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1. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis

Author: Ishigaki, Kazuyoshi, Sakaue, Saori, Terao, Chikashi, Luo, Yang, Sonehara, Kyuto, Yamaguchi, Kensuke, Amariuta, Tiffany, Too, Chun Lai, Laufer, Vincent A., Scott, Ian C., Viatte, Sebastien, Takahashi, Meiko, Ohmura, Koichiro, Murasawa, Akira, Hashimoto, Motomu, Ito, Hiromu, Hammoudeh, Mohammed, Emadi, Samar Al, Masri, Basel K., Halabi, Hussein, Badsha, Humeira, Uthman, Imad W., Wu, Xin, Lin, Li, Li, Ting, Plant, Darren, Barton, Anne, Orozco, Gisela, Verstappen, Suzanne M. M., Bowes, John, MacGregor, Alexander J., Honda, Suguru, Koido, Masaru, Tomizuka, Kohei, Kamatani, Yoichiro, Tanaka, Hiroaki, Tanaka, Eiichi, Suzuki, Akari, Maeda, Yuichi, Yamamoto, Kenichi, Miyawaki, Satoru, Xie, Gang, Zhang, Jinyi, Amos, Christopher I., Keystone, Edward, Wolbink, Gertjan, van der Horst-Bruinsma, Irene, Cui, Jing, Liao, Katherine P., Carroll, Robert J., Lee, Hye-Soon, Bang, So-Young, Siminovitch, Katherine A., de Vries, Niek, Alfredsson, Lars, Rantapää-Dahlqvist, Solbritt, Karlson, Elizabeth W., Bae, Sang-Cheol, Kimberly, Robert P., Edberg, Jeffrey C., Mariette, Xavier, Huizinga, Tom, Dieudé, Philippe, Schneider, Matthias, Kerick, Martin, Denny, Joshua C., Matsuda, Koichi, Matsuo, Keitaro, Mimori, Tsuneyo, Matsuda, Fumihiko, Fujio, Keishi, Tanaka, Yoshiya, Kumanogoh, Atsushi, Traylor, Matthew, Lewis, Cathryn M., Eyre, Stephen, Xu, Huji, Saxena, Richa, Arayssi, Thurayya, Kochi, Yuta, Ikari, Katsunori, Harigai, Masayoshi, Gregersen, Peter K., Yamamoto, Kazuhiko, Louis Bridges, S., Padyukov, Leonid, Martin, Javier, Klareskog, Lars, Okada, Yukinori, Raychaudhuri, Soumya, Ishigaki, Kazuyoshi, Sakaue, Saori, Terao, Chikashi, Luo, Yang, Sonehara, Kyuto, Yamaguchi, Kensuke, Amariuta, Tiffany, Too, Chun Lai, Laufer, Vincent A., Scott, Ian C., Viatte, Sebastien, Takahashi, Meiko, Ohmura, Koichiro, Murasawa, Akira, Hashimoto, Motomu, Ito, Hiromu, Hammoudeh, Mohammed, Emadi, Samar Al, Masri, Basel K., Halabi, Hussein, Badsha, Humeira, Uthman, Imad W., Wu, Xin, Lin, Li, Li, Ting, Plant, Darren, Barton, Anne, Orozco, Gisela, Verstappen, Suzanne M. M., Bowes, John, MacGregor, Alexander J., Honda, Suguru, Koido, Masaru, Tomizuka, Kohei, Kamatani, Yoichiro, Tanaka, Hiroaki, Tanaka, Eiichi, Suzuki, Akari, Maeda, Yuichi, Yamamoto, Kenichi, Miyawaki, Satoru, Xie, Gang, Zhang, Jinyi, Amos, Christopher I., Keystone, Edward, Wolbink, Gertjan, van der Horst-Bruinsma, Irene, Cui, Jing, Liao, Katherine P., Carroll, Robert J., Lee, Hye-Soon, Bang, So-Young, Siminovitch, Katherine A., de Vries, Niek, Alfredsson, Lars, Rantapää-Dahlqvist, Solbritt, Karlson, Elizabeth W., Bae, Sang-Cheol, Kimberly, Robert P., Edberg, Jeffrey C., Mariette, Xavier, Huizinga, Tom, Dieudé, Philippe, Schneider, Matthias, Kerick, Martin, Denny, Joshua C., Matsuda, Koichi, Matsuo, Keitaro, Mimori, Tsuneyo, Matsuda, Fumihiko, Fujio, Keishi, Tanaka, Yoshiya, Kumanogoh, Atsushi, Traylor, Matthew, Lewis, Cathryn M., Eyre, Stephen, Xu, Huji, Saxena, Richa, Arayssi, Thurayya, Kochi, Yuta, Ikari, Katsunori, Harigai, Masayoshi, Gregersen, Peter K., Yamamoto, Kazuhiko, Louis Bridges, S., Padyukov, Leonid, Martin, Javier, Klareskog, Lars, Okada, Yukinori, and Raychaudhuri, Soumya
Abstract: Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10−8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
Published: 2022
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2. Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes.

Author: Robertson, Catherine C, Robertson, Catherine C, Inshaw, Jamie RJ, Onengut-Gumuscu, Suna, Chen, Wei-Min, Santa Cruz, David Flores, Yang, Hanzhi, Cutler, Antony J, Crouch, Daniel JM, Farber, Emily, Bridges, S Louis, Edberg, Jeffrey C, Kimberly, Robert P, Buckner, Jane H, Deloukas, Panos, Divers, Jasmin, Dabelea, Dana, Lawrence, Jean M, Marcovina, Santica, Shah, Amy S, Greenbaum, Carla J, Atkinson, Mark A, Gregersen, Peter K, Oksenberg, Jorge R, Pociot, Flemming, Rewers, Marian J, Steck, Andrea K, Dunger, David B, Type 1 Diabetes Genetics Consortium, Wicker, Linda S, Concannon, Patrick, Todd, John A, Rich, Stephen S, Robertson, Catherine C, Robertson, Catherine C, Inshaw, Jamie RJ, Onengut-Gumuscu, Suna, Chen, Wei-Min, Santa Cruz, David Flores, Yang, Hanzhi, Cutler, Antony J, Crouch, Daniel JM, Farber, Emily, Bridges, S Louis, Edberg, Jeffrey C, Kimberly, Robert P, Buckner, Jane H, Deloukas, Panos, Divers, Jasmin, Dabelea, Dana, Lawrence, Jean M, Marcovina, Santica, Shah, Amy S, Greenbaum, Carla J, Atkinson, Mark A, Gregersen, Peter K, Oksenberg, Jorge R, Pociot, Flemming, Rewers, Marian J, Steck, Andrea K, Dunger, David B, Type 1 Diabetes Genetics Consortium, Wicker, Linda S, Concannon, Patrick, Todd, John A, and Rich, Stephen S
Abstract: We report the largest and most diverse genetic study of type 1 diabetes (T1D) to date (61,427 participants), yielding 78 genome-wide-significant (P < 5 × 10-8) regions, including 36 that are new. We define credible sets of T1D-associated variants and show that they are enriched in immune-cell accessible chromatin, particularly CD4+ effector T cells. Using chromatin-accessibility profiling of CD4+ T cells from 115 individuals, we map chromatin-accessibility quantitative trait loci and identify five regions where T1D risk variants co-localize with chromatin-accessibility quantitative trait loci. We highlight rs72928038 in BACH2 as a candidate causal T1D variant leading to decreased enhancer accessibility and BACH2 expression in T cells. Finally, we prioritize potential drug targets by integrating genetic evidence, functional genomic maps and immune protein-protein interactions, identifying 12 genes implicated in T1D that have been targeted in clinical trials for autoimmune diseases. These findings provide an expanded genomic landscape for T1D.
Published: 2021

3. Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes.

Author: Robertson, Catherine C, Robertson, Catherine C, Inshaw, Jamie RJ, Onengut-Gumuscu, Suna, Chen, Wei-Min, Santa Cruz, David Flores, Yang, Hanzhi, Cutler, Antony J, Crouch, Daniel JM, Farber, Emily, Bridges, S Louis, Edberg, Jeffrey C, Kimberly, Robert P, Buckner, Jane H, Deloukas, Panos, Divers, Jasmin, Dabelea, Dana, Lawrence, Jean M, Marcovina, Santica, Shah, Amy S, Greenbaum, Carla J, Atkinson, Mark A, Gregersen, Peter K, Oksenberg, Jorge R, Pociot, Flemming, Rewers, Marian J, Steck, Andrea K, Dunger, David B, Type 1 Diabetes Genetics Consortium, Wicker, Linda S, Concannon, Patrick, Todd, John A, Rich, Stephen S, Robertson, Catherine C, Robertson, Catherine C, Inshaw, Jamie RJ, Onengut-Gumuscu, Suna, Chen, Wei-Min, Santa Cruz, David Flores, Yang, Hanzhi, Cutler, Antony J, Crouch, Daniel JM, Farber, Emily, Bridges, S Louis, Edberg, Jeffrey C, Kimberly, Robert P, Buckner, Jane H, Deloukas, Panos, Divers, Jasmin, Dabelea, Dana, Lawrence, Jean M, Marcovina, Santica, Shah, Amy S, Greenbaum, Carla J, Atkinson, Mark A, Gregersen, Peter K, Oksenberg, Jorge R, Pociot, Flemming, Rewers, Marian J, Steck, Andrea K, Dunger, David B, Type 1 Diabetes Genetics Consortium, Wicker, Linda S, Concannon, Patrick, Todd, John A, and Rich, Stephen S
Abstract: We report the largest and most diverse genetic study of type 1 diabetes (T1D) to date (61,427 participants), yielding 78 genome-wide-significant (P < 5 × 10-8) regions, including 36 that are new. We define credible sets of T1D-associated variants and show that they are enriched in immune-cell accessible chromatin, particularly CD4+ effector T cells. Using chromatin-accessibility profiling of CD4+ T cells from 115 individuals, we map chromatin-accessibility quantitative trait loci and identify five regions where T1D risk variants co-localize with chromatin-accessibility quantitative trait loci. We highlight rs72928038 in BACH2 as a candidate causal T1D variant leading to decreased enhancer accessibility and BACH2 expression in T cells. Finally, we prioritize potential drug targets by integrating genetic evidence, functional genomic maps and immune protein-protein interactions, identifying 12 genes implicated in T1D that have been targeted in clinical trials for autoimmune diseases. These findings provide an expanded genomic landscape for T1D.
Published: 2021

4. Complement genes contribute sex-biased vulnerability in diverse disorders.

Author: Kamitaki, Nolan, Kamitaki, Nolan, Sekar, Aswin, Handsaker, Robert E, de Rivera, Heather, Tooley, Katherine, Morris, David L, Taylor, Kimberly E, Whelan, Christopher W, Tombleson, Philip, Loohuis, Loes M Olde, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke, Michael, Kimberly, Robert P, Kaufman, Kenneth M, Harley, John B, Langefeld, Carl D, Seidman, Christine E, Pato, Michele T, Pato, Carlos N, Ophoff, Roel A, Graham, Robert R, Criswell, Lindsey A, Vyse, Timothy J, McCarroll, Steven A, Kamitaki, Nolan, Kamitaki, Nolan, Sekar, Aswin, Handsaker, Robert E, de Rivera, Heather, Tooley, Katherine, Morris, David L, Taylor, Kimberly E, Whelan, Christopher W, Tombleson, Philip, Loohuis, Loes M Olde, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke, Michael, Kimberly, Robert P, Kaufman, Kenneth M, Harley, John B, Langefeld, Carl D, Seidman, Christine E, Pato, Michele T, Pato, Carlos N, Ophoff, Roel A, Graham, Robert R, Criswell, Lindsey A, Vyse, Timothy J, and McCarroll, Steven A
Abstract: Many common illnesses, for reasons that have not been identified, differentially affect men and women. For instance, the autoimmune diseases systemic lupus erythematosus (SLE) and Sjögren's syndrome affect nine times more women than men1, whereas schizophrenia affects men with greater frequency and severity relative to women2. All three illnesses have their strongest common genetic associations in the major histocompatibility complex (MHC) locus, an association that in SLE and Sjögren's syndrome has long been thought to arise from alleles of the human leukocyte antigen (HLA) genes at that locus3-6. Here we show that variation of the complement component 4 (C4) genes C4A and C4B, which are also at the MHC locus and have been linked to increased risk for schizophrenia7, generates 7-fold variation in risk for SLE and 16-fold variation in risk for Sjögren's syndrome among individuals with common C4 genotypes, with C4A protecting more strongly than C4B in both illnesses. The same alleles that increase risk for schizophrenia greatly reduce risk for SLE and Sjögren's syndrome. In all three illnesses, C4 alleles act more strongly in men than in women: common combinations of C4A and C4B generated 14-fold variation in risk for SLE, 31-fold variation in risk for Sjögren's syndrome, and 1.7-fold variation in schizophrenia risk among men (versus 6-fold, 15-fold and 1.26-fold variation in risk among women, respectively). At a protein level, both C4 and its effector C3 were present at higher levels in cerebrospinal fluid and plasma8,9 in men than in women among adults aged between 20 and 50 years, corresponding to the ages of differential disease vulnerability. Sex differences in complement protein levels may help to explain the more potent effects of C4 alleles in men, women's greater risk of SLE and Sjögren's syndrome and men's greater vulnerability to schizophrenia. These results implicate the complement system as a source of sexual dimorphism in vulnerability to diverse illnes
Published: 2020

5. Complement genes contribute sex-biased vulnerability in diverse disorders.

Author: Kamitaki, Nolan, Kamitaki, Nolan, Sekar, Aswin, Handsaker, Robert E, de Rivera, Heather, Tooley, Katherine, Morris, David L, Taylor, Kimberly E, Whelan, Christopher W, Tombleson, Philip, Loohuis, Loes M Olde, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke, Michael, Kimberly, Robert P, Kaufman, Kenneth M, Harley, John B, Langefeld, Carl D, Seidman, Christine E, Pato, Michele T, Pato, Carlos N, Ophoff, Roel A, Graham, Robert R, Criswell, Lindsey A, Vyse, Timothy J, McCarroll, Steven A, Kamitaki, Nolan, Kamitaki, Nolan, Sekar, Aswin, Handsaker, Robert E, de Rivera, Heather, Tooley, Katherine, Morris, David L, Taylor, Kimberly E, Whelan, Christopher W, Tombleson, Philip, Loohuis, Loes M Olde, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Boehnke, Michael, Kimberly, Robert P, Kaufman, Kenneth M, Harley, John B, Langefeld, Carl D, Seidman, Christine E, Pato, Michele T, Pato, Carlos N, Ophoff, Roel A, Graham, Robert R, Criswell, Lindsey A, Vyse, Timothy J, and McCarroll, Steven A
Abstract: Many common illnesses, for reasons that have not been identified, differentially affect men and women. For instance, the autoimmune diseases systemic lupus erythematosus (SLE) and Sjögren's syndrome affect nine times more women than men1, whereas schizophrenia affects men with greater frequency and severity relative to women2. All three illnesses have their strongest common genetic associations in the major histocompatibility complex (MHC) locus, an association that in SLE and Sjögren's syndrome has long been thought to arise from alleles of the human leukocyte antigen (HLA) genes at that locus3-6. Here we show that variation of the complement component 4 (C4) genes C4A and C4B, which are also at the MHC locus and have been linked to increased risk for schizophrenia7, generates 7-fold variation in risk for SLE and 16-fold variation in risk for Sjögren's syndrome among individuals with common C4 genotypes, with C4A protecting more strongly than C4B in both illnesses. The same alleles that increase risk for schizophrenia greatly reduce risk for SLE and Sjögren's syndrome. In all three illnesses, C4 alleles act more strongly in men than in women: common combinations of C4A and C4B generated 14-fold variation in risk for SLE, 31-fold variation in risk for Sjögren's syndrome, and 1.7-fold variation in schizophrenia risk among men (versus 6-fold, 15-fold and 1.26-fold variation in risk among women, respectively). At a protein level, both C4 and its effector C3 were present at higher levels in cerebrospinal fluid and plasma8,9 in men than in women among adults aged between 20 and 50 years, corresponding to the ages of differential disease vulnerability. Sex differences in complement protein levels may help to explain the more potent effects of C4 alleles in men, women's greater risk of SLE and Sjögren's syndrome and men's greater vulnerability to schizophrenia. These results implicate the complement system as a source of sexual dimorphism in vulnerability to diverse illnes
Published: 2020

