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1. Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes

Author

Glessner, Joseph T, Ningappa, Mylarappa B, Ngo, Kim A, Zahid, Maliha, So, Juhoon, Higgs, Brandon W, Sleiman, Patrick MA, Narayanan, Tejaswini, Ranganathan, Sarangarajan, March, Michael, Prasadan, Krishna, Vaccaro, Courtney, Reyes-Mugica, Miguel, Velazquez, Jeremy, Salgado, Claudia M, Ebrahimkhani, Mo R, Schmitt, Lori, Rajasundaram, Dhivyaa, Paul, Morgan, Pellegrino, Renata, Gittes, George K, Li, Dong, Wang, Xiang, Billings, Jonathan, Squires, Robert, Ashokkumar, Chethan, Sharif, Khalid, Kelly, Deirdre, Dhawan, Anil, Horslen, Simon, Lo, Cecilia W, Shin, Donghun, Subramaniam, Shankar, Hakonarson, Hakon, and Sindhi, Rakesh

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Genetics, Digestive Diseases, Human Genome, Congenital Structural Anomalies, Prevention, Liver Disease, Infant Mortality, Pediatric, Rare Diseases, Perinatal Period - Conditions Originating in Perinatal Period, Chronic Liver Disease and Cirrhosis, Aetiology, 2.1 Biological and endogenous factors, Child, Animals, Mice, Humans, Biliary Atresia, Genome-Wide Association Study, Genetic Predisposition to Disease, Zebrafish, Canada, Ciliogenesis, Polygenic Susceptibility, Portal Vein, Tube Morphogenesis, Vascular Development, Public Health and Health Services, Gastroenterology & Hepatology, Clinical sciences
Abstract

Background & aimsBiliary atresia (BA) is poorly understood and leads to liver transplantation (LT), with the requirement for and associated risks of lifelong immunosuppression, in most children. We performed a genome-wide association study (GWAS) to determine the genetic basis of BA.MethodsWe performed a GWAS in 811 European BA cases treated with LT in US, Canadian and UK centers, and 4,654 genetically matched controls. Whole-genome sequencing of 100 cases evaluated synthetic association with rare variants. Functional studies included whole liver transcriptome analysis of 64 BA cases and perturbations in experimental models.ResultsA GWAS of common single nucleotide polymorphisms (SNPs), i.e. allele frequencies >1%, identified intronic SNPs rs6446628 in AFAP1 with genome-wide significance (p = 3.93E-8) and rs34599046 in TUSC3 at sub-threshold genome-wide significance (p = 1.34E-7), both supported by credible peaks of neighboring SNPs. Like other previously reported BA-associated genes, AFAP1 and TUSC3 are ciliogenesis and planar polarity effectors (CPLANE). In gene-set-based GWAS, BA was associated with 6,005 SNPs in 102 CPLANE genes (p = 5.84E-15). Compared with non-CPLANE genes, more CPLANE genes harbored rare variants (allele frequency

Published
2023

2. Genetic correlations among psychiatric and immune‐related phenotypes based on genome‐wide association data

Author

Tylee, Daniel S, Sun, Jiayin, Hess, Jonathan L, Tahir, Muhammad A, Sharma, Esha, Malik, Rainer, Worrall, Bradford B, Levine, Andrew J, Martinson, Jeremy J, Nejentsev, Sergey, Speed, Doug, Fischer, Annegret, Mick, Eric, Walker, Brian R, Crawford, Andrew, Grant, Struan FA, Polychronakos, Constantin, Bradfield, Jonathan P, Sleiman, Patrick MA, Hakonarson, Hakon, Ellinghaus, Eva, Elder, James T, Tsoi, Lam C, Trembath, Richard C, Barker, Jonathan N, Franke, Andre, Dehghan, Abbas, Team, The 23 and Me Research, Consortium, The Inflammation Working Group of the CHARGE, Consortium, The METASTROKE Consortium of the International Stroke Genetics, Registry, The Netherlands Twin, Group, The neuroCHARGE Working, Consortium, The Obsessive Compulsive and Tourette Syndrome Working Group of the Psychiatric Genomics, Faraone, Stephen V, and Glatt, Stephen J