6. Individualized decision aid for diverse women with lupus nephritis (IDEA-WON): A randomized controlled trial.

Author: Singh, Jasvinder A, Singh, Jasvinder A, Fraenkel, Liana, Green, Candace, Alarcón, Graciela S, Barton, Jennifer L, Saag, Kenneth G, Hanrahan, Leslie M, Raymond, Sandra C, Kimberly, Robert P, Leong, Amye L, Reyes, Elyse, Street, Richard L, Suarez-Almazor, Maria E, Eakin, Guy S, Marrow, Laura, Morgan, Charity J, Caro, Brennda, Sloan, Jeffrey A, Jandali, Bochra, Garcia, Salvador R, Grossman, Jennifer, Winthrop, Kevin L, Trupin, Laura, Dall'Era, Maria, Meara, Alexa, Rizvi, Tara, Chatham, W Winn, Yazdany, Jinoos, Singh, Jasvinder A, Singh, Jasvinder A, Fraenkel, Liana, Green, Candace, Alarcón, Graciela S, Barton, Jennifer L, Saag, Kenneth G, Hanrahan, Leslie M, Raymond, Sandra C, Kimberly, Robert P, Leong, Amye L, Reyes, Elyse, Street, Richard L, Suarez-Almazor, Maria E, Eakin, Guy S, Marrow, Laura, Morgan, Charity J, Caro, Brennda, Sloan, Jeffrey A, Jandali, Bochra, Garcia, Salvador R, Grossman, Jennifer, Winthrop, Kevin L, Trupin, Laura, Dall'Era, Maria, Meara, Alexa, Rizvi, Tara, Chatham, W Winn, and Yazdany, Jinoos
Abstract: BackgroundTreatment decision-making regarding immunosuppressive therapy is challenging for individuals with lupus. We assessed the effectiveness of a decision aid for immunosuppressive therapy in lupus nephritis.Methods and findingsIn a United States multicenter, open-label, randomized controlled trial (RCT), adult women with lupus nephritis, mostly from racial/ethnic minority backgrounds with low socioeconomic status (SES), seen in in- or outpatient settings, were randomized to an individualized, culturally tailored, computerized decision aid versus American College of Rheumatology (ACR) lupus pamphlet (1:1 ratio), using computer-generated randomization. We hypothesized that the co-primary outcomes of decisional conflict and informed choice regarding immunosuppressive medications would improve more in the decision aid group. Of 301 randomized women, 298 were analyzed; 47% were African-American, 26% Hispanic, and 15% white. Mean age (standard deviation [SD]) was 37 (12) years, 57% had annual income of <$40,000, and 36% had a high school education or less. Compared with the provision of the ACR lupus pamphlet (n = 147), participants randomized to the decision aid (n = 151) had (1) a clinically meaningful and statistically significant reduction in decisional conflict, 21.8 (standard error [SE], 2.5) versus 12.7 (SE, 2.0; p = 0.005) and (2) no difference in informed choice in the main analysis, 41% versus 31% (p = 0.08), but clinically meaningful and statistically significant difference in sensitivity analysis (net values for immunosuppressives positive [in favor] versus negative [against]), 50% versus 35% (p = 0.006). Unresolved decisional conflict was lower in the decision aid versus pamphlet groups, 22% versus 44% (p < 0.001). Significantly more patients in the decision aid versus pamphlet group rated information to be excellent for understanding lupus nephritis (49% versus 33%), risk factors (43% versus 27%), medication options (50% versus 33%; p ≤ 0.003 for
Published: 2019

7. Individualized decision aid for diverse women with lupus nephritis (IDEA-WON): A randomized controlled trial.

Author: Singh, Jasvinder A, Taal, Maarten W1, Singh, Jasvinder A, Fraenkel, Liana, Green, Candace, Alarcón, Graciela S, Barton, Jennifer L, Saag, Kenneth G, Hanrahan, Leslie M, Raymond, Sandra C, Kimberly, Robert P, Leong, Amye L, Reyes, Elyse, Street, Richard L, Suarez-Almazor, Maria E, Eakin, Guy S, Marrow, Laura, Morgan, Charity J, Caro, Brennda, Sloan, Jeffrey A, Jandali, Bochra, Garcia, Salvador R, Grossman, Jennifer, Winthrop, Kevin L, Trupin, Laura, Dall'Era, Maria, Meara, Alexa, Rizvi, Tara, Chatham, W Winn, Yazdany, Jinoos, Singh, Jasvinder A, Taal, Maarten W1, Singh, Jasvinder A, Fraenkel, Liana, Green, Candace, Alarcón, Graciela S, Barton, Jennifer L, Saag, Kenneth G, Hanrahan, Leslie M, Raymond, Sandra C, Kimberly, Robert P, Leong, Amye L, Reyes, Elyse, Street, Richard L, Suarez-Almazor, Maria E, Eakin, Guy S, Marrow, Laura, Morgan, Charity J, Caro, Brennda, Sloan, Jeffrey A, Jandali, Bochra, Garcia, Salvador R, Grossman, Jennifer, Winthrop, Kevin L, Trupin, Laura, Dall'Era, Maria, Meara, Alexa, Rizvi, Tara, Chatham, W Winn, and Yazdany, Jinoos
Abstract: BackgroundTreatment decision-making regarding immunosuppressive therapy is challenging for individuals with lupus. We assessed the effectiveness of a decision aid for immunosuppressive therapy in lupus nephritis.Methods and findingsIn a United States multicenter, open-label, randomized controlled trial (RCT), adult women with lupus nephritis, mostly from racial/ethnic minority backgrounds with low socioeconomic status (SES), seen in in- or outpatient settings, were randomized to an individualized, culturally tailored, computerized decision aid versus American College of Rheumatology (ACR) lupus pamphlet (1:1 ratio), using computer-generated randomization. We hypothesized that the co-primary outcomes of decisional conflict and informed choice regarding immunosuppressive medications would improve more in the decision aid group. Of 301 randomized women, 298 were analyzed; 47% were African-American, 26% Hispanic, and 15% white. Mean age (standard deviation [SD]) was 37 (12) years, 57% had annual income of <$40,000, and 36% had a high school education or less. Compared with the provision of the ACR lupus pamphlet (n = 147), participants randomized to the decision aid (n = 151) had (1) a clinically meaningful and statistically significant reduction in decisional conflict, 21.8 (standard error [SE], 2.5) versus 12.7 (SE, 2.0; p = 0.005) and (2) no difference in informed choice in the main analysis, 41% versus 31% (p = 0.08), but clinically meaningful and statistically significant difference in sensitivity analysis (net values for immunosuppressives positive [in favor] versus negative [against]), 50% versus 35% (p = 0.006). Unresolved decisional conflict was lower in the decision aid versus pamphlet groups, 22% versus 44% (p < 0.001). Significantly more patients in the decision aid versus pamphlet group rated information to be excellent for understanding lupus nephritis (49% versus 33%), risk factors (43% versus 27%), medication options (50% versus 33%; p ≤ 0.003 for
Published: 2019

8. Type 1 Diabetes Risk in African-Ancestry Participants and Utility of an Ancestry-Specific Genetic Risk Score.

Author: Onengut-Gumuscu, Suna, Onengut-Gumuscu, Suna, Chen, Wei-Min, Robertson, Catherine C, Bonnie, Jessica K, Farber, Emily, Zhu, Zhennan, Oksenberg, Jorge R, Brant, Steven R, Bridges, S Louis, Edberg, Jeffrey C, Kimberly, Robert P, Gregersen, Peter K, Rewers, Marian J, Steck, Andrea K, Black, Mary H, Dabelea, Dana, Pihoker, Catherine, Atkinson, Mark A, Wagenknecht, Lynne E, Divers, Jasmin, Bell, Ronny A, SEARCH for Diabetes in Youth, Type 1 Diabetes Genetics Consortium, Erlich, Henry A, Concannon, Patrick, Rich, Stephen S, Onengut-Gumuscu, Suna, Onengut-Gumuscu, Suna, Chen, Wei-Min, Robertson, Catherine C, Bonnie, Jessica K, Farber, Emily, Zhu, Zhennan, Oksenberg, Jorge R, Brant, Steven R, Bridges, S Louis, Edberg, Jeffrey C, Kimberly, Robert P, Gregersen, Peter K, Rewers, Marian J, Steck, Andrea K, Black, Mary H, Dabelea, Dana, Pihoker, Catherine, Atkinson, Mark A, Wagenknecht, Lynne E, Divers, Jasmin, Bell, Ronny A, SEARCH for Diabetes in Youth, Type 1 Diabetes Genetics Consortium, Erlich, Henry A, Concannon, Patrick, and Rich, Stephen S
Abstract: ObjectiveGenetic risk scores (GRS) have been developed that differentiate individuals with type 1 diabetes from those with other forms of diabetes and are starting to be used for population screening; however, most studies were conducted in European-ancestry populations. This study identifies novel genetic variants associated with type 1 diabetes risk in African-ancestry participants and develops an African-specific GRS.Research design and methodsWe generated single nucleotide polymorphism (SNP) data with the ImmunoChip on 1,021 African-ancestry participants with type 1 diabetes and 2,928 control participants. HLA class I and class II alleles were imputed using SNP2HLA. Logistic regression models were used to identify genome-wide significant (P < 5.0 × 10-8) SNPs associated with type 1 diabetes in the African-ancestry samples and validate SNPs associated with risk in known European-ancestry loci (P < 2.79 × 10-5).ResultsAfrican-specific (HLA-DQA1*03:01-HLA-DQB1*02:01) and known European-ancestry HLA haplotypes (HLA-DRB1*03:01-HLA-DQA1*05:01-HLA-DQB1*02:01, HLA-DRB1*04:01-HLA-DQA1*03:01-HLA-DQB1*03:02) were significantly associated with type 1 diabetes risk. Among European-ancestry defined non-HLA risk loci, six risk loci were significantly associated with type 1 diabetes in subjects of African ancestry. An African-specific GRS provided strong prediction of type 1 diabetes risk (area under the curve 0.871), performing significantly better than a European-based GRS and two polygenic risk scores in independent discovery and validation cohorts.ConclusionsGenetic risk of type 1 diabetes includes ancestry-specific, disease-associated variants. The GRS developed here provides improved prediction of type 1 diabetes in African-ancestry subjects and a means to identify groups of individuals who would benefit from immune monitoring for early detection of islet autoimmunity.
Published: 2019

9. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

10. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

11. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

12. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

13. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

14. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P amp;lt; 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE., Funding Agencies|Alliance for Lupus Research; Arthritis Research UK Special Strategic Award [19289]; George Koukis; National Institute for Health Research (NIHR) Biomedical Research Centre based at Guys and St Thomas NHS Foundation Trust; Kings College London; NIH [AR049084]; International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN) [AI083194, CA141700, AR058621]; Proyecto de Excelencia; Consejeria de Andalucia; MUSC [UL1RR029882, 5P60AR062755]; US National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health (NIH) [K01 AR067280, P60 AR062755, N01AR22265]; APPLE Investigators; NIAMS/NIH [P50-AR055503]; RILITE foundation; Genentech; [AR043814]; [AR-065626]; [AR060366]; [MD007909]; [AI107176]; [AR-057172]; [RC2 AR058959]; [U19 A1082714]; [R01 AR063124]; [P30 GM110766]; [R01 AR056360]; [P60 AR053308]; [R01AR43727]; [NIH AR 043727]; [069572]
Published: 2017
Full Text: View/download PDF

15. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

16. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P amp;lt; 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE., Funding Agencies|Alliance for Lupus Research; Arthritis Research UK Special Strategic Award [19289]; George Koukis; National Institute for Health Research (NIHR) Biomedical Research Centre based at Guys and St Thomas NHS Foundation Trust; Kings College London; NIH [AR049084]; International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN) [AI083194, CA141700, AR058621]; Proyecto de Excelencia; Consejeria de Andalucia; MUSC [UL1RR029882, 5P60AR062755]; US National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health (NIH) [K01 AR067280, P60 AR062755, N01AR22265]; APPLE Investigators; NIAMS/NIH [P50-AR055503]; RILITE foundation; Genentech; [AR043814]; [AR-065626]; [AR060366]; [MD007909]; [AI107176]; [AR-057172]; [RC2 AR058959]; [U19 A1082714]; [R01 AR063124]; [P30 GM110766]; [R01 AR056360]; [P60 AR053308]; [R01AR43727]; [NIH AR 043727]; [069572]
Published: 2017
Full Text: View/download PDF

17. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlöf, Jonas Carlsson, Acevedo Vásquez, Eduardo M., Alarcón, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho Venegas, Jorge M., Dahlqvist, Solbritt Rantapää, D’Alfonso, Sandra, Da Silva, Berta Martins, De la Rúa Figueroa, Iñigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emőke, Esquivel Valerio, Jorge Antonio, Fortin, Paul R., Freedman, Barry I., Frostegård, Johan, García, Mercedes A., García de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovács, László, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan Zhen, Maradiaga Ceceña, Marco A., Martín, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, José F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, José M., Aguilar Salinas, Carlos Alberto, Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusié Luna, Teresa, Vasconcelos, Carlos, Vilá, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcón Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlöf, Jonas Carlsson, Acevedo Vásquez, Eduardo M., Alarcón, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho Venegas, Jorge M., Dahlqvist, Solbritt Rantapää, D’Alfonso, Sandra, Da Silva, Berta Martins, De la Rúa Figueroa, Iñigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emőke, Esquivel Valerio, Jorge Antonio, Fortin, Paul R., Freedman, Barry I., Frostegård, Johan, García, Mercedes A., García de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovács, László, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan Zhen, Maradiaga Ceceña, Marco A., Martín, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, José F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, José M., Aguilar Salinas, Carlos Alberto, Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusié Luna, Teresa, Vasconcelos, Carlos, Vilá, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcón Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (B50% of these regions have multiple independent associations); these include 24 novel SLE regions (Po5 10 8), reﬁned association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identiﬁes both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE
Published: 2017

18. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

19. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P amp;lt; 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE., Funding Agencies|Alliance for Lupus Research; Arthritis Research UK Special Strategic Award [19289]; George Koukis; National Institute for Health Research (NIHR) Biomedical Research Centre based at Guys and St Thomas NHS Foundation Trust; Kings College London; NIH [AR049084]; International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN) [AI083194, CA141700, AR058621]; Proyecto de Excelencia; Consejeria de Andalucia; MUSC [UL1RR029882, 5P60AR062755]; US National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health (NIH) [K01 AR067280, P60 AR062755, N01AR22265]; APPLE Investigators; NIAMS/NIH [P50-AR055503]; RILITE foundation; Genentech; [AR043814]; [AR-065626]; [AR060366]; [MD007909]; [AI107176]; [AR-057172]; [RC2 AR058959]; [U19 A1082714]; [R01 AR063124]; [P30 GM110766]; [R01 AR056360]; [P60 AR053308]; [R01AR43727]; [NIH AR 043727]; [069572]
Published: 2017
Full Text: View/download PDF

20. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlöf, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann-Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

21. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
Full Text: View/download PDF

22. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: National Institute for Health Research (UK), Arthritis Research UK, Alliance for Lupus Research, Junta de Andalucía, National Institute of Arthritis and Musculoskeletal and Skin Diseases (US), National Institutes of Health (US), RILITE Foundation, Genentech Foundation, Langefeld, C. D., Ainsworth, H. C., Kelly, J. A., Comeau, M. E., Marion, M. C., Howard, T. D., Ramos, P. S., Croker, J. A., Morris, D. L., Sandling, J. K., Almlöf, J. C., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, José Mario, Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, C., Vilá, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcón-Riquelme, M. E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, P. M., Vyse, Timothy J., Acevedo-Vásquez, E. M., Alarcón, G. S., Babini, A. M., Baca, V., Bengtsson, A. A., Berbotto, G. A., Bij, l. M., Brown, E. E., Brunner, H.I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegård, Johan, García, Mercedes A., García de la Torre, Ignacio, Gilkeson, G. S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, D. L., Karp, David R., Kaufman, Kenneth M, Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martín, J., McCune, Joseph M., McWilliams, David R, Merrill, Joan T, Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, N., Petri, Michelle, Pineau, Christian A., National Institute for Health Research (UK), Arthritis Research UK, Alliance for Lupus Research, Junta de Andalucía, National Institute of Arthritis and Musculoskeletal and Skin Diseases (US), National Institutes of Health (US), RILITE Foundation, Genentech Foundation, Langefeld, C. D., Ainsworth, H. C., Kelly, J. A., Comeau, M. E., Marion, M. C., Howard, T. D., Ramos, P. S., Croker, J. A., Morris, D. L., Sandling, J. K., Almlöf, J. C., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, José Mario, Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, C., Vilá, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcón-Riquelme, M. E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, P. M., Vyse, Timothy J., Acevedo-Vásquez, E. M., Alarcón, G. S., Babini, A. M., Baca, V., Bengtsson, A. A., Berbotto, G. A., Bij, l. M., Brown, E. E., Brunner, H.I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Dahlqvist, Solbritt Rantapaa, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegård, Johan, García, Mercedes A., García de la Torre, Ignacio, Gilkeson, G. S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, D. L., Karp, David R., Kaufman, Kenneth M, Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martín, J., McCune, Joseph M., McWilliams, David R, Merrill, Joan T, Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, N., Petri, Michelle, and Pineau, Christian A.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017

23. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P amp;lt; 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE., Funding Agencies|Alliance for Lupus Research; Arthritis Research UK Special Strategic Award [19289]; George Koukis; National Institute for Health Research (NIHR) Biomedical Research Centre based at Guys and St Thomas NHS Foundation Trust; Kings College London; NIH [AR049084]; International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN) [AI083194, CA141700, AR058621]; Proyecto de Excelencia; Consejeria de Andalucia; MUSC [UL1RR029882, 5P60AR062755]; US National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health (NIH) [K01 AR067280, P60 AR062755, N01AR22265]; APPLE Investigators; NIAMS/NIH [P50-AR055503]; RILITE foundation; Genentech; [AR043814]; [AR-065626]; [AR060366]; [MD007909]; [AI107176]; [AR-057172]; [RC2 AR058959]; [U19 A1082714]; [R01 AR063124]; [P30 GM110766]; [R01 AR056360]; [P60 AR053308]; [R01AR43727]; [NIH AR 043727]; [069572]
Published: 2017
Full Text: View/download PDF

24. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Carlsson Almlof, Jonas, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapaa Dahlqvist, Solbritt, DAlfonso, Sandra, Martins Da Silva, Berta, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P amp;lt; 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE., Funding Agencies|Alliance for Lupus Research; Arthritis Research UK Special Strategic Award [19289]; George Koukis; National Institute for Health Research (NIHR) Biomedical Research Centre based at Guys and St Thomas NHS Foundation Trust; Kings College London; NIH [AR049084]; International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN) [AI083194, CA141700, AR058621]; Proyecto de Excelencia; Consejeria de Andalucia; MUSC [UL1RR029882, 5P60AR062755]; US National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health (NIH) [K01 AR067280, P60 AR062755, N01AR22265]; APPLE Investigators; NIAMS/NIH [P50-AR055503]; RILITE foundation; Genentech; [AR043814]; [AR-065626]; [AR060366]; [MD007909]; [AI107176]; [AR-057172]; [RC2 AR058959]; [U19 A1082714]; [R01 AR063124]; [P30 GM110766]; [R01 AR056360]; [P60 AR053308]; [R01AR43727]; [NIH AR 043727]; [069572]
Published: 2017
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25. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlöf, Jonas Carlsson, Acevedo Vásquez, Eduardo M., Alarcón, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho Venegas, Jorge M., Dahlqvist, Solbritt Rantapää, D’Alfonso, Sandra, Da Silva, Berta Martins, De la Rúa Figueroa, Iñigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emőke, Esquivel Valerio, Jorge Antonio, Fortin, Paul R., Freedman, Barry I., Frostegård, Johan, García, Mercedes A., García de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovács, László, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan Zhen, Maradiaga Ceceña, Marco A., Martín, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, José F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, José M., Aguilar Salinas, Carlos Alberto, Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusié Luna, Teresa, Vasconcelos, Carlos, Vilá, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcón Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Cunninghame Graham, Deborah S., Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlöf, Jonas Carlsson, Acevedo Vásquez, Eduardo M., Alarcón, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho Venegas, Jorge M., Dahlqvist, Solbritt Rantapää, D’Alfonso, Sandra, Da Silva, Berta Martins, De la Rúa Figueroa, Iñigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emőke, Esquivel Valerio, Jorge Antonio, Fortin, Paul R., Freedman, Barry I., Frostegård, Johan, García, Mercedes A., García de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovács, László, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan Zhen, Maradiaga Ceceña, Marco A., Martín, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, José F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, José M., Aguilar Salinas, Carlos Alberto, Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjöwall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusié Luna, Teresa, Vasconcelos, Carlos, Vilá, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvänen, Ann Christine, Rönnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcón Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (B50% of these regions have multiple independent associations); these include 24 novel SLE regions (Po5 10 8), reﬁned association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identiﬁes both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE
Published: 2017

26. Transancestral mapping and genetic load in systemic lupus erythematosus

Author: Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., Vyse, Timothy J., Langefeld, Carl D., Ainsworth, Hannah C., Graham, Deborah S. Cunninghame, Kelly, Jennifer A., Comeau, Mary E., Marion, Miranda C., Howard, Timothy D., Ramos, Paula S., Croker, Jennifer A., Morris, David L., Sandling, Johanna K., Almlof, Jonas Carlsson, Acevedo-Vasquez, Eduardo M., Alarcon, Graciela S., Babini, Alejandra M., Baca, Vicente, Bengtsson, Anders A., Berbotto, Guillermo A., Bijl, Marc, Brown, Elizabeth E., Brunner, Hermine I., Cardiel, Mario H., Catoggio, Luis, Cervera, Ricard, Cucho-Venegas, Jorge M., Rantapää Dahlqvist, Solbritt, D'Alfonso, Sandra, Da Silva, Berta Martins, de la Rua Figueroa, Inigo, Doria, Andrea, Edberg, Jeffrey C., Endreffy, Emoke, Esquivel-Valerio, Jorge A., Fortin, Paul R., Freedman, Barry I., Frostegard, Johan, Garcia, Mercedes A., Garcia de la Torre, Ignacio, Gilkeson, Gary S., Gladman, Dafna D., Gunnarsson, Iva, Guthridge, Joel M., Huggins, Jennifer L., James, Judith A., Kallenberg, Cees G. M., Kamen, Diane L., Karp, David R., Kaufman, Kenneth M., Kottyan, Leah C., Kovacs, Laszlo, Laustrup, Helle, Lauwerys, Bernard R., Li, Quan-Zhen, Maradiaga-Cecena, Marco A., Martin, Javier, McCune, Joseph M., McWilliams, David R., Merrill, Joan T., Miranda, Pedro, Moctezuma, Jose F., Nath, Swapan K., Niewold, Timothy B., Orozco, Lorena, Ortego-Centeno, Norberto, Petri, Michelle, Pineau, Christian A., Pons-Estel, Bernardo A., Pope, Janet, Raj, Prithvi, Ramsey-Goldman, Rosalind, Reveille, John D., Russell, Laurie P., Sabio, Jose M., Aguilar-Salinas, Carlos A., Scherbarth, Hugo R., Scorza, Raffaella, Seldin, Michael F., Sjowall, Christopher, Svenungsson, Elisabet, Thompson, Susan D., Toloza, Sergio M. A., Truedsson, Lennart, Tusie-Luna, Teresa, Vasconcelos, Carlos, Vila, Luis M., Wallace, Daniel J., Weisman, Michael H., Wither, Joan E., Bhangale, Tushar, Oksenberg, Jorge R., Rioux, John D., Gregersen, Peter K., Syvanen, Ann-Christine, Ronnblom, Lars, Criswell, Lindsey A., Jacob, Chaim O., Sivils, Kathy L., Tsao, Betty P., Schanberg, Laura E., Behrens, Timothy W., Silverman, Earl D., Alarcon-Riquelme, Marta E., Kimberly, Robert P., Harley, John B., Wakeland, Edward K., Graham, Robert R., Gaffney, Patrick M., and Vyse, Timothy J.
Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.
Published: 2017
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27. X Chromosome Dose and Sex Bias in Autoimmune Diseases : Increased 47,XXX in Systemic Lupus Erythematosus and Sjögren's Syndrome

Author: Liu, Ke, Kurien, Biji T, Zimmerman, Sarah L, Kaufman, Kenneth M, Taft, Diana H, Kottyan, Leah C, Lazaro, Sara, Weaver, Carrie A, Ice, John A, Adler, Adam J, Chodosh, James, Radfar, Lida, Rasmussen, Astrid, Stone, Donald U, Lewis, David M, Li, Shibo, Koelsch, Kristi A, Igoe, Ann, Talsania, Mitali, Kumar, Jay, Maier-Moore, Jacen S, Harris, Valerie M, Gopalakrishnan, Rajaram, Jonsson, Roland, Lessard, James A, Lu, Xianglan, Gottenberg, Jacques-Eric, Anaya, Juan-Manuel, Cunninghame-Graham, Deborah S, Huang, Andrew J W, Brennan, Michael T, Hughes, Pamela, Illei, Gabor G, Miceli-Richard, Corinne, Keystone, Edward C, Bykerk, Vivian P, Hirschfield, Gideon, Xie, Gang, Ng, Wan-Fai, Nordmark, Gunnel, Eriksson, Per, Omdal, Roald, Rhodus, Nelson L, Rischmueller, Maureen, Rohrer, Michael, Segal, Barbara M, Vyse, Timothy J, Wahren-Herlenius, Marie, Witte, Torsten, Pons-Estel, Bernardo, Alarcon-Riquelme, Marta E, Guthridge, Joel M, James, Judith A, Lessard, Christopher J, Kelly, Jennifer A, Thompson, Susan D, Gaffney, Patrick M, Montgomery, Courtney G, Edberg, Jeffrey C, Kimberly, Robert P, Alarcón, Graciela S, Langefeld, Carl L, Gilkeson, Gary S, Kamen, Diane L, Tsao, Betty P, McCune, W Joseph, Salmon, Jane E, Merrill, Joan T, Weisman, Michael H, Wallace, Daniel J, Utset, Tammy O, Bottinger, Erwin P, Amos, Christopher I, Siminovitch, Katherine A, Mariette, Xavier, Sivils, Kathy L, Harley, John B, Scofield, R Hal, Liu, Ke, Kurien, Biji T, Zimmerman, Sarah L, Kaufman, Kenneth M, Taft, Diana H, Kottyan, Leah C, Lazaro, Sara, Weaver, Carrie A, Ice, John A, Adler, Adam J, Chodosh, James, Radfar, Lida, Rasmussen, Astrid, Stone, Donald U, Lewis, David M, Li, Shibo, Koelsch, Kristi A, Igoe, Ann, Talsania, Mitali, Kumar, Jay, Maier-Moore, Jacen S, Harris, Valerie M, Gopalakrishnan, Rajaram, Jonsson, Roland, Lessard, James A, Lu, Xianglan, Gottenberg, Jacques-Eric, Anaya, Juan-Manuel, Cunninghame-Graham, Deborah S, Huang, Andrew J W, Brennan, Michael T, Hughes, Pamela, Illei, Gabor G, Miceli-Richard, Corinne, Keystone, Edward C, Bykerk, Vivian P, Hirschfield, Gideon, Xie, Gang, Ng, Wan-Fai, Nordmark, Gunnel, Eriksson, Per, Omdal, Roald, Rhodus, Nelson L, Rischmueller, Maureen, Rohrer, Michael, Segal, Barbara M, Vyse, Timothy J, Wahren-Herlenius, Marie, Witte, Torsten, Pons-Estel, Bernardo, Alarcon-Riquelme, Marta E, Guthridge, Joel M, James, Judith A, Lessard, Christopher J, Kelly, Jennifer A, Thompson, Susan D, Gaffney, Patrick M, Montgomery, Courtney G, Edberg, Jeffrey C, Kimberly, Robert P, Alarcón, Graciela S, Langefeld, Carl L, Gilkeson, Gary S, Kamen, Diane L, Tsao, Betty P, McCune, W Joseph, Salmon, Jane E, Merrill, Joan T, Weisman, Michael H, Wallace, Daniel J, Utset, Tammy O, Bottinger, Erwin P, Amos, Christopher I, Siminovitch, Katherine A, Mariette, Xavier, Sivils, Kathy L, Harley, John B, and Scofield, R Hal
Abstract: OBJECTIVE: More than 80% of autoimmune disease is female dominant, but the mechanism for this female bias is poorly understood. We suspected an X chromosome dose effect and hypothesized that trisomy X (47,XXX, 1 in ∼1,000 live female births) would be increased in female predominant diseases (e.g. systemic lupus erythematosus [SLE], primary Sjögren's syndrome [SS], primary biliary cirrhosis [PBC] and rheumatoid arthritis [RA]) compared to diseases without female predominance (sarcoidosis) and controls. METHODS: We identified 47,XXX subjects using aggregate data from single nucleotide polymorphism (SNP) arrays and confirmed, when possible, by fluorescent in situ hybridization (FISH) or quantitative polymerase chain reaction (q-PCR). RESULTS: We found 47,XXX in seven of 2,826 SLE and three of 1,033 SS female patients, but only in two of the 7,074 female controls (p=0.003, OR=8.78, 95% CI: 1.67-86.79 and p=0.02, OR=10.29, 95% CI: 1.18-123.47; respectively). One 47,XXX subject was present for ∼404 SLE women and ∼344 SS women. 47,XXX was present in excess among SLE and SS subjects. CONCLUSION: The estimated prevalence of SLE and SS in women with 47,XXX was respectively ∼2.5 and ∼2.9 times higher than in 46,XX women and ∼25 and ∼41 times higher than in 46,XY men. No statistically significant increase of 47,XXX was observed in other female-biased diseases (PBC or RA), supporting the idea of multiple pathways to sex bias in autoimmunity. This article is protected by copyright. All rights reserved.
Published: 2016
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28. X Chromosome Dose and Sex Bias in Autoimmune Diseases