Subjects
Pharmacology and Pharmaceutical Sciences, Biological Sciences, Biomedical and Clinical Sciences, Genetics, Serious Mental Illness, Human Genome, Genetic Testing, Brain Disorders, Schizophrenia, Digestive Diseases, Prevention, Mental Health, Clinical Research, Autoimmune Disease, 2.1 Biological and endogenous factors, Aetiology, Mental health, Autoimmune Diseases, Comorbidity, Databases, Factual, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Male, Mental Disorders, Multifactorial Inheritance, Polymorphism, Single Nucleotide, White People, allergy, anorexia nervosa, attention deficit-hyperactivity disorder, autoimmune disorder, bipolar disorder, celiac disease, childhood ear infection, C-reactive protein, Crohn's disease, genetic correlation, genome-wide association, hypothyroidism, major depression, neuroticism, obsessive schizophrenia, primary biliary cirrhosis, rheumatoid arthritis, smoking, systemic lupus erythematosus, Tourette syndrome, tuberculosis susceptibility, type 1 diabetes, ulcerative colitis, and Me Research Team, Inflammation Working Group of the CHARGE Consortium, METASTROKE Consortium of the International Stroke Genetics Consortium, Netherlands Twin Registry, neuroCHARGE Working Group, Obsessive Compulsive and Tourette Syndrome Working Group of the Psychiatric Genomics Consortium, Clinical Sciences, Neurosciences, Clinical sciences
Abstract

Individuals with psychiatric disorders have elevated rates of autoimmune comorbidity and altered immune signaling. It is unclear whether these altered immunological states have a shared genetic basis with those psychiatric disorders. The present study sought to use existing summary-level data from previous genome-wide association studies to determine if commonly varying single nucleotide polymorphisms are shared between psychiatric and immune-related phenotypes. We estimated heritability and examined pair-wise genetic correlations using the linkage disequilibrium score regression (LDSC) and heritability estimation from summary statistics methods. Using LDSC, we observed significant genetic correlations between immune-related disorders and several psychiatric disorders, including anorexia nervosa, attention deficit-hyperactivity disorder, bipolar disorder, major depression, obsessive compulsive disorder, schizophrenia, smoking behavior, and Tourette syndrome. Loci significantly mediating genetic correlations were identified for schizophrenia when analytically paired with Crohn's disease, primary biliary cirrhosis, systemic lupus erythematosus, and ulcerative colitis. We report significantly correlated loci and highlight those containing genome-wide associations and candidate genes for respective disorders. We also used the LDSC method to characterize genetic correlations among the immune-related phenotypes. We discuss our findings in the context of relevant genetic and epidemiological literature, as well as the limitations and caveats of the study.

Published
2018

3. Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network

Author

Chen, Zhao, Tang, Hua, Qayyum, Rehan, Schick, Ursula M, Nalls, Michael A, Handsaker, Robert, Li, Jin, Lu, Yingchang, Yanek, Lisa R, Keating, Brendan, Meng, Yan, van Rooij, Frank JA, Okada, Yukinori, Kubo, Michiaki, Rasmussen-Torvik, Laura, Keller, Margaux F, Lange, Leslie, Evans, Michele, Bottinger, Erwin P, Linderman, Michael D, Ruderfer, Douglas M, Hakonarson, Hakon, Papanicolaou, George, Zonderman, Alan B, Gottesman, Omri, Project, CHARGE Consortium BioBank Japan, Thomson, Cynthia, Ziv, Elad, Singleton, Andrew B, Loos, Ruth JF, Sleiman, Patrick MA, Ganesh, Santhi, McCarroll, Steven, Becker, Diane M, Wilson, James G, Lettre, Guillaume, and Reiner, Alexander P