Author: Liu, Ke, Kurien, Biji T., Zimmerman, Sarah L., Kaufman, Kenneth M., Taft, Diana H., Kottyan, Leah C., Lazaro, Sara, Weaver, Carrie A., Ice, John A., Adler, Adam J., Chodosh, James, Radfar, Lida, Rasmussen, Astrid, Stone, Donald U., Lewis, David M., Li, Shibo, Koelsch, Kristi A., Igoe, Ann, Talsania, Mitali, Kumar, Jay, Maier-Moore, Jacen S., Harris, Valerie M., Gopalakrishnan, Rajaram, Jonsson, Roland, Lessard, James A., Lu, Xianglan, Eric Gottenberg, Jacques, Manuel Anaya, Juan, Cunninghame-Graham, Deborah S., Huang, Andrew J. W., Brennan, Michael T., Hughes, Pamela, Mei, Gabor G., Miceli-Richard, Corinne, Keystone, Edward C., Bykerk, Vivian P., Hirschfield, Gideon, Xie, Gang, Ng, Wan-Fai, Nordmark, Gunnel, Eriksson, Per, Omda, Roald, Rhodus, Nelson L., Rischmueller, Maureen, Rohrer, Michael, Sega, Barbara M., Vvse, Timothy J., Wahren-Herlenius, Marie, Witte, Torsten, Pons-Este, Bernardo, Alarcon-Riquelme, Marta E., Guthridge, Joel M., James, Judith A., Lessard, Christopher J., Kelly, Jennifer A., Thompson, Susan D., Gaffney, Patrick M., Montgomery, Courtney G., Edberg, Jeffrey C., Kimberly, Robert P., Alarcon, Gracicla S., Langefeld, Carl L., Gilkeson, Gary S., Kamen, Diane L., Tsao, Betty P., Joseph McCune, W., Salmon, Jane E., Merrill, Joan T., Weisman, Michael H., Wallace, Daniel J., Utset, Tammy, Bottinger, Erwin P., Amos, Christopher I., Siminovitch, Katherine A., Mariette, Xavier, Sivils, Kathy L., Harley, John B., Hal Scofield, R., Liu, Ke, Kurien, Biji T., Zimmerman, Sarah L., Kaufman, Kenneth M., Taft, Diana H., Kottyan, Leah C., Lazaro, Sara, Weaver, Carrie A., Ice, John A., Adler, Adam J., Chodosh, James, Radfar, Lida, Rasmussen, Astrid, Stone, Donald U., Lewis, David M., Li, Shibo, Koelsch, Kristi A., Igoe, Ann, Talsania, Mitali, Kumar, Jay, Maier-Moore, Jacen S., Harris, Valerie M., Gopalakrishnan, Rajaram, Jonsson, Roland, Lessard, James A., Lu, Xianglan, Eric Gottenberg, Jacques, Manuel Anaya, Juan, Cunninghame-Graham, Deborah S., Huang, Andrew J. W., Brennan, Michael T., Hughes, Pamela, Mei, Gabor G., Miceli-Richard, Corinne, Keystone, Edward C., Bykerk, Vivian P., Hirschfield, Gideon, Xie, Gang, Ng, Wan-Fai, Nordmark, Gunnel, Eriksson, Per, Omda, Roald, Rhodus, Nelson L., Rischmueller, Maureen, Rohrer, Michael, Sega, Barbara M., Vvse, Timothy J., Wahren-Herlenius, Marie, Witte, Torsten, Pons-Este, Bernardo, Alarcon-Riquelme, Marta E., Guthridge, Joel M., James, Judith A., Lessard, Christopher J., Kelly, Jennifer A., Thompson, Susan D., Gaffney, Patrick M., Montgomery, Courtney G., Edberg, Jeffrey C., Kimberly, Robert P., Alarcon, Gracicla S., Langefeld, Carl L., Gilkeson, Gary S., Kamen, Diane L., Tsao, Betty P., Joseph McCune, W., Salmon, Jane E., Merrill, Joan T., Weisman, Michael H., Wallace, Daniel J., Utset, Tammy, Bottinger, Erwin P., Amos, Christopher I., Siminovitch, Katherine A., Mariette, Xavier, Sivils, Kathy L., Harley, John B., and Hal Scofield, R.
Abstract: Objective. More than 80% of autoimmune disease predominantly affects females, but the mechanism for this female bias is poorly understood. We suspected that an X chromosome dose effect accounts for this, and we undertook this study to test our hypothesis that trisomy X (47, XXX; occurring in similar to 1 in 1,000 live female births) would be increased in patients with female-predominant diseases (systemic lupus erythematosus [SLE], primary Sjogrens syndrome [SS], primary biliary cirrhosis, and rheumatoid arthritis [RA]) compared to patients with diseases without female predominance (sarcoidosis) and compared to controls. Methods. All subjects in this study were female. We identified subjects with 47, XXX using aggregate data from single-nucleotide polymorphism arrays, and, when possible, we confirmed the presence of 47, XXX using fluorescence in situ hybridization or quantitative polymerase chain reaction. Results. We found 47, XXX in 7 of 2,826 SLE patients and in 3 of 1,033 SS patients, but in only 2 of 7,074 controls (odds ratio in the SLE and primary SS groups 8.78 [95% confidence interval 1.67-86.79], P = 0.003 and odds ratio 10.29 [95% confidence interval 1.18-123.47], P = 0.02, respectively). One in 404 women with SLE and 1 in 344 women with SS had 47, XXX. There was an excess of 47, XXX among SLE and SS patients. Conclusion. The estimated prevalence of SLE and SS in women with 47, XXX was similar to 2.5 and similar to 2.9 times higher, respectively, than that in women with 46, XX and similar to 25 and similar to 41 times higher, respectively, than that in men with 46, XY. No statistically significant increase of 47, XXX was observed in other female-biased diseases (primary biliary cirrhosis or RA), supporting the idea of multiple pathways to sex bias in autoimmunity., Funding Agencies|NIH [AR-062755, AI-024717, AI-031584, AI-062629, AI-063274, AI-082714, AI-083194, AI-101934]; NIH (National Institute of Dental and Craniofacial Research Intramural Research Program); University of Oklahoma Health Sciences Center (Clinical and Translational Science OCTSI Summer Scholar Program); US Department of Veterans Affairs [IMMA9]; US Department of Defense [PR094002]; Alliance for Lupus Research; Kirkland Scholar Program; Strategic Research Program at Helse Bergen; Western Norway Regional Health Authority; Broegelmann Foundation; French Ministry of Health (EvASSESS Programme Hospitalier de Recherche Clinique); Swedish Rheumatism Foundation; Arthritis Australia; Research to Prevent Blindness; Medical Research Council, UK [G0800629]; DFG [KFO 250 WI 1031/6-1]; Canadian Institutes of Health Research [MOP89955, MOP74621]; Ontario Research Fund [RE05-075]; Canada Research Chair Program; Instituto de Salud Carlos III (ISCIII through FEDER) [02558]; Allergan; Lilly; UCB; The NIH [AR-042460, AR-048204, AR-048940, AR-049084, AR-052125, AR-053483, AR-053734, AR-056360, AR-058959, AR-062277, AR-043814, AR-065626, DE-015223, DE-018209, RR-020143, GM-103510, GM-104938, HG-008667, TR-001475, HG-006828]
Published: 2016
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29. Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans.

Author: Huang, Chengrui, Huang, Chengrui, Haritunians, Talin, Okou, David T, Cutler, David J, Zwick, Michael E, Taylor, Kent D, Datta, Lisa W, Maranville, Joseph C, Liu, Zhenqiu, Ellis, Shannon, Chopra, Pankaj, Alexander, Jonathan S, Baldassano, Robert N, Cross, Raymond K, Dassopoulos, Themistocles, Dhere, Tanvi A, Duerr, Richard H, Hanson, John S, Hou, Jason K, Hussain, Sunny Z, Isaacs, Kim L, Kachelries, Kelly E, Kader, Howard, Kappelman, Michael D, Katz, Jeffrey, Kellermayer, Richard, Kirschner, Barbara S, Kuemmerle, John F, Kumar, Archana, Kwon, John H, Lazarev, Mark, Mannon, Peter, Moulton, Dedrick E, Osuntokun, Bankole O, Patel, Ashish, Rioux, John D, Rotter, Jerome I, Saeed, Shehzad, Scherl, Ellen J, Silverberg, Mark S, Silverman, Ann, Targan, Stephan R, Valentine, John F, Wang, Ming-Hsi, Simpson, Claire L, Bridges, S Louis, Kimberly, Robert P, Rich, Stephen S, Cho, Judy H, Rienzo, Anna Di, Kao, Linda WH, McGovern, Dermot PB, Brant, Steven R, Kugathasan, Subra, Huang, Chengrui, Huang, Chengrui, Haritunians, Talin, Okou, David T, Cutler, David J, Zwick, Michael E, Taylor, Kent D, Datta, Lisa W, Maranville, Joseph C, Liu, Zhenqiu, Ellis, Shannon, Chopra, Pankaj, Alexander, Jonathan S, Baldassano, Robert N, Cross, Raymond K, Dassopoulos, Themistocles, Dhere, Tanvi A, Duerr, Richard H, Hanson, John S, Hou, Jason K, Hussain, Sunny Z, Isaacs, Kim L, Kachelries, Kelly E, Kader, Howard, Kappelman, Michael D, Katz, Jeffrey, Kellermayer, Richard, Kirschner, Barbara S, Kuemmerle, John F, Kumar, Archana, Kwon, John H, Lazarev, Mark, Mannon, Peter, Moulton, Dedrick E, Osuntokun, Bankole O, Patel, Ashish, Rioux, John D, Rotter, Jerome I, Saeed, Shehzad, Scherl, Ellen J, Silverberg, Mark S, Silverman, Ann, Targan, Stephan R, Valentine, John F, Wang, Ming-Hsi, Simpson, Claire L, Bridges, S Louis, Kimberly, Robert P, Rich, Stephen S, Cho, Judy H, Rienzo, Anna Di, Kao, Linda WH, McGovern, Dermot PB, Brant, Steven R, and Kugathasan, Subra
Abstract: Background & aimsInflammatory bowel disease (IBD) has familial aggregation in African Americans (AAs), but little is known about the molecular genetic susceptibility. Mapping studies using the Immunochip genotyping array expand the number of susceptibility loci for IBD in Caucasians to 163, but the contribution of the 163 loci and European admixture to IBD risk in AAs is unclear. We performed a genetic mapping study using the Immunochip to determine whether IBD susceptibility loci in Caucasians also affect risk in AAs and identify new associated loci.MethodsWe recruited AAs with IBD and without IBD (controls) from 34 IBD centers in the United States; additional controls were collected from 4 other Immunochip studies. Association and admixture loci were mapped for 1088 patients with Crohn's disease, 361 with ulcerative colitis, 62 with IBD type unknown, and 1797 controls; 130,241 autosomal single-nucleotide polymorphisms (SNPs) were analyzed.ResultsThe strongest associations were observed between ulcerative colitis and HLA rs9271366 (P = 7.5 × 10(-6)), Crohn's disease and 5p13.1 rs4286721 (P = 3.5 × 10(-6)), and IBD and KAT2A rs730086 (P = 2.3 × 10(-6)). Additional suggestive associations (P < 4.2 × 10(-5)) were observed between Crohn's disease and IBD and African-specific SNPs in STAT5A and STAT3; between IBD and SNPs in IL23R, IL12B, and C2orf43; and between ulcerative colitis and SNPs near HDAC11 and near LINC00994. The latter 3 loci have not been previously associated with IBD, but require replication. Established Caucasian associations were replicated in AAs (P < 3.1 × 10(-4)) at NOD2, IL23R, 5p15.3, and IKZF3. Significant admixture (P < 3.9 × 10(-4)) was observed for 17q12-17q21.31 (IZKF3 through STAT3), 10q11.23-10q21.2, 15q22.2-15q23, and 16p12.2-16p12.1. Network analyses showed significant enrichment (false discovery rate <1 × 10(-5)) in genes that encode members of the JAK-STAT, cytokine, and chemokine signaling pathways, as w
Published: 2015

30. Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans.

Author: Huang, Chengrui, Huang, Chengrui, Haritunians, Talin, Okou, David T, Cutler, David J, Zwick, Michael E, Taylor, Kent D, Datta, Lisa W, Maranville, Joseph C, Liu, Zhenqiu, Ellis, Shannon, Chopra, Pankaj, Alexander, Jonathan S, Baldassano, Robert N, Cross, Raymond K, Dassopoulos, Themistocles, Dhere, Tanvi A, Duerr, Richard H, Hanson, John S, Hou, Jason K, Hussain, Sunny Z, Isaacs, Kim L, Kachelries, Kelly E, Kader, Howard, Kappelman, Michael D, Katz, Jeffrey, Kellermayer, Richard, Kirschner, Barbara S, Kuemmerle, John F, Kumar, Archana, Kwon, John H, Lazarev, Mark, Mannon, Peter, Moulton, Dedrick E, Osuntokun, Bankole O, Patel, Ashish, Rioux, John D, Rotter, Jerome I, Saeed, Shehzad, Scherl, Ellen J, Silverberg, Mark S, Silverman, Ann, Targan, Stephan R, Valentine, John F, Wang, Ming-Hsi, Simpson, Claire L, Bridges, S Louis, Kimberly, Robert P, Rich, Stephen S, Cho, Judy H, Rienzo, Anna Di, Kao, Linda WH, McGovern, Dermot PB, Brant, Steven R, Kugathasan, Subra, Huang, Chengrui, Huang, Chengrui, Haritunians, Talin, Okou, David T, Cutler, David J, Zwick, Michael E, Taylor, Kent D, Datta, Lisa W, Maranville, Joseph C, Liu, Zhenqiu, Ellis, Shannon, Chopra, Pankaj, Alexander, Jonathan S, Baldassano, Robert N, Cross, Raymond K, Dassopoulos, Themistocles, Dhere, Tanvi A, Duerr, Richard H, Hanson, John S, Hou, Jason K, Hussain, Sunny Z, Isaacs, Kim L, Kachelries, Kelly E, Kader, Howard, Kappelman, Michael D, Katz, Jeffrey, Kellermayer, Richard, Kirschner, Barbara S, Kuemmerle, John F, Kumar, Archana, Kwon, John H, Lazarev, Mark, Mannon, Peter, Moulton, Dedrick E, Osuntokun, Bankole O, Patel, Ashish, Rioux, John D, Rotter, Jerome I, Saeed, Shehzad, Scherl, Ellen J, Silverberg, Mark S, Silverman, Ann, Targan, Stephan R, Valentine, John F, Wang, Ming-Hsi, Simpson, Claire L, Bridges, S Louis, Kimberly, Robert P, Rich, Stephen S, Cho, Judy H, Rienzo, Anna Di, Kao, Linda WH, McGovern, Dermot PB, Brant, Steven R, and Kugathasan, Subra
Abstract: Background & aimsInflammatory bowel disease (IBD) has familial aggregation in African Americans (AAs), but little is known about the molecular genetic susceptibility. Mapping studies using the Immunochip genotyping array expand the number of susceptibility loci for IBD in Caucasians to 163, but the contribution of the 163 loci and European admixture to IBD risk in AAs is unclear. We performed a genetic mapping study using the Immunochip to determine whether IBD susceptibility loci in Caucasians also affect risk in AAs and identify new associated loci.MethodsWe recruited AAs with IBD and without IBD (controls) from 34 IBD centers in the United States; additional controls were collected from 4 other Immunochip studies. Association and admixture loci were mapped for 1088 patients with Crohn's disease, 361 with ulcerative colitis, 62 with IBD type unknown, and 1797 controls; 130,241 autosomal single-nucleotide polymorphisms (SNPs) were analyzed.ResultsThe strongest associations were observed between ulcerative colitis and HLA rs9271366 (P = 7.5 × 10(-6)), Crohn's disease and 5p13.1 rs4286721 (P = 3.5 × 10(-6)), and IBD and KAT2A rs730086 (P = 2.3 × 10(-6)). Additional suggestive associations (P < 4.2 × 10(-5)) were observed between Crohn's disease and IBD and African-specific SNPs in STAT5A and STAT3; between IBD and SNPs in IL23R, IL12B, and C2orf43; and between ulcerative colitis and SNPs near HDAC11 and near LINC00994. The latter 3 loci have not been previously associated with IBD, but require replication. Established Caucasian associations were replicated in AAs (P < 3.1 × 10(-4)) at NOD2, IL23R, 5p15.3, and IKZF3. Significant admixture (P < 3.9 × 10(-4)) was observed for 17q12-17q21.31 (IZKF3 through STAT3), 10q11.23-10q21.2, 15q22.2-15q23, and 16p12.2-16p12.1. Network analyses showed significant enrichment (false discovery rate <1 × 10(-5)) in genes that encode members of the JAK-STAT, cytokine, and chemokine signaling pathways, as w
Published: 2015

31. Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression.

Author: Lu, Xiaoming, Lu, Xiaoming, Zoller, Erin E, Weirauch, Matthew T, Wu, Zhiguo, Namjou, Bahram, Williams, Adrienne H, Ziegler, Julie T, Comeau, Mary E, Marion, Miranda C, Glenn, Stuart B, Adler, Adam, Shen, Nan, Nath, Swapan K, Stevens, Anne M, Freedman, Barry I, Tsao, Betty P, Jacob, Chaim O, Kamen, Diane L, Brown, Elizabeth E, Gilkeson, Gary S, Alarcón, Graciela S, Reveille, John D, Anaya, Juan-Manuel, James, Judith A, Sivils, Kathy L, Criswell, Lindsey A, Vilá, Luis M, Alarcón-Riquelme, Marta E, Petri, Michelle, Scofield, R Hal, Kimberly, Robert P, Ramsey-Goldman, Rosalind, Joo, Young Bin, Choi, Jeongim, Bae, Sang-Cheol, Boackle, Susan A, Graham, Deborah Cunninghame, Vyse, Timothy J, Guthridge, Joel M, Gaffney, Patrick M, Langefeld, Carl D, Kelly, Jennifer A, Greis, Kenneth D, Kaufman, Kenneth M, Harley, John B, Kottyan, Leah C, Lu, Xiaoming, Lu, Xiaoming, Zoller, Erin E, Weirauch, Matthew T, Wu, Zhiguo, Namjou, Bahram, Williams, Adrienne H, Ziegler, Julie T, Comeau, Mary E, Marion, Miranda C, Glenn, Stuart B, Adler, Adam, Shen, Nan, Nath, Swapan K, Stevens, Anne M, Freedman, Barry I, Tsao, Betty P, Jacob, Chaim O, Kamen, Diane L, Brown, Elizabeth E, Gilkeson, Gary S, Alarcón, Graciela S, Reveille, John D, Anaya, Juan-Manuel, James, Judith A, Sivils, Kathy L, Criswell, Lindsey A, Vilá, Luis M, Alarcón-Riquelme, Marta E, Petri, Michelle, Scofield, R Hal, Kimberly, Robert P, Ramsey-Goldman, Rosalind, Joo, Young Bin, Choi, Jeongim, Bae, Sang-Cheol, Boackle, Susan A, Graham, Deborah Cunninghame, Vyse, Timothy J, Guthridge, Joel M, Gaffney, Patrick M, Langefeld, Carl D, Kelly, Jennifer A, Greis, Kenneth D, Kaufman, Kenneth M, Harley, John B, and Kottyan, Leah C
Abstract: Genetic variants at chromosomal region 11q23.3, near the gene ETS1, have been associated with systemic lupus erythematosus (SLE), or lupus, in independent cohorts of Asian ancestry. Several recent studies have implicated ETS1 as a critical driver of immune cell function and differentiation, and mice deficient in ETS1 develop an SLE-like autoimmunity. We performed a fine-mapping study of 14,551 subjects from multi-ancestral cohorts by starting with genotyped variants and imputing to all common variants spanning ETS1. By constructing genetic models via frequentist and Bayesian association methods, we identified 16 variants that are statistically likely to be causal. We functionally assessed each of these variants on the basis of their likelihood of affecting transcription factor binding, miRNA binding, or chromatin state. Of the four variants that we experimentally examined, only rs6590330 differentially binds lysate from B cells. Using mass spectrometry, we found more binding of the transcription factor signal transducer and activator of transcription 1 (STAT1) to DNA near the risk allele of rs6590330 than near the non-risk allele. Immunoblot analysis and chromatin immunoprecipitation of pSTAT1 in B cells heterozygous for rs6590330 confirmed that the risk allele increased binding to the active form of STAT1. Analysis with expression quantitative trait loci indicated that the risk allele of rs6590330 is associated with decreased ETS1 expression in Han Chinese, but not other ancestral cohorts. We propose a model in which the risk allele of rs6590330 is associated with decreased ETS1 expression and increases SLE risk by enhancing the binding of pSTAT1.
Published: 2015

32. Genetic associations of leptin-related polymorphisms with systemic lupus erythematosus.

Author: Zhao, Jian, Zhao, Jian, Wu, Hui, Langefeld, Carl D, Kaufman, Kenneth M, Kelly, Jennifer A, Bae, Sang-Cheol, Marta E. Alarcón-Riquelme for the BIOLUPUS and GENLES networks, Alarcón, Graciela S, Anaya, Juan-Manuel, Criswell, Lindsey A, Freedman, Barry I, Kamen, Diane L, Gilkeson, Gary S, Jacob, Chaim O, James, Judith A, Merrill, Joan T, Gaffney, Patrick M, Sivils, Kathy Moser, Niewold, Timothy B, Petri, Michelle A, Song, Seung Taek, Jeong, Hye-Jin, Ramsey-Goldman, Rosalind, Reveille, John D, Scofield, R Hal, Stevens, Anne M, Boackle, Susan A, Vilá, Luis M, Chang, Deh-Ming, Song, Yeong Wook, Vyse, Timothy J, Harley, John B, Brown, Elizabeth E, Edberg, Jeffrey C, Kimberly, Robert P, Hahn, Bevra H, Grossman, Jennifer M, Tsao, Betty P, La Cava, Antonio, Zhao, Jian, Zhao, Jian, Wu, Hui, Langefeld, Carl D, Kaufman, Kenneth M, Kelly, Jennifer A, Bae, Sang-Cheol, Marta E. Alarcón-Riquelme for the BIOLUPUS and GENLES networks, Alarcón, Graciela S, Anaya, Juan-Manuel, Criswell, Lindsey A, Freedman, Barry I, Kamen, Diane L, Gilkeson, Gary S, Jacob, Chaim O, James, Judith A, Merrill, Joan T, Gaffney, Patrick M, Sivils, Kathy Moser, Niewold, Timothy B, Petri, Michelle A, Song, Seung Taek, Jeong, Hye-Jin, Ramsey-Goldman, Rosalind, Reveille, John D, Scofield, R Hal, Stevens, Anne M, Boackle, Susan A, Vilá, Luis M, Chang, Deh-Ming, Song, Yeong Wook, Vyse, Timothy J, Harley, John B, Brown, Elizabeth E, Edberg, Jeffrey C, Kimberly, Robert P, Hahn, Bevra H, Grossman, Jennifer M, Tsao, Betty P, and La Cava, Antonio
Abstract: Leptin is abnormally elevated in the plasma of patients with systemic lupus erythematosus (SLE), where it is thought to promote and/or sustain pro-inflammatory responses. Whether this association could reflect an increased genetic susceptibility to develop SLE is not known, and studies of genetic associations with leptin-related polymorphisms in SLE patients have been so far inconclusive. Here we genotyped DNA samples from 15,706 SLE patients and healthy matched controls from four different ancestral groups, to correlate polymorphisms of genes of the leptin pathway to risk for SLE. It was found that although several SNPs showed weak associations, those associations did not remain significant after correction for multiple testing. These data do not support associations between defined leptin-related polymorphisms and increased susceptibility to develop SLE.
Published: 2015

33. End-stage renal disease in African Americans with lupus nephritis is associated with APOL1.

Author: Freedman, Barry I, Freedman, Barry I, Langefeld, Carl D, Andringa, Kelly K, Croker, Jennifer A, Williams, Adrienne H, Garner, Neva E, Birmingham, Daniel J, Hebert, Lee A, Hicks, Pamela J, Segal, Mark S, Edberg, Jeffrey C, Brown, Elizabeth E, Alarcón, Graciela S, Costenbader, Karen H, Comeau, Mary E, Criswell, Lindsey A, Harley, John B, James, Judith A, Kamen, Diane L, Lim, S Sam, Merrill, Joan T, Sivils, Kathy L, Niewold, Timothy B, Patel, Neha M, Petri, Michelle, Ramsey-Goldman, Rosalind, Reveille, John D, Salmon, Jane E, Tsao, Betty P, Gibson, Keisha L, Byers, Joyce R, Vinnikova, Anna K, Lea, Janice P, Julian, Bruce A, Kimberly, Robert P, Lupus Nephritis–End‐Stage Renal Disease Consortium, Freedman, Barry I, Freedman, Barry I, Langefeld, Carl D, Andringa, Kelly K, Croker, Jennifer A, Williams, Adrienne H, Garner, Neva E, Birmingham, Daniel J, Hebert, Lee A, Hicks, Pamela J, Segal, Mark S, Edberg, Jeffrey C, Brown, Elizabeth E, Alarcón, Graciela S, Costenbader, Karen H, Comeau, Mary E, Criswell, Lindsey A, Harley, John B, James, Judith A, Kamen, Diane L, Lim, S Sam, Merrill, Joan T, Sivils, Kathy L, Niewold, Timothy B, Patel, Neha M, Petri, Michelle, Ramsey-Goldman, Rosalind, Reveille, John D, Salmon, Jane E, Tsao, Betty P, Gibson, Keisha L, Byers, Joyce R, Vinnikova, Anna K, Lea, Janice P, Julian, Bruce A, Kimberly, Robert P, and Lupus Nephritis–End‐Stage Renal Disease Consortium
Abstract: ObjectiveLupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE) that exhibits familial aggregation and may progress to end-stage renal disease (ESRD). LN is more prevalent among African Americans than among European Americans. This study was undertaken to investigate the hypothesis that the apolipoprotein L1 gene (APOL1) nephropathy risk alleles G1/G2, common in African Americans and rare in European Americans, contribute to the ethnic disparity in risk.MethodsAPOL1 G1 and G2 nephropathy alleles were genotyped in 855 African American SLE patients with LN-ESRD (cases) and 534 African American SLE patients without nephropathy (controls) and tested for association under a recessive genetic model, by logistic regression.ResultsNinety percent of the SLE patients were female. The mean ± SD age at SLE diagnosis was significantly lower in LN-ESRD cases than in SLE non-nephropathy controls (27.3 ± 10.9 years versus 39.5 ± 12.2 years). The mean ± SD time from SLE diagnosis to development of LN-ESRD in cases was 7.3 ± 7.2 years. The G1/G2 risk alleles were strongly associated with SLE-ESRD, with 25% of cases and 12% of controls having 2 nephropathy alleles (odds ratio [OR] 2.57, recessive model P = 1.49 × 10(-9)), and after adjustment for age, sex, and ancestry admixture (OR 2.72, P = 6.23 × 10(-6)). The age-, sex-, and admixture-adjusted population attributable risk for ESRD among patients with G1/G2 polymorphisms was 0.26, compared to 0.003 among European American patients. The mean time from SLE diagnosis to ESRD development was ∼2 years earlier among individuals with APOL1 risk genotypes (P = 0.01).ConclusionAPOL1 G1/G2 alleles strongly impact the risk of LN-ESRD in African Americans, as well as the time to progression to ESRD. The high frequency of these alleles in African Americans with near absence in European Americans explains an important proportion of the increased risk of LN-ESRD in African Americans.
Published: 2014

34. Two functional lupus-associated BLK promoter variants control cell-type- and developmental-stage-specific transcription.

Author: Guthridge, Joel M, Guthridge, Joel M, Lu, Rufei, Sun, Harry, Sun, Celi, Wiley, Graham B, Dominguez, Nicolas, Macwana, Susan R, Lessard, Christopher J, Kim-Howard, Xana, Cobb, Beth L, Kaufman, Kenneth M, Kelly, Jennifer A, Langefeld, Carl D, Adler, Adam J, Harley, Isaac TW, Merrill, Joan T, Gilkeson, Gary S, Kamen, Diane L, Niewold, Timothy B, Brown, Elizabeth E, Edberg, Jeffery C, Petri, Michelle A, Ramsey-Goldman, Rosalind, Reveille, John D, Vilá, Luis M, Kimberly, Robert P, Freedman, Barry I, Stevens, Anne M, Boackle, Susan A, Criswell, Lindsey A, Vyse, Tim J, Behrens, Timothy W, Jacob, Chaim O, Alarcón-Riquelme, Marta E, Sivils, Kathy L, Choi, Jiyoung, Joo, Young Bin, Bang, So-Young, Lee, Hye-Soon, Bae, Sang-Cheol, Shen, Nan, Qian, Xiaoxia, Tsao, Betty P, Scofield, R Hal, Harley, John B, Webb, Carol F, Wakeland, Edward K, James, Judith A, Nath, Swapan K, Graham, Robert R, Gaffney, Patrick M, Guthridge, Joel M, Guthridge, Joel M, Lu, Rufei, Sun, Harry, Sun, Celi, Wiley, Graham B, Dominguez, Nicolas, Macwana, Susan R, Lessard, Christopher J, Kim-Howard, Xana, Cobb, Beth L, Kaufman, Kenneth M, Kelly, Jennifer A, Langefeld, Carl D, Adler, Adam J, Harley, Isaac TW, Merrill, Joan T, Gilkeson, Gary S, Kamen, Diane L, Niewold, Timothy B, Brown, Elizabeth E, Edberg, Jeffery C, Petri, Michelle A, Ramsey-Goldman, Rosalind, Reveille, John D, Vilá, Luis M, Kimberly, Robert P, Freedman, Barry I, Stevens, Anne M, Boackle, Susan A, Criswell, Lindsey A, Vyse, Tim J, Behrens, Timothy W, Jacob, Chaim O, Alarcón-Riquelme, Marta E, Sivils, Kathy L, Choi, Jiyoung, Joo, Young Bin, Bang, So-Young, Lee, Hye-Soon, Bae, Sang-Cheol, Shen, Nan, Qian, Xiaoxia, Tsao, Betty P, Scofield, R Hal, Harley, John B, Webb, Carol F, Wakeland, Edward K, James, Judith A, Nath, Swapan K, Graham, Robert R, and Gaffney, Patrick M
Abstract: Efforts to identify lupus-associated causal variants in the FAM167A/BLK locus on 8p21 are hampered by highly associated noncausal variants. In this report, we used a trans-population mapping and sequencing strategy to identify a common variant (rs922483) in the proximal BLK promoter and a tri-allelic variant (rs1382568) in the upstream alternative BLK promoter as putative causal variants for association with systemic lupus erythematosus. The risk allele (T) at rs922483 reduced proximal promoter activity and modulated alternative promoter usage. Allelic differences at rs1382568 resulted in altered promoter activity in B progenitor cell lines. Thus, our results demonstrated that both lupus-associated functional variants contribute to the autoimmune disease association by modulating transcription of BLK in B cells and thus potentially altering immune responses.
Published: 2014

35. Brief Report: Single-nucleotide polymorphisms in VKORC1 are risk factors for systemic lupus erythematosus in Asians.

Author: Kaiser, Rachel, Kaiser, Rachel, Taylor, Kimberly E, Deng, Yun, Zhao, Jian, Li, Yonghong, Nititham, Joanne, Chang, Monica, Catanese, Joseph, Begovich, Ann B, Brown, Elizabeth E, Edberg, Jeffrey C, McGwin, Gerald, Alarcón, Graciela S, Ramsey-Goldman, Rosalind, Reveille, John D, Vila, Luis M, Petri, Michelle, Kimberly, Robert P, Feng, Xuebing, Sun, Lingyun, Shen, Nan, Li, Wei, Lu, Jian-Xin, Wakeland, Edward K, Li, Quan-Zhen, Yang, Wanling, Lau, Yu-Lung, Liu, Fei-Lan, Chang, Deh-Ming, Yu, Chack-Yung, Song, Yeong W, Tsao, Betty P, Criswell, Lindsey A, Hwee Siew Howe and the Tan Tock Seng Hospital Systemic Lupus Erythematosus Study Group, Kaiser, Rachel, Kaiser, Rachel, Taylor, Kimberly E, Deng, Yun, Zhao, Jian, Li, Yonghong, Nititham, Joanne, Chang, Monica, Catanese, Joseph, Begovich, Ann B, Brown, Elizabeth E, Edberg, Jeffrey C, McGwin, Gerald, Alarcón, Graciela S, Ramsey-Goldman, Rosalind, Reveille, John D, Vila, Luis M, Petri, Michelle, Kimberly, Robert P, Feng, Xuebing, Sun, Lingyun, Shen, Nan, Li, Wei, Lu, Jian-Xin, Wakeland, Edward K, Li, Quan-Zhen, Yang, Wanling, Lau, Yu-Lung, Liu, Fei-Lan, Chang, Deh-Ming, Yu, Chack-Yung, Song, Yeong W, Tsao, Betty P, Criswell, Lindsey A, and Hwee Siew Howe and the Tan Tock Seng Hospital Systemic Lupus Erythematosus Study Group
Abstract: ObjectiveThe increased risk of thrombosis in systemic lupus erythematosus (SLE) may be partially explained by interrelated genetic pathways for thrombosis and SLE. The present study was undertaken to investigate whether 33 established and novel single-nucleotide polymorphisms (SNPs) in 20 genes involved in hemostasis pathways that have been associated with deep venous thrombosis (DVT) in the general population are risk factors for SLE among Asian subjects.MethodsPatients in the discovery cohort were enrolled in 1 of 2 North American SLE cohorts. Patients in the replication cohort were enrolled in 1 of 4 Asian or 2 North American cohorts. We first genotyped 263 Asian patients with SLE and 357 healthy Asian control subjects for 33 SNPs in the discovery phase, and then genotyped 5 SNPs in up to an additional 1,496 patients and 993 controls in the replication phase. Patients were compared to controls for bivariate association with minor alleles. Principal components analysis was used to control for intra-Asian ancestry in the replication cohort.ResultsTwo genetic variants in the gene VKORC1 were highly significant in both the discovery and replication cohorts: rs9934438 (in the discovery cohort, odds ratio [OR] 2.45, P=2×10(-9); in the replication cohort, OR 1.54, P=4×10(-6)) and rs9923231 (in the discovery cohort, OR 2.40, P=6×10(-9); in the replication cohort, OR 1.53, P=5×10(-6)). These associations were significant in the replication cohort after adjustment for intra-Asian ancestry: for rs9934438, OR 1.34, P=0.0029; for rs9923231, OR 1.34, P=0.0032.ConclusionGenetic variants in VKORC1, which are involved in vitamin K reduction and associated with DVT, correlate with SLE development in Asian subjects. These results suggest that there may be intersecting genetic pathways for the development of SLE and thrombosis.
Published: 2013

36. Variable association of reactive intermediate genes with systemic lupus erythematosus in populations with different African ancestry.