Subjects
Biological Sciences, Genetics, Human Genome, Clinical Research, Hematology, Aetiology, 2.1 Biological and endogenous factors, Blood, Adolescent, Adult, Black or African American, Child, Chromosomes, Human, Pair 16, Cohort Studies, Erythrocyte Count, Erythrocyte Indices, Erythrocytes, Female, Genome-Wide Association Study, Hemoglobins, Humans, Male, Polymorphism, Single Nucleotide, White People, Young Adult, alpha-Globins, BioBank Japan Project, CHARGE Consortium, Medical and Health Sciences, Genetics & Heredity
Abstract

Laboratory red blood cell (RBC) measurements are clinically important, heritable and differ among ethnic groups. To identify genetic variants that contribute to RBC phenotypes in African Americans (AAs), we conducted a genome-wide association study in up to ~16 500 AAs. The alpha-globin locus on chromosome 16pter [lead SNP rs13335629 in ITFG3 gene; P < 1E-13 for hemoglobin (Hgb), RBC count, mean corpuscular volume (MCV), MCH and MCHC] and the G6PD locus on Xq28 [lead SNP rs1050828; P < 1E - 13 for Hgb, hematocrit (Hct), MCV, RBC count and red cell distribution width (RDW)] were each associated with multiple RBC traits. At the alpha-globin region, both the common African 3.7 kb deletion and common single nucleotide polymorphisms (SNPs) appear to contribute independently to RBC phenotypes among AAs. In the 2p21 region, we identified a novel variant of PRKCE distinctly associated with Hct in AAs. In a genome-wide admixture mapping scan, local European ancestry at the 6p22 region containing HFE and LRRC16A was associated with higher Hgb. LRRC16A has been previously associated with the platelet count and mean platelet volume in AAs, but not with Hgb. Finally, we extended to AAs the findings of association of erythrocyte traits with several loci previously reported in Europeans and/or Asians, including CD164 and HBS1L-MYB. In summary, this large-scale genome-wide analysis in AAs has extended the importance of several RBC-associated genetic loci to AAs and identified allelic heterogeneity and pleiotropy at several previously known genetic loci associated with blood cell traits in AAs.

Published
2013

4. A genome-wide association meta-analysis identifies new childhood obesity loci

Author

Bradfield, Jonathan P, Taal, H Rob, Timpson, Nicholas J, Scherag, Andre, Lecoeur, Cecile, Warrington, Nicole M, Hypponen, Elina, Holst, Claus, Valcarcel, Beatriz, Thiering, Elisabeth, Salem, Rany M, Schumacher, Fredrick R, Cousminer, Diana L, Sleiman, Patrick MA, Zhao, Jianhua, Berkowitz, Robert I, Vimaleswaran, Karani S, Jarick, Ivonne, Pennell, Craig E, Evans, David M, St Pourcain, Beate, Berry, Diane J, Mook-Kanamori, Dennis O, Hofman, Albert, Rivadeneira, Fernando, Uitterlinden, Andre G, van Duijn, Cornelia M, van der Valk, Ralf JP, de Jongste, Johan C, Postma, Dirkje S, Boomsma, Dorret I, Gauderman, W James, Hassanein, Mohamed T, Lindgren, Cecilia M, Magi, Reedik, Boreham, Colin AG, Neville, Charlotte E, Moreno, Luis A, Elliott, Paul, Pouta, Anneli, Hartikainen, Anna-Liisa, Li, Mingyao, Raitakari, Olli, Lehtimaki, Terho, Eriksson, Johan G, Palotie, Aarno, Dallongeville, Jean, Das, Shikta, Deloukas, Panos, McMahon, George, Ring, Susan M, Kemp, John P, Buxton, Jessica L, Blakemore, Alexandra IF, Bustamante, Mariona, Guxens, Monica, Hirschhorn, Joel N, Gillman, Matthew W, Kreiner-Moller, Eskil, Bisgaard, Hans, Gilliland, Frank D, Heinrich, Joachim, Wheeler, Eleanor, Barroso, Ines, O'Rahilly, Stephen, Meirhaeghe, Aline, Sorensen, Thorkild IA, Power, Chris, Palmer, Lyle J, Hinney, Anke, Widen, Elisabeth, Farooqi, I Sadaf, McCarthy, Mark I, Froguel, Philippe, Meyre, David, Hebebrand, Johannes, Jarvelin, Marjo-Riitta, Jaddoe, Vincent WV, Smith, George Davey, Hakonarson, Hakon, and Grant, Struan FA

Subjects
Biological Sciences, Genetics, Pediatric, Nutrition, Obesity, Human Genome, Metabolic and endocrine, Oral and gastrointestinal, Stroke, Cancer, Cardiovascular, Adolescent, Adult, Body Mass Index, Case-Control Studies, Genetic Loci, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Young Adult, Early Growth Genetics Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Multiple genetic variants have been associated with adult obesity and a few with severe obesity in childhood; however, less progress has been made in establishing genetic influences on common early-onset obesity. We performed a North American, Australian and European collaborative meta-analysis of 14 studies consisting of 5,530 cases (≥95th percentile of body mass index (BMI)) and 8,318 controls (

Published
2012

5. Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy

Author

Höglinger, Günter U, Melhem, Nadine M, Dickson, Dennis W, Sleiman, Patrick MA, Wang, Li-San, Klei, Lambertus, Rademakers, Rosa, de Silva, Rohan, Litvan, Irene, Riley, David E, van Swieten, John C, Heutink, Peter, Wszolek, Zbigniew K, Uitti, Ryan J, Vandrovcova, Jana, Hurtig, Howard I, Gross, Rachel G, Maetzler, Walter, Goldwurm, Stefano, Tolosa, Eduardo, Borroni, Barbara, Pastor, Pau, Cantwell, Laura B, Han, Mi Ryung, Dillman, Allissa, van der Brug, Marcel P, Gibbs, J Raphael, Cookson, Mark R, Hernandez, Dena G, Singleton, Andrew B, Farrer, Matthew J, Yu, Chang-En, Golbe, Lawrence I, Revesz, Tamas, Hardy, John, Lees, Andrew J, Devlin, Bernie, Hakonarson, Hakon, Müller, Ulrich, and Schellenberg, Gerard D

Subjects
Biological Sciences, Genetics, Pediatric, Prevention, Cerebral Palsy, Rare Diseases, Neurodegenerative, Brain Disorders, Acquired Cognitive Impairment, Human Genome, Perinatal Period - Conditions Originating in Perinatal Period, Frontotemporal Dementia (FTD), Dementia, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Neurological, Case-Control Studies, Chromosomes, Human, Cohort Studies, Genetic Loci, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Prognosis, Risk Factors, Supranuclear Palsy, Progressive, Tauopathies, tau Proteins, PSP Genetics Study Group, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Progressive supranuclear palsy (PSP) is a movement disorder with prominent tau neuropathology. Brain diseases with abnormal tau deposits are called tauopathies, the most common of which is Alzheimer's disease. Environmental causes of tauopathies include repetitive head trauma associated with some sports. To identify common genetic variation contributing to risk for tauopathies, we carried out a genome-wide association study of 1,114 individuals with PSP (cases) and 3,247 controls (stage 1) followed by a second stage in which we genotyped 1,051 cases and 3,560 controls for the stage 1 SNPs that yielded P ≤ 10(-3). We found significant previously unidentified signals (P < 5 × 10(-8)) associated with PSP risk at STX6, EIF2AK3 and MOBP. We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT brain expression. The genes implicated encode proteins for vesicle-membrane fusion at the Golgi-endosomal interface, for the endoplasmic reticulum unfolded protein response and for a myelin structural component.