Author: Ramos, Paula S, Ramos, Paula S, Oates, James C, Kamen, Diane L, Williams, Adrienne H, Gaffney, Patrick M, Kelly, Jennifer A, Kaufman, Kenneth M, Kimberly, Robert P, Niewold, Timothy B, Jacob, Chaim O, Tsao, Betty P, Alarcón, Graciela S, Brown, Elizabeth E, Edberg, Jeffrey C, Petri, Michelle A, Ramsey-Goldman, Rosalind, Reveille, John D, Vilá, Luis M, James, Judith A, Guthridge, Joel M, Merrill, Joan T, Boackle, Susan A, Freedman, Barry I, Scofield, R Hal, Stevens, Anne M, Vyse, Timothy J, Criswell, Lindsey A, Moser, Kathy L, Alarcón-Riquelme, Marta E, Langefeld, Carl D, Harley, John B, Gilkeson, Gary S, Ramos, Paula S, Ramos, Paula S, Oates, James C, Kamen, Diane L, Williams, Adrienne H, Gaffney, Patrick M, Kelly, Jennifer A, Kaufman, Kenneth M, Kimberly, Robert P, Niewold, Timothy B, Jacob, Chaim O, Tsao, Betty P, Alarcón, Graciela S, Brown, Elizabeth E, Edberg, Jeffrey C, Petri, Michelle A, Ramsey-Goldman, Rosalind, Reveille, John D, Vilá, Luis M, James, Judith A, Guthridge, Joel M, Merrill, Joan T, Boackle, Susan A, Freedman, Barry I, Scofield, R Hal, Stevens, Anne M, Vyse, Timothy J, Criswell, Lindsey A, Moser, Kathy L, Alarcón-Riquelme, Marta E, Langefeld, Carl D, Harley, John B, and Gilkeson, Gary S
Abstract: ObjectiveLittle is known about the genetic etiology of systemic lupus erythematosus (SLE) in individuals of African ancestry, despite its higher prevalence and greater disease severity. Overproduction of nitric oxide (NO) and reactive oxygen species are implicated in the pathogenesis and severity of SLE, making NO synthases and other reactive intermediate-related genes biological candidates for disease susceptibility. We analyzed variation in reactive intermediate genes for association with SLE in 2 populations with African ancestry.MethodsA total of 244 single-nucleotide polymorphisms (SNP) from 53 regions were analyzed in non-Gullah African Americans (AA; 1432 cases and 1687 controls) and the genetically more homogeneous Gullah of the Sea Islands of South Carolina (133 cases and 112 controls). Single-marker, haplotype, and 2-locus interaction tests were computed for these populations.ResultsThe glutathione reductase gene GSR (rs2253409; p = 0.0014, OR 1.26, 95% CI 1.09-1.44) was the most significant single SNP association in AA. In the Gullah, the NADH dehydrogenase NDUFS4 (rs381575; p = 0.0065, OR 2.10, 95% CI 1.23-3.59) and NO synthase gene NOS1 (rs561712; p = 0.0072, OR 0.62, 95% CI 0.44-0.88) were most strongly associated with SLE. When both populations were analyzed together, GSR remained the most significant effect (rs2253409; p = 0.00072, OR 1.26, 95% CI 1.10-1.44). Haplotype and 2-locus interaction analyses also uncovered different loci in each population.ConclusionThese results suggest distinct patterns of association with SLE in African-derived populations; specific loci may be more strongly associated within select population groups.
Published: 2013

37. Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as Susceptibility Loci for Systemic Lupus Erythematosus in a Large-Scale Multiracial Replication Study

Author: Lessard, Christopher J., Adrianto, Indra, Ice, John A., Wiley, Graham B., Kelly, Jennifer A., Glenn, Stuart B., Adler, Adam J., Li, He, Rasmussen, Astrid, Williams, Adrienne H., Ziegler, Julie, Comeau, Mary E., Marion, Miranda, Wakeland, Benjamin E., Liang, Chaoying, Ramos, Paula S., Grundahl, Kiely M., Gallant, Caroline J., Alarcon-Riquelme, Marta E., Alarcon, Graciela S., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Chang, Deh-Ming, Cho, Soo-Kyung, Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Kim, Jae-Hoon, Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Scofield, R. Hal, Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Kaufman, Kenneth M., Harley, John B., Wakeland, Edward K., Langefeld, Carl D., Gaffney, Patrick M., Montgomery, Courtney G., Moser, Kathy L., Lessard, Christopher J., Adrianto, Indra, Ice, John A., Wiley, Graham B., Kelly, Jennifer A., Glenn, Stuart B., Adler, Adam J., Li, He, Rasmussen, Astrid, Williams, Adrienne H., Ziegler, Julie, Comeau, Mary E., Marion, Miranda, Wakeland, Benjamin E., Liang, Chaoying, Ramos, Paula S., Grundahl, Kiely M., Gallant, Caroline J., Alarcon-Riquelme, Marta E., Alarcon, Graciela S., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Chang, Deh-Ming, Cho, Soo-Kyung, Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Kim, Jae-Hoon, Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Scofield, R. Hal, Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Kaufman, Kenneth M., Harley, John B., Wakeland, Edward K., Langefeld, Carl D., Gaffney, Patrick M., Montgomery, Courtney G., and Moser, Kathy L.
Abstract: Systemic lupus erythematosus (SLE) is a chronic heterogeneous autoimmune disorder characterized by the loss of tolerance to self-antigens and dysregulated interferon responses. The etiology of SLE is complex, involving both heritable and environmental factors. Candidate-gene studies and genome-wide association (GWA) scans have been successful in identifying new loci that contribute to disease susceptibility; however, much of the heritable risk has yet to be identified. In this study, we sought to replicate 1,580 variants showing suggestive association with SLE in a previously published GWA scan of European Americans; we tested a multiethnic population consisting of 7,998 SLE cases and 7,492 controls of European, African American, Asian, Hispanic, Gullah, and Amerindian ancestry to find association with the disease. Several genes relevant to immunological pathways showed association with SLE. Three loci exceeded the genome-wide significance threshold: interferon regulatory factor 8 (IRF8; rs11644034; p(meta-Euro) = 2.08 x 10(-10)), transmembrane protein 39A (TMEM39A; rs1132200; p(meta-all) 8.62 x 10(-9)), and 17q21 (rs1453560; p(meta-all) = 3.48 x 10(-10)) between IKAROS family of zinc finger 3 (AIOLOS; IKZF3) and zona pellucida binding protein 2 (ZPBP2). Fine mapping, resequencing, imputation, and haplotype analysis of IRF8 indicated that three independent effects tagged by rs8046526, rs450443, and rs4843869, respectively, were required for risk in individuals of European ancestry. Eleven additional replicated effects (5 x 10(-8) < p(meta-Euro) < 9.99 x 10(-5)) were observed with CFHR1, CADM2, LOC730109/IL12A, LPP, LOC63920, SLU7, ADAMTSL1, C10orf64, OR8D4 FAM19A2, and STXBP6. The results of this study increase the number of confirmed SLE risk loci and identify others warranting further investigation.
Published: 2012
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38. Evaluation of TRAF6 in a large multiancestral lupus cohort

Author: Namjou, Bahram, Choi, Chan-Bum, Harley, Isaac T. W., Alarcon-Riquelme, Marta E., Kelly, Jennifer A., Glenn, Stuart B., Ojwang, Joshua O., Adler, Adam, Kim, Kwangwoo, Gallant, Caroline J., Boackle, Susan A., Criswell, Lindsey A., Kimberly, Robert P., Brown, Elizabeth E., Edberg, Jeffrey, Alarcon, Graciela S., Stevens, Anne M., Jacob, Chaim O., Gilkeson, Gary S., Kamen, Diane L., Tsao, Betty P., Anaya, Juan-Manuel, Kim, Eun-Mi, Park, So-Yeon, Sung, Yoon-Kyoung, Guthridge, Joel M., Merrill, Joan T., Petri, Michelle, Ramsey-Goldman, Rosalind, Vila, Luis M., Niewold, Timothy B., Martin, Javier, Pons-Estel, Bernardo A., Vyse, Timothy J., Freedman, Barry I., Moser, Kathy L., Gaffney, Patrick M., Williams, Adrienne H., Comeau, Mary E., Reveille, John D., Kang, Changwon, James, Judith A., Scofield, R. Hal, Langefeld, Carl D., Kaufman, Kenneth M., Harley, John B., Bae, Sang-Cheol, Namjou, Bahram, Choi, Chan-Bum, Harley, Isaac T. W., Alarcon-Riquelme, Marta E., Kelly, Jennifer A., Glenn, Stuart B., Ojwang, Joshua O., Adler, Adam, Kim, Kwangwoo, Gallant, Caroline J., Boackle, Susan A., Criswell, Lindsey A., Kimberly, Robert P., Brown, Elizabeth E., Edberg, Jeffrey, Alarcon, Graciela S., Stevens, Anne M., Jacob, Chaim O., Gilkeson, Gary S., Kamen, Diane L., Tsao, Betty P., Anaya, Juan-Manuel, Kim, Eun-Mi, Park, So-Yeon, Sung, Yoon-Kyoung, Guthridge, Joel M., Merrill, Joan T., Petri, Michelle, Ramsey-Goldman, Rosalind, Vila, Luis M., Niewold, Timothy B., Martin, Javier, Pons-Estel, Bernardo A., Vyse, Timothy J., Freedman, Barry I., Moser, Kathy L., Gaffney, Patrick M., Williams, Adrienne H., Comeau, Mary E., Reveille, John D., Kang, Changwon, James, Judith A., Scofield, R. Hal, Langefeld, Carl D., Kaufman, Kenneth M., Harley, John B., and Bae, Sang-Cheol
Abstract: Objective Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with significant immune system aberrations resulting from complex heritable genetics as well as environmental factors. We undertook to study the role of TRAF6 as a candidate gene for SLE, since it plays a major role in several signaling pathways that are important for immunity and organ development. Methods Fifteen single-nucleotide polymorphisms (SNPs) across TRAF6 were evaluated in 7,490 SLE patients and 6,780 control subjects from different ancestries. Population-based casecontrol association analyses and meta-analyses were performed. P values, false discovery rate q values, and odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated. Results Evidence of associations was detected in multiple SNPs. The best overall P values were obtained for SNPs rs5030437 and rs4755453 (P = 7.85 x 10(-5) and P = 4.73 x 10(-5), respectively) without significant heterogeneity among populations (P = 0.67 and P = 0.50, respectively, in Q statistic). In addition, SNP rs540386, which was previously reported to be associated with rheumatoid arthritis (RA), was found to be in linkage disequilibrium with these 2 SNPs (r2 = 0.95) and demonstrated evidence of association with SLE in the same direction (meta-analysis P = 9.15 x 10(-4), OR 0.89 [95% CI 0.830.95]). The presence of thrombocytopenia improved the overall results in different populations (meta-analysis P = 1.99 x 10(-6), OR 0.57 [95% CI 0.450.72], for rs5030470). Finally, evidence of family-based association in 34 African American pedigrees with the presence of thrombocytopenia was detected in 1 available SNP (rs5030437) with a Z score magnitude of 2.28 (P = 0.02) under a dominant model. Conclusion Our data indicate the presence of association of TRAF6 with SLE, consistent with the previous report of association with RA. These data provide further support for the involvement of TRAF6 in the pathogenesis of autoimmunity.
Published: 2012
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39. Analysis of autosomal genes reveals gene-sex interactions and higher total genetic risk in men with systemic lupus erythematosus

Author: UCL - SSS/DDUV - Institut de Duve, UCL - (SLuc) Service de rhumatologie, Hughes, Travis, Adler, Adam, Merrill, Joan T, Kelly, Jennifer A, Kaufman, Kenneth M, Williams, Adrienne, Langefeld, Carl D, Gilkeson, Gary S, Sanchez, Elena, Martin, Javier, Boackle, Susan A, Stevens, Anne M, Alarcón, Graciela S, Niewold, Timothy B, Brown, Elizabeth E, Kimberly, Robert P, Edberg, Jeffrey C, Ramsey-Goldman, Rosalind, Petri, Michelle, Reveille, John D, Criswell, Lindsey A, Vilá, Luis M, Jacob, Chaim O, Gaffney, Patrick M, Moser, Kathy L, Vyse, Timothy J, Alarcón-Riquelme, Marta E, BIOLUPUS Network, James, Judith A, Tsao, Betty P, Scofield, R Hal, Harley, John B, Richardson, Bruce C, Sawalha, Amr H, Lauwerys, Bernard, UCL - SSS/DDUV - Institut de Duve, UCL - (SLuc) Service de rhumatologie, Hughes, Travis, Adler, Adam, Merrill, Joan T, Kelly, Jennifer A, Kaufman, Kenneth M, Williams, Adrienne, Langefeld, Carl D, Gilkeson, Gary S, Sanchez, Elena, Martin, Javier, Boackle, Susan A, Stevens, Anne M, Alarcón, Graciela S, Niewold, Timothy B, Brown, Elizabeth E, Kimberly, Robert P, Edberg, Jeffrey C, Ramsey-Goldman, Rosalind, Petri, Michelle, Reveille, John D, Criswell, Lindsey A, Vilá, Luis M, Jacob, Chaim O, Gaffney, Patrick M, Moser, Kathy L, Vyse, Timothy J, Alarcón-Riquelme, Marta E, BIOLUPUS Network, James, Judith A, Tsao, Betty P, Scofield, R Hal, Harley, John B, Richardson, Bruce C, Sawalha, Amr H, and Lauwerys, Bernard
Abstract: Objectives: Systemic lupus erythematosus (SLE) is a sexually dimorphic autoimmune disease which is more common in women, but affected men often experience a more severe disease. The genetic basis of sexual dimorphism in SLE is not clearly defined. A study was undertaken to examine sex-specific genetic effects among SLE susceptibility loci. Methods: A total of 18 autosomal genetic susceptibility loci for SLE were genotyped in a large set of patients with SLE and controls of European descent, consisting of 5932 female and 1495 male samples. Sex-specific genetic association analyses were performed. The sex-gene interaction was further validated using parametric and non-parametric methods. Aggregate differences in sex-specific genetic risk were examined by calculating a cumulative genetic risk score for SLE in each individual and comparing the average genetic risk between male and female patients. Results: A significantly higher cumulative genetic risk for SLE was observed in men than in women. (P=4.52x10 -8) A significant sex-gene interaction was seen primarily in the human leucocyte antigen (HLA) region but also in IRF5, whereby men with SLE possess a significantly higher frequency of risk alleles than women. The genetic effect observed in KIAA1542 is specific to women with SLE and does not seem to have a role in men. Conclusions: The data indicate that men require a higher cumulative genetic load than women to develop SLE. These observations suggest that sex bias in autoimmunity could be influenced by autosomal genetic susceptibility loci.
Published: 2012

40. Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study

Author: Lessard, Christopher J., Adrianto, Indra, Ice, John A., Wiley, Graham B., Kelly, Jennifer A., Glenn, Stuart B., Adler, Adam J., Li, He, Rasmussen, Astrid, Williams, Adrienne H., Ziegler, Julie, Comeau, Mary, Marion, Miranda, Wakeland, Benjamin E., Liang, Chaoying, Ramos, Paula S., Grundahl, Kiely M., Gallant, Caroline J., Alarcón-Riquelme, Marta E., Alarcón, Graciela S., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan, Brown, Elizabeth E., Chang, Deh-Ming, Cho, Soo-Kyung, Criswel, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Kim, Jae-Hoon, Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Scofield, Robert H., Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Kaufman, Kenneth M., Harley, John B., Wakeland, Edward K., Langefeld, Carl D., Gaffney, Patrick M., Montgomery, Courtney G., Moser, Kathy L., Lessard, Christopher J., Adrianto, Indra, Ice, John A., Wiley, Graham B., Kelly, Jennifer A., Glenn, Stuart B., Adler, Adam J., Li, He, Rasmussen, Astrid, Williams, Adrienne H., Ziegler, Julie, Comeau, Mary, Marion, Miranda, Wakeland, Benjamin E., Liang, Chaoying, Ramos, Paula S., Grundahl, Kiely M., Gallant, Caroline J., Alarcón-Riquelme, Marta E., Alarcón, Graciela S., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan, Brown, Elizabeth E., Chang, Deh-Ming, Cho, Soo-Kyung, Criswel, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Kim, Jae-Hoon, Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Scofield, Robert H., Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Kaufman, Kenneth M., Harley, John B., Wakeland, Edward K., Langefeld, Carl D., Gaffney, Patrick M., Montgomery, Courtney G., and Moser, Kathy L.
Abstract: Systemic lupus erythematosus (SLE) is a chronic heterogeneous autoimmune disorder characterized by the loss of tolerance to self-antigens and dysregulated interferon responses. The etiology of SLE is complex, involving both heritable and environmental factors. Candidate-gene studies and genome-wide association (GWA) scans have been successful in identifying new loci that contribute to disease susceptibility; however, much of the heritable risk has yet to be identified. In this study, we sought to replicate 1,580 variants showing suggestive association with SLE in a previously published GWA scan of European Americans; we tested a multiethnic population consisting of 7,998 SLE cases and 7,492 controls of European, African American, Asian, Hispanic, Gullah, and Amerindian ancestry to find association with the disease. Several genes relevant to immunological pathways showed association with SLE. Three loci exceeded the genome-wide significance threshold: interferon regulatory factor 8 (IRF8; rs11644034; p meta-Euro = 2.08 × 10 -10), transmembrane protein 39A (TMEM39A; rs1132200; p meta-all = 8.62 × 10 -9), and 17q21 (rs1453560; p meta-all = 3.48 × 10 -10) between IKAROS family of zinc finger 3 (AIOLOS; IKZF3) and zona pellucida binding protein 2 (ZPBP2). Fine mapping, resequencing, imputation, and haplotype analysis of IRF8 indicated that three independent effects tagged by rs8046526, rs450443, and rs4843869, respectively, were required for risk in individuals of European ancestry. Eleven additional replicated effects (5 × 10 -8 < p meta-Euro < 9.99 × 10 -5) were observed with CFHR1, CADM2, LOC730109/IL12A, LPP, LOC63920, SLU7, ADAMTSL1, C10orf64, OR8D4, FAM19A2, and STXBP6. The results of this study increase the number of confirmed SLE risk loci and identify others warranting further investigation. © 2012 The American Society of Human Genetics.
Published: 2012