Published
2011

6. Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions

Author

Van Deerlin, Vivianna M, Sleiman, Patrick MA, Martinez-Lage, Maria, Chen-Plotkin, Alice, Wang, Li-San, Graff-Radford, Neill R, Dickson, Dennis W, Rademakers, Rosa, Boeve, Bradley F, Grossman, Murray, Arnold, Steven E, Mann, David MA, Pickering-Brown, Stuart M, Seelaar, Harro, Heutink, Peter, van Swieten, John C, Murrell, Jill R, Ghetti, Bernardino, Spina, Salvatore, Grafman, Jordan, Hodges, John, Spillantini, Maria Grazia, Gilman, Sid, Lieberman, Andrew P, Kaye, Jeffrey A, Woltjer, Randall L, Bigio, Eileen H, Mesulam, Marsel, al-Sarraj, Safa, Troakes, Claire, Rosenberg, Roger N, White, Charles L, Ferrer, Isidro, Lladó, Albert, Neumann, Manuela, Kretzschmar, Hans A, Hulette, Christine Marie, Welsh-Bohmer, Kathleen A, Miller, Bruce L, Alzualde, Ainhoa, de Munain, Adolfo Lopez, McKee, Ann C, Gearing, Marla, Levey, Allan I, Lah, James J, Hardy, John, Rohrer, Jonathan D, Lashley, Tammaryn, Mackenzie, Ian RA, Feldman, Howard H, Hamilton, Ronald L, Dekosky, Steven T, van der Zee, Julie, Kumar-Singh, Samir, Van Broeckhoven, Christine, Mayeux, Richard, Vonsattel, Jean Paul G, Troncoso, Juan C, Kril, Jillian J, Kwok, John BJ, Halliday, Glenda M, Bird, Thomas D, Ince, Paul G, Shaw, Pamela J, Cairns, Nigel J, Morris, John C, McLean, Catriona Ann, DeCarli, Charles, Ellis, William G, Freeman, Stefanie H, Frosch, Matthew P, Growdon, John H, Perl, Daniel P, Sano, Mary, Bennett, David A, Schneider, Julie A, Beach, Thomas G, Reiman, Eric M, Woodruff, Bryan K, Cummings, Jeffrey, Vinters, Harry V, Miller, Carol A, Chui, Helena C, Alafuzoff, Irina, Hartikainen, Päivi, Seilhean, Danielle, Galasko, Douglas, Masliah, Eliezer, Cotman, Carl W, Tuñón, M Teresa, Martínez, M Cristina Caballero, Munoz, David G, Carroll, Steven L, Marson, Daniel, Riederer, Peter F, Bogdanovic, Nenad, Schellenberg, Gerard D, Hakonarson, Hakon, Trojanowski, John Q, and Lee, Virginia M-Y

Subjects
Biological Sciences, Genetics, Frontotemporal Dementia (FTD), Neurodegenerative, Dementia, Rare Diseases, Brain Disorders, Neurosciences, Acquired Cognitive Impairment, Aetiology, 2.1 Biological and endogenous factors, Case-Control Studies, Chromosomes, Human, Pair 7, DNA-Binding Proteins, Frontotemporal Lobar Degeneration, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Inclusion Bodies, Intercellular Signaling Peptides and Proteins, Linkage Disequilibrium, Membrane Proteins, Polymorphism, Single Nucleotide, Progranulins, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Frontotemporal lobar degeneration (FTLD) is the second most common cause of presenile dementia. The predominant neuropathology is FTLD with TAR DNA-binding protein (TDP-43) inclusions (FTLD-TDP). FTLD-TDP is frequently familial, resulting from mutations in GRN (which encodes progranulin). We assembled an international collaboration to identify susceptibility loci for FTLD-TDP through a genome-wide association study of 515 individuals with FTLD-TDP. We found that FTLD-TDP associates with multiple SNPs mapping to a single linkage disequilibrium block on 7p21 that contains TMEM106B. Three SNPs retained genome-wide significance following Bonferroni correction (top SNP rs1990622, P = 1.08 x 10(-11); odds ratio, minor allele (C) 0.61, 95% CI 0.53-0.71). The association replicated in 89 FTLD-TDP cases (rs1990622; P = 2 x 10(-4)). TMEM106B variants may confer risk of FTLD-TDP by increasing TMEM106B expression. TMEM106B variants also contribute to genetic risk for FTLD-TDP in individuals with mutations in GRN. Our data implicate variants in TMEM106B as a strong risk factor for FTLD-TDP, suggesting an underlying pathogenic mechanism.

Published
2010

10. Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations.

Author

Li, Yun Rose, Glessner, Joseph T, Coe, Bradley P, Li, Jin, Mohebnasab, Maede, Chang, Xiao, Connolly, John, Kao, Charlly, Wei, Zhi, Bradfield, Jonathan, Kim, Cecilia, Hou, Cuiping, Khan, Munir, Mentch, Frank, Qiu, Haijun, Bakay, Marina, Cardinale, Christopher, Lemma, Maria, Abrams, Debra, Bridglall-Jhingoor, Andrew, Behr, Meckenzie, Harrison, Shanell, Otieno, George, Thomas, Alexandria, Wang, Fengxiang, Chiavacci, Rosetta, Wu, Lawrence, Hadley, Dexter, Goldmuntz, Elizabeth, Elia, Josephine, Maris, John, Grundmeier, Robert, Devoto, Marcella, Keating, Brendan, March, Michael, Pellagrino, Renata, Grant, Struan FA, Sleiman, Patrick MA, Li, Mingyao, Eichler, Evan E, Hakonarson, Hakon, Li, Yun Rose, Glessner, Joseph T, Coe, Bradley P, Li, Jin, Mohebnasab, Maede, Chang, Xiao, Connolly, John, Kao, Charlly, Wei, Zhi, Bradfield, Jonathan, Kim, Cecilia, Hou, Cuiping, Khan, Munir, Mentch, Frank, Qiu, Haijun, Bakay, Marina, Cardinale, Christopher, Lemma, Maria, Abrams, Debra, Bridglall-Jhingoor, Andrew, Behr, Meckenzie, Harrison, Shanell, Otieno, George, Thomas, Alexandria, Wang, Fengxiang, Chiavacci, Rosetta, Wu, Lawrence, Hadley, Dexter, Goldmuntz, Elizabeth, Elia, Josephine, Maris, John, Grundmeier, Robert, Devoto, Marcella, Keating, Brendan, March, Michael, Pellagrino, Renata, Grant, Struan FA, Sleiman, Patrick MA, Li, Mingyao, Eichler, Evan E, and Hakonarson, Hakon

Abstract

Copy number variants (CNVs) are suggested to have a widespread impact on the human genome and phenotypes. To understand the role of CNVs across human diseases, we examine the CNV genomic landscape of 100,028 unrelated individuals of European ancestry, using SNP and CGH array datasets. We observe an average CNV burden of ~650 kb, identifying a total of 11,314 deletion, 5625 duplication, and 2746 homozygous deletion CNV regions (CNVRs). In all, 13.7% are unreported, 58.6% overlap with at least one gene, and 32.8% interrupt coding exons. These CNVRs are significantly more likely to overlap OMIM genes (2.94-fold), GWAS loci (1.52-fold), and non-coding RNAs (1.44-fold), compared with random distribution (P < 1 × 10-3). We uncover CNV associations with four major disease categories, including autoimmune, cardio-metabolic, oncologic, and neurological/psychiatric diseases, and identify several drug-repurposing opportunities. Our results demonstrate robust frequency definition for large-scale rare variant association studies, identify CNVs associated with major disease categories, and illustrate the pleiotropic impact of CNVs in human disease.