41. Evidence for gene???gene epistatic interactions among susceptibility loci for systemic lupus erythematosus

Author: University of Michigan and Ann Arbor VA Medical Center, Ann Arbor, University of Puerto Rico, San Juan, Puerto Rico, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Oklahoma City VA Medical Center, Oklahoma City, Wake Forest University Health Sciences Center, Winston???Salem, North Carolina, University of Alabama at Birmingham, Northwestern University Feinberg School of Medicine, Chicago, Illinois, Johns Hopkins University School of Medicine, Baltimore, Maryland, University of Colorado Denver School of Medicine, Aurora, University of Washington and Seattle Children's Research Institute, Seattle, University of Texas Health Science Center at Houston, Instituto de Parasitolog??a y Biomedicina L??pez???Neyra, CSIC, Granada, Spain, University of Chicago, Chicago, Illinois, Medical University of South Carolina, Charleston, University of California, San Francisco, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, University of Southern California, Los Angeles, University of California, Los Angeles, King's College London and Guy's Hospital, London, UK, Cincinnati Children's Hospital Medical Center and Cincinnati VA Medical Center, Cincinnati, Ohio, Center for Genomics and Oncological Research Pfizer???University of Granada???Junta de Andalucia, Granada, Spain, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, MS#24, Oklahoma City, OK 73104, Hughes, Travis, Adler, Adam, Kelly, Jennifer A., Kaufman, Kenneth M., Williams, Adrienne H., Langefeld, Carl D., Brown, Elizabeth E., Alarc??n, Graciela S., Kimberly, Robert P., Edberg, Jeffrey C., Ramsey???goldman, Rosalind, Petri, Michelle, Boackle, Susan A., Stevens, Anne M., Reveille, John D., Sanchez, Elena, Mart??n, Javier, Niewold, Timothy B., Vil??, Luis M., Scofield, R. Hal, Gilkeson, Gary S., Gaffney, Patrick M., Criswell, Lindsey A., Moser, Kathy L., Merrill, Joan T., Jacob, Chaim O., Tsao, Betty P., James, Judith A., Vyse, Timothy J., Alarc??n???riquelme, Marta E., Harley, John B., Richardson, Bruce C., Sawalha, Amr H., University of Michigan and Ann Arbor VA Medical Center, Ann Arbor, University of Puerto Rico, San Juan, Puerto Rico, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Oklahoma City VA Medical Center, Oklahoma City, Wake Forest University Health Sciences Center, Winston???Salem, North Carolina, University of Alabama at Birmingham, Northwestern University Feinberg School of Medicine, Chicago, Illinois, Johns Hopkins University School of Medicine, Baltimore, Maryland, University of Colorado Denver School of Medicine, Aurora, University of Washington and Seattle Children's Research Institute, Seattle, University of Texas Health Science Center at Houston, Instituto de Parasitolog??a y Biomedicina L??pez???Neyra, CSIC, Granada, Spain, University of Chicago, Chicago, Illinois, Medical University of South Carolina, Charleston, University of California, San Francisco, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, University of Southern California, Los Angeles, University of California, Los Angeles, King's College London and Guy's Hospital, London, UK, Cincinnati Children's Hospital Medical Center and Cincinnati VA Medical Center, Cincinnati, Ohio, Center for Genomics and Oncological Research Pfizer???University of Granada???Junta de Andalucia, Granada, Spain, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, MS#24, Oklahoma City, OK 73104, Hughes, Travis, Adler, Adam, Kelly, Jennifer A., Kaufman, Kenneth M., Williams, Adrienne H., Langefeld, Carl D., Brown, Elizabeth E., Alarc??n, Graciela S., Kimberly, Robert P., Edberg, Jeffrey C., Ramsey???goldman, Rosalind, Petri, Michelle, Boackle, Susan A., Stevens, Anne M., Reveille, John D., Sanchez, Elena, Mart??n, Javier, Niewold, Timothy B., Vil??, Luis M., Scofield, R. Hal, Gilkeson, Gary S., Gaffney, Patrick M., Criswell, Lindsey A., Moser, Kathy L., Merrill, Joan T., Jacob, Chaim O., Tsao, Betty P., James, Judith A., Vyse, Timothy J., Alarc??n???riquelme, Marta E., Harley, John B., Richardson, Bruce C., and Sawalha, Amr H.
Abstract: Objective Several confirmed genetic susceptibility loci for lupus have been described. To date, no clear evidence for genetic epistasis in lupus has been established. The aim of this study was to test for gene???gene interactions in a number of known lupus susceptibility loci. Methods Eighteen single???nucleotide polymorphisms tagging independent and confirmed lupus susceptibility loci were genotyped in a set of 4,248 patients with lupus and 3,818 normal healthy control subjects of European descent. Epistasis was tested by a 2???step approach using both parametric and nonparametric methods. The false discovery rate (FDR) method was used to correct for multiple testing. Results We detected and confirmed gene???gene interactions between the HLA region and CTLA4 , IRF5 , and ITGAM and between PDCD1 and IL21 in patients with lupus. The most significant interaction detected by parametric analysis was between rs3131379 in the HLA region and rs231775 in CTLA4 (interaction odds ratio 1.19, Z = 3.95, P = 7.8 ?? 10 ???5 [FDR ???0.05], P for multifactor dimensionality reduction = 5.9 ?? 10 ???45 ). Importantly, our data suggest that in patients with lupus, the presence of the HLA lupus risk alleles in rs1270942 and rs3131379 increases the odds of also carrying the lupus risk allele in IRF5 (rs2070197) by 17% and 16%, respectively ( P = 0.0028 and P = 0.0047, respectively). Conclusion We provide evidence for gene???gene epistasis in systemic lupus erythematosus. These findings support a role for genetic interaction contributing to the complexity of lupus heritability.
Published: 2012

42. Genetic risk factors for thrombosis in systemic lupus erythematosus.

Author: Kaiser, Rachel, Kaiser, Rachel, Li, Yonghong, Chang, Monica, Catanese, Joseph, Begovich, Ann B, Brown, Elizabeth E, Edberg, Jeffrey C, McGwin, Gerald, Alarcón, Graciela S, Ramsey-Goldman, Rosalind, Reveille, John D, Vilá, Luis M, Petri, Michelle A, Kimberly, Robert P, Taylor, Kimberly E, Criswell, Lindsey A, Kaiser, Rachel, Kaiser, Rachel, Li, Yonghong, Chang, Monica, Catanese, Joseph, Begovich, Ann B, Brown, Elizabeth E, Edberg, Jeffrey C, McGwin, Gerald, Alarcón, Graciela S, Ramsey-Goldman, Rosalind, Reveille, John D, Vilá, Luis M, Petri, Michelle A, Kimberly, Robert P, Taylor, Kimberly E, and Criswell, Lindsey A
Abstract: ObjectiveThrombosis is a serious complication of systemic lupus erythematosus (SLE). We investigated whether genetic variants implicated in thrombosis pathways are associated with thrombosis among 2 ethnically diverse SLE cohorts.MethodsOur discovery cohort consisted of 1698 patients with SLE enrolled in the University of California, San Francisco, Lupus Genetics Project and our replication cohort included 1361 patients with SLE enrolled in the PROFILE cohort. Patients fulfilled American College of Rheumatology SLE criteria, and data relevant to thrombosis were available. Thirty-three single nucleotide polymorphisms (SNP) previously shown to be associated with risk of deep venous thrombosis in the general population or implicated in thrombosis pathways were genotyped and tested for association with thrombosis in bivariate allelic analyses. SNP with p < 0.1 in the bivariate analyses were further tested in multivariable logistic regression models adjusted for age, sex, disease duration, antiphospholipid antibody status, smoking, nephritis, and medications.ResultsIn the discovery cohort, 23% of patients with SLE experienced a thrombotic event. SNP in the following genes demonstrated association with thrombosis risk overall in the discovery or replication cohorts and were assessed using metaanalytic methods: factor V Leiden (FVL) rs6025 (OR 1.85, p = 0.02) and methylenetetrahydrofolate reductase (MTHFR) rs1801133 (OR 0.75, p = 0.04) in whites, and fibrinogen gamma (FGG) rs2066865 (OR 1.91, p = 0.01) in Hispanic Americans. SNP in these genes showed association with venous thrombosis risk in whites: MTHFR rs1801131 (OR 1.51, p = 0.01), MTHFR rs1801133 (OR 0.70, p = 0.04), FVL rs6025 (OR 2.69, p = 0.002), and FGG rs2066865 (OR 1.49, p = 0.02) in whites. A SNP in FGG rs2066865 (OR 2.19, p = 0.003) demonstrated association with arterial thrombosis risk in Hispanics.ConclusionOur results implicate specific genetic risk factors for thrombosis in patients with SLE and sugges
Published: 2012

43. Impact of genetic ancestry and sociodemographic status on the clinical expression of systemic lupus erythematosus in American Indian-European populations.

Author: Sánchez, Elena, Sánchez, Elena, Rasmussen, Astrid, Riba, Laura, Acevedo-Vasquez, Eduardo, Kelly, Jennifer A, Langefeld, Carl D, Williams, Adrianne H, Ziegler, Julie T, Comeau, Mary E, Marion, Miranda C, García-De La Torre, Ignacio, Maradiaga-Ceceña, Marco A, Cardiel, Mario H, Esquivel-Valerio, Jorge A, Rodriguez-Amado, Jacqueline, Moctezuma, José Francisco, Miranda, Pedro, Perandones, Carlos E, Castel, Cecilia, Laborde, Hugo A, Alba, Paula, Musuruana, Jorge L, Goecke, I Annelise, Anaya, Juan-Manuel, Kaufman, Kenneth M, Adler, Adam, Glenn, Stuart B, Brown, Elizabeth E, Alarcón, Graciela S, Kimberly, Robert P, Edberg, Jeffrey C, Vilá, Luis M, Criswell, Lindsey A, Gilkeson, Gary S, Niewold, Timothy B, Martín, Javier, Vyse, Timothy J, Boackle, Susan A, Ramsey-Goldman, Rosalind, Scofield, R Hal, Petri, Michelle, Merrill, Joan T, Reveille, John D, Tsao, Betty P, Orozco, Lorena, Baca, Vicente, Moser, Kathy L, Gaffney, Patrick M, James, Judith A, Harley, John B, Tusié-Luna, Teresa, Pons-Estel, Bernardo A, Jacob, Chaim O, Alarcón-Riquelme, Marta E, Sánchez, Elena, Sánchez, Elena, Rasmussen, Astrid, Riba, Laura, Acevedo-Vasquez, Eduardo, Kelly, Jennifer A, Langefeld, Carl D, Williams, Adrianne H, Ziegler, Julie T, Comeau, Mary E, Marion, Miranda C, García-De La Torre, Ignacio, Maradiaga-Ceceña, Marco A, Cardiel, Mario H, Esquivel-Valerio, Jorge A, Rodriguez-Amado, Jacqueline, Moctezuma, José Francisco, Miranda, Pedro, Perandones, Carlos E, Castel, Cecilia, Laborde, Hugo A, Alba, Paula, Musuruana, Jorge L, Goecke, I Annelise, Anaya, Juan-Manuel, Kaufman, Kenneth M, Adler, Adam, Glenn, Stuart B, Brown, Elizabeth E, Alarcón, Graciela S, Kimberly, Robert P, Edberg, Jeffrey C, Vilá, Luis M, Criswell, Lindsey A, Gilkeson, Gary S, Niewold, Timothy B, Martín, Javier, Vyse, Timothy J, Boackle, Susan A, Ramsey-Goldman, Rosalind, Scofield, R Hal, Petri, Michelle, Merrill, Joan T, Reveille, John D, Tsao, Betty P, Orozco, Lorena, Baca, Vicente, Moser, Kathy L, Gaffney, Patrick M, James, Judith A, Harley, John B, Tusié-Luna, Teresa, Pons-Estel, Bernardo A, Jacob, Chaim O, and Alarcón-Riquelme, Marta E
Abstract: ObjectiveAmerican Indian-Europeans, Asians, and African Americans have an excess morbidity from systemic lupus erythematosus (SLE) and a higher prevalence of lupus nephritis than do Caucasians. The aim of this study was to analyze the relationship between genetic ancestry and sociodemographic characteristics and clinical features in a large cohort of American Indian-European SLE patients.MethodsA total of 2,116 SLE patients of American Indian-European origin and 4,001 SLE patients of European descent for whom we had clinical data were included in the study. Genotyping of 253 continental ancestry-informative markers was performed on the Illumina platform. Structure and Admixture software were used to determine genetic ancestry proportions of each individual. Logistic regression was used to test the association between genetic ancestry and sociodemographic and clinical characteristics. Odds ratios (ORs) were calculated with 95% confidence intervals (95% CIs).ResultsThe average American Indian genetic ancestry of 2,116 SLE patients was 40.7%. American Indian genetic ancestry conferred increased risks of renal involvement (P < 0.0001, OR 3.50 [95% CI 2.63- 4.63]) and early age at onset (P < 0.0001). American Indian ancestry protected against photosensitivity (P < 0.0001, OR 0.58 [95% CI 0.44-0.76]), oral ulcers (P < 0.0001, OR 0.55 [95% CI 0.42-0.72]), and serositis (P < 0.0001, OR 0.56 [95% CI 0.41-0.75]) after adjustment for age, sex, and age at onset. However, age and sex had stronger effects than genetic ancestry on malar rash, discoid rash, arthritis, and neurologic involvement.ConclusionIn general, American Indian genetic ancestry correlates with lower sociodemographic status and increases the risk of developing renal involvement and SLE at an earlier age.
Published: 2012

44. Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

Author: Adrianto, Indra, Wen, Feng, Templeton, Amanda, Wiley, Graham, King, Jarrod B., Lessard, Christopher J., Bates, Jared S., Hu, Yanqing, Kelly, Jennifer A., Kaufman, Kenneth M., Guthridge, Joel M., Alarcon-Riquelme, Marta E., Anaya, Juan-Manuel, Bae, Sang-Cheol, Bang, So-Young, Boackle, Susan A., Brown, Elizabeth E., Petri, Michelle A., Gallant, Caroline, Ramsey-Goldman, Rosalind, Reveille, John D., Vila, Luis M., Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gregersen, Peter K., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Pons-Estel, Bernardo A., Scofield, R. Hal, Stevens, Anne M., Tsao, Betty P., Vyse, Timothy J., Langefeld, Carl D., Harley, John B., Moser, Kathy L., Webb, Carol F., Humphrey, Mary Beth, Montgomery, Courtney Gray, Gaffney, Patrick M., Adrianto, Indra, Wen, Feng, Templeton, Amanda, Wiley, Graham, King, Jarrod B., Lessard, Christopher J., Bates, Jared S., Hu, Yanqing, Kelly, Jennifer A., Kaufman, Kenneth M., Guthridge, Joel M., Alarcon-Riquelme, Marta E., Anaya, Juan-Manuel, Bae, Sang-Cheol, Bang, So-Young, Boackle, Susan A., Brown, Elizabeth E., Petri, Michelle A., Gallant, Caroline, Ramsey-Goldman, Rosalind, Reveille, John D., Vila, Luis M., Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gregersen, Peter K., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Pons-Estel, Bernardo A., Scofield, R. Hal, Stevens, Anne M., Tsao, Betty P., Vyse, Timothy J., Langefeld, Carl D., Harley, John B., Moser, Kathy L., Webb, Carol F., Humphrey, Mary Beth, Montgomery, Courtney Gray, and Gaffney, Patrick M.
Abstract: Systemic lupus erythematosus (SLE, MIM152700) is an autoimmune disease characterized by self-reactive antibodies resulting in systemic inflammation and organ failure. TNFAIP3, encoding the ubiquitin-modifying enzyme A20, is an established susceptibility locus for SLE. By fine mapping and genomic re-sequencing in ethnically diverse populations, we fully characterized the TNFAIP3 risk haplotype and identified a TT>A polymorphic dinucleotide (deletion T followed by a T to A transversion) associated with SLE in subjects of European (P = 1.58 x 10(-8), odds ratio = 1.70) and Korean (P = 8.33 x 10(-10), odds ratio = 2.54) ancestry. This variant, located in a region of high conservation and regulatory potential, bound a nuclear protein complex composed of NF-kappa B subunits with reduced avidity. Further, compared with the non-risk haplotype, the haplotype carrying this variant resulted in reduced TNFAIP3 mRNA and A20 protein expression. These results establish this TT>A variant as the most likely functional polymorphism responsible for the association between TNFAIP3 and SLE.
Published: 2011
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45. Identification of a Systemic Lupus Erythematosus Susceptibility Locus at 11p13 between PDHX and CD44 in a Multiethnic Study

Author: Lessard, Christopher J., Adrianto, Indra, Kelly, Jennifer A., Kaufman, Kenneth M., Grundahl, Kiely M., Adler, Adam, Williams, Adrienne H., Gallant, Caroline J., Alarcon-Riquelme, Marta E., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Chang, Deh-Ming, Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gregersen, Peter K., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Bruner, Gail R., Langefeld, Carl D., Montgomery, Courtney, Harley, John B., Scofield, R. Hal, Gaffney, Patrick M., Moser, Kathy L., Lessard, Christopher J., Adrianto, Indra, Kelly, Jennifer A., Kaufman, Kenneth M., Grundahl, Kiely M., Adler, Adam, Williams, Adrienne H., Gallant, Caroline J., Alarcon-Riquelme, Marta E., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Chang, Deh-Ming, Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gregersen, Peter K., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Bruner, Gail R., Langefeld, Carl D., Montgomery, Courtney, Harley, John B., Scofield, R. Hal, Gaffney, Patrick M., and Moser, Kathy L.
Abstract: Systemic lupus erythematosus (SLE) is considered to be the prototypic autoimmune disease, with a complex genetic architecture influenced by environmental factors. We sought to replicate a putative association at 11p13 not yet exceeding genome-wide significance (p < 5 x 10(-8)) identified in a genome-wide association study (GWAS). Our GWA scan identified two intergenic SNPs located between PDHX and CD44 showing suggestive evidence of association with SLE in cases of European descent (rs2732552, p = 0.004, odds ratio [OR] = 0.78; rs387619, p = 0.003, OR = 0.78). The replication cohort consisted of >15,000 subjects, including 3562 SLE cases and 3491 controls of European ancestry, 1527 cases and 1811 controls of African American (AA) descent, and 1265 cases and 1260 controls of Asian origin. We observed robust association at both rs2732552 (p = 9.03 x 10(-8), OR = 0.83) and rs387619 (p = 7.7 x 10(-7), OR = 0.83) in the European samples with p(meta) = 1.82 x 10(-9) for rs2732552. The AA and Asian SLE cases also demonstrated association at rs2732552 (p = 5 x 10(-3), OR = 0.81 and p = 4.3 x 10(-4), OR = 0.80, respectively). A meta-analysis of rs2732552 for all racial and ethnic groups studied produced p(meta) = 2.36 x 10(-13). This locus contains multiple regulatory sites that could potentially affect expression and functions of CD44, a cell-surface glycoprotein influencing immunologic, inflammatory, and oncologic phenotypes, or PDHX, a subunit of the pyruvate dehydrogenase complex.
Published: 2011
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46. A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap.

Author: Ramos, Paula S, Ramos, Paula S, Criswell, Lindsey A, Moser, Kathy L, Comeau, Mary E, Williams, Adrienne H, Pajewski, Nicholas M, Chung, Sharon A, Graham, Robert R, Zidovetzki, Raphael, Kelly, Jennifer A, Kaufman, Kenneth M, Jacob, Chaim O, Vyse, Timothy J, Tsao, Betty P, Kimberly, Robert P, Gaffney, Patrick M, Alarcón-Riquelme, Marta E, Harley, John B, Langefeld, Carl D, International Consortium on the Genetics of Systemic Erythematosus, Ramos, Paula S, Ramos, Paula S, Criswell, Lindsey A, Moser, Kathy L, Comeau, Mary E, Williams, Adrienne H, Pajewski, Nicholas M, Chung, Sharon A, Graham, Robert R, Zidovetzki, Raphael, Kelly, Jennifer A, Kaufman, Kenneth M, Jacob, Chaim O, Vyse, Timothy J, Tsao, Betty P, Kimberly, Robert P, Gaffney, Patrick M, Alarcón-Riquelme, Marta E, Harley, John B, Langefeld, Carl D, and International Consortium on the Genetics of Systemic Erythematosus
Abstract: In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non-Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02×10(-06)) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn's disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non-MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared
Published: 2011

47. Association of genetic variants in complement factor H and factor H-related genes with systemic lupus erythematosus susceptibility

Author: Zhao, Jian, Wu, Hui, Khosravi, Melanie, Cui, Huijuan, Qian, Xiaoxia, Kelly, Jennifer A., Kaufman, Kenneth M., Langefeld, Carl D., Williams, Adrienne H., Comeau, Mary, Ziegler, Julie T., Marion, Miranda C., Adler, Adam, Glenn, Stuart B., Alarcón-Riquelme, Marta E., Pons-Estel, Bernardo A., Harley, John B., Bae, Sang-Cheol, Bang, So-Young, Cho, Soo-Kyung, Jacob, Chaim O., Vyse, Timothy J., Niewold, Timothy B., Gaffney, Patrick M., Moser, Kathy L., Kimberly, Robert P., Edberg, Jeffrey C., Brown, Elizabeth E., Alarcón, Graciela S., Petri, Michelle A., Ramsey-Goldman, Rosalind, Vilá, Luis M., Reveille, John D., James, Judith A., Gilkeson, Gary S., Kamen, Diane L., Freedman, Barry I., Anaya, Juan-Manuel, Merrill, Joan T., Criswell, Lindsey A., Scofield, Robert H., Stevens, Anne M., Guthridge, Joel M., Chang, Deh-Ming, Song, Yeong Wook, Park, Ji Ah, Young Lee, Eun, Boackle, Susan, Grossman, Jennifer M., Hahn, Bevra H., Goodship, Timothy H. J., Cantor, Rita M., Yu, Chack-Yung, Shen, Nan, Tsao, Betty P., Zhao, Jian, Wu, Hui, Khosravi, Melanie, Cui, Huijuan, Qian, Xiaoxia, Kelly, Jennifer A., Kaufman, Kenneth M., Langefeld, Carl D., Williams, Adrienne H., Comeau, Mary, Ziegler, Julie T., Marion, Miranda C., Adler, Adam, Glenn, Stuart B., Alarcón-Riquelme, Marta E., Pons-Estel, Bernardo A., Harley, John B., Bae, Sang-Cheol, Bang, So-Young, Cho, Soo-Kyung, Jacob, Chaim O., Vyse, Timothy J., Niewold, Timothy B., Gaffney, Patrick M., Moser, Kathy L., Kimberly, Robert P., Edberg, Jeffrey C., Brown, Elizabeth E., Alarcón, Graciela S., Petri, Michelle A., Ramsey-Goldman, Rosalind, Vilá, Luis M., Reveille, John D., James, Judith A., Gilkeson, Gary S., Kamen, Diane L., Freedman, Barry I., Anaya, Juan-Manuel, Merrill, Joan T., Criswell, Lindsey A., Scofield, Robert H., Stevens, Anne M., Guthridge, Joel M., Chang, Deh-Ming, Song, Yeong Wook, Park, Ji Ah, Young Lee, Eun, Boackle, Susan, Grossman, Jennifer M., Hahn, Bevra H., Goodship, Timothy H. J., Cantor, Rita M., Yu, Chack-Yung, Shen, Nan, and Tsao, Betty P.
Abstract: Systemic lupus erythematosus (SLE), a complex polygenic autoimmune disease, is associated with increased complement activation. Variants of genes encoding complement regulator factor H (CFH) and five CFH-related proteins (CFHR1-CFHR5) within the chromosome 1q32 locus linked to SLE, have been associated with multiple human diseases and may contribute to dysregulated complement activation predisposing to SLE. We assessed 60 SNPs covering the CFH-CFHRs region for association with SLE in 15,864 case-control subjects derived from four ethnic groups. Significant allelic associations with SLE were detected in European Americans (EA) and African Americans (AA), which could be attributed to an intronic CFH SNP (rs6677604, in intron 11, Pmeta = 6.6×10-8, OR = 1.18) and an intergenic SNP between CFHR1 and CFHR4 (rs16840639, Pmeta = 2.9×10-7, OR = 1.17) rather than to previously identified disease-associated CFH exonic SNPs, including I62V, Y402H, A474A, and D936E. In addition, allelic association of rs6677604 with SLE was subsequently confirmed in Asians (AS). Haplotype analysis revealed that the underlying causal variant, tagged by rs6677604 and rs16840639, was localized to a ~146 kb block extending from intron 9 of CFH to downstream of CFHR1. Within this block, the deletion of CFHR3 and CFHR1 (CFHR3-1Δ), a likely causal variant measured using multiplex ligation-dependent probe amplification, was tagged by rs6677604 in EA and AS and rs16840639 in AA, respectively. Deduced from genotypic associations of tag SNPs in EA, AA, and AS, homozygous deletion of CFHR3-1Δ (Pmeta = 3.2×10-7, OR = 1.47) conferred a higher risk of SLE than heterozygous deletion (Pmeta = 3.5×10-4, OR = 1.14). These results suggested that the CFHR3-1Δ deletion within the SLE-associated block, but not the previously described exonic SNPs of CFH, might contribute to the development of SLE in EA, AA, and AS, providing new insights into the role of complement regulators in the pathogenesis of SLE.
Published: 2011

48. A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap.

Author: Ramos, Paula S, Dermitzakis, Emmanouil T1, Ramos, Paula S, Criswell, Lindsey A, Moser, Kathy L, Comeau, Mary E, Williams, Adrienne H, Pajewski, Nicholas M, Chung, Sharon A, Graham, Robert R, Zidovetzki, Raphael, Kelly, Jennifer A, Kaufman, Kenneth M, Jacob, Chaim O, Vyse, Timothy J, Tsao, Betty P, Kimberly, Robert P, Gaffney, Patrick M, Alarcón-Riquelme, Marta E, Harley, John B, Langefeld, Carl D, International Consortium on the Genetics of Systemic Erythematosus, Ramos, Paula S, Dermitzakis, Emmanouil T1, Ramos, Paula S, Criswell, Lindsey A, Moser, Kathy L, Comeau, Mary E, Williams, Adrienne H, Pajewski, Nicholas M, Chung, Sharon A, Graham, Robert R, Zidovetzki, Raphael, Kelly, Jennifer A, Kaufman, Kenneth M, Jacob, Chaim O, Vyse, Timothy J, Tsao, Betty P, Kimberly, Robert P, Gaffney, Patrick M, Alarcón-Riquelme, Marta E, Harley, John B, Langefeld, Carl D, and International Consortium on the Genetics of Systemic Erythematosus
Abstract: In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non-Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02×10(-06)) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn's disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non-MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared
Published: 2011

49. The Role of Genetic Variation Near Interferon-Kappa in Systemic Lupus Erythematosus

Author: Harley, Isaac T. W., Niewold, Timothy B., Stormont, Rebecca M., Kaufman, Kenneth M., Glenn, Stuart B., Franek, Beverly S., Kelly, Jennifer A., Kilpatrick, Jeffrey R., Hutchings, David, Divers, Jasmin, Bruner, Gail R., Edberg, Jeffrey C., McGwin, Gerald, Jr., Petri, Michelle A., Ramsey-Goldman, Rosalind, Reveille, John D., Vila-Perez, Luis M., Merrill, Joan T., Gilkeson, Gary S., Vyse, Timothy J., Alarcón-Riquelme, Marta E., Cho, Soo-Kyung, Jacob, Chaim O., Alarcon, Graciela S., Moser, Kathy L., Gaffney, Patrick M., Kimberly, Robert P., Bae, Sang-Cheol, Langefeld, Carl D., Harley, John B., Guthridge, Joel M., James, Judith A., Harley, Isaac T. W., Niewold, Timothy B., Stormont, Rebecca M., Kaufman, Kenneth M., Glenn, Stuart B., Franek, Beverly S., Kelly, Jennifer A., Kilpatrick, Jeffrey R., Hutchings, David, Divers, Jasmin, Bruner, Gail R., Edberg, Jeffrey C., McGwin, Gerald, Jr., Petri, Michelle A., Ramsey-Goldman, Rosalind, Reveille, John D., Vila-Perez, Luis M., Merrill, Joan T., Gilkeson, Gary S., Vyse, Timothy J., Alarcón-Riquelme, Marta E., Cho, Soo-Kyung, Jacob, Chaim O., Alarcon, Graciela S., Moser, Kathy L., Gaffney, Patrick M., Kimberly, Robert P., Bae, Sang-Cheol, Langefeld, Carl D., Harley, John B., Guthridge, Joel M., and James, Judith A.
Abstract: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by increased type I interferons (IFNs) and multiorgan inflammation frequently targeting the skin. IFN-kappa is a type I IFN expressed in skin. A pooled genome-wide scan implicated the IFNK locus in SLE susceptibility. We studied IFNK single nucleotide polymorphisms (SNPs) in 3982 SLE cases and 4275 controls, composed of European (EA), African-American (AA), and Asian ancestry. rs12553951C was associated with SLE in EA males (odds ratio = 1.93, P = 2.5 x 10(-4)), but not females. Suggestive associations with skin phenotypes in EA and AA females were found, and these were also sex-specific. IFNK SNPs were associated with increased serum type I IFN in EA and AA SLE patients. Our data suggest a sex-dependent association between IFNK SNPs and SLE and skin phenotypes. The serum IFN association suggests that IFNK variants could influence type I IFN producing plasmacytoid dendritic cells in affected skin.
Published: 2010
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50. Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus

Author: Webb, Ryan, Wren, Jonathan D., Jeffries, Matlock, Kelly, Jennifer A., Kaufman, Kenneth M., Tang, Yuhong, Frank, Mark Barton, Merrill, Joan, Kimberly, Robert P., Edberg, Jeffrey C., Ramsey-Goldman, Rosalind, Petri, Michelle, Reveille, John D., Alarcón, Graciela S., Vilá, Luis M., Alarcón-Riquelme, Marta E., James, Judith A., Vyse, Timothy J., Moser, Kathy L., Gaffney, Patrick M., Gilkeson, Gary S., Harley, John B., Sawalha, Amr H., Webb, Ryan, Wren, Jonathan D., Jeffries, Matlock, Kelly, Jennifer A., Kaufman, Kenneth M., Tang, Yuhong, Frank, Mark Barton, Merrill, Joan, Kimberly, Robert P., Edberg, Jeffrey C., Ramsey-Goldman, Rosalind, Petri, Michelle, Reveille, John D., Alarcón, Graciela S., Vilá, Luis M., Alarcón-Riquelme, Marta E., James, Judith A., Vyse, Timothy J., Moser, Kathy L., Gaffney, Patrick M., Gilkeson, Gary S., Harley, John B., and Sawalha, Amr H.
Abstract: OBJECTIVE: Both genetic and epigenetic factors play an important role in the pathogenesis of lupus. The aim of this study was to examine methyl-CpG-binding protein 2 gene (MECP2) polymorphisms in a large cohort of patients with lupus and control subjects, and to determine the functional consequences of the lupus-associated MECP2 haplotype. METHODS: We genotyped 18 single-nucleotide polymorphisms within MECP2, located on chromosome Xq28, in a large cohort of patients with lupus and control subjects of European descent. We studied the functional effects of the lupus-associated MECP2 haplotype by determining gene expression profiles in B cell lines in female lupus patients with and those without the lupus-associated MECP2 risk haplotype. RESULTS: We confirmed, replicated, and extended the genetic association between lupus and genetic markers within MECP2 in a large independent cohort of lupus patients and control subjects of European descent (odds ratio 1.35, P = 6.65 x 10(-11)). MECP2 is a dichotomous transcription regulator that either activates or represses gene expression. We identified 128 genes that are differentially expressed in lupus patients with the disease-associated MECP2 haplotype; most ( approximately 81%) were up-regulated. Genes that were up-regulated had significantly more CpG islands in their promoter regions compared with genes that were down-regulated. Gene ontology analysis using the differentially expressed genes revealed significant association with epigenetic regulatory mechanisms, suggesting that these genes are targets for MECP2 regulation in B cells. Furthermore, at least 13 of the 104 up-regulated genes are regulated by interferon. The disease-risk MECP2 haplotype was associated with increased expression of the MECP2 transcription coactivator CREB1 and decreased expression of the corepressor histone deacetylase 1. CONCLUSION: Polymorphism in the MECP2 locus is associated with lupus and, at least in part, contributes to the interferon signat
Published: 2009
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