Published
2019

11. Genetic sharing and heritability of paediatric age of onset autoimmune diseases.

Author

Li, Yun R, Zhao, Sihai D, Li, Jin, Bradfield, Jonathan P, Mohebnasab, Maede, Steel, Laura, Kobie, Julie, Abrams, Debra J, Mentch, Frank D, Glessner, Joseph T, Guo, Yiran, Wei, Zhi, Connolly, John J, Cardinale, Christopher J, Bakay, Marina, Li, Dong, Maggadottir, S Melkorka, Thomas, Kelly A, Qui, Haijun, Chiavacci, Rosetta M, Kim, Cecilia E, Wang, Fengxiang, Snyder, James, Flatø, Berit, Førre, Øystein, Denson, Lee A, Thompson, Susan D, Becker, Mara L, Guthery, Stephen L, Latiano, Anna, Perez, Elena, Resnick, Elena, Strisciuglio, Caterina, Staiano, Annamaria, Miele, Erasmo, Silverberg, Mark S, Lie, Benedicte A, Punaro, Marilynn, Russell, Richard K, Wilson, David C, Dubinsky, Marla C, Monos, Dimitri S, Annese, Vito, Munro, Jane E, Wise, Carol, Chapel, Helen, Cunningham-Rundles, Charlotte, Orange, Jordan S, Behrens, Edward M, Sullivan, Kathleen E, Kugathasan, Subra, Griffiths, Anne M, Satsangi, Jack, Grant, Struan FA, Sleiman, Patrick MA, Finkel, Terri H, Polychronakos, Constantin, Baldassano, Robert N, Luning Prak, Eline T, Ellis, Justine A, Li, Hongzhe, Keating, Brendan J, Hakonarson, Hakon, Li, Yun R, Zhao, Sihai D, Li, Jin, Bradfield, Jonathan P, Mohebnasab, Maede, Steel, Laura, Kobie, Julie, Abrams, Debra J, Mentch, Frank D, Glessner, Joseph T, Guo, Yiran, Wei, Zhi, Connolly, John J, Cardinale, Christopher J, Bakay, Marina, Li, Dong, Maggadottir, S Melkorka, Thomas, Kelly A, Qui, Haijun, Chiavacci, Rosetta M, Kim, Cecilia E, Wang, Fengxiang, Snyder, James, Flatø, Berit, Førre, Øystein, Denson, Lee A, Thompson, Susan D, Becker, Mara L, Guthery, Stephen L, Latiano, Anna, Perez, Elena, Resnick, Elena, Strisciuglio, Caterina, Staiano, Annamaria, Miele, Erasmo, Silverberg, Mark S, Lie, Benedicte A, Punaro, Marilynn, Russell, Richard K, Wilson, David C, Dubinsky, Marla C, Monos, Dimitri S, Annese, Vito, Munro, Jane E, Wise, Carol, Chapel, Helen, Cunningham-Rundles, Charlotte, Orange, Jordan S, Behrens, Edward M, Sullivan, Kathleen E, Kugathasan, Subra, Griffiths, Anne M, Satsangi, Jack, Grant, Struan FA, Sleiman, Patrick MA, Finkel, Terri H, Polychronakos, Constantin, Baldassano, Robert N, Luning Prak, Eline T, Ellis, Justine A, Li, Hongzhe, Keating, Brendan J, and Hakonarson, Hakon

Abstract

Autoimmune diseases (AIDs) are polygenic diseases affecting 7-10% of the population in the Western Hemisphere with few effective therapies. Here, we quantify the heritability of paediatric AIDs (pAIDs), including JIA, SLE, CEL, T1D, UC, CD, PS, SPA and CVID, attributable to common genomic variations (SNP-h(2)). SNP-h(2) estimates are most significant for T1D (0.863±s.e. 0.07) and JIA (0.727±s.e. 0.037), more modest for UC (0.386±s.e. 0.04) and CD (0.454±0.025), largely consistent with population estimates and are generally greater than that previously reported by adult GWAS. On pairwise analysis, we observed that the diseases UC-CD (0.69±s.e. 0.07) and JIA-CVID (0.343±s.e. 0.13) are the most strongly correlated. Variations across the MHC strongly contribute to SNP-h(2) in T1D and JIA, but does not significantly contribute to the pairwise rG. Together, our results partition contributions of shared versus disease-specific genomic variations to pAID heritability, identifying pAIDs with unexpected risk sharing, while recapitulating known associations between autoimmune diseases previously reported in adult cohorts.

Published
2015

12. Genetic polymorphisms and associated susceptibility to asthma

Author

March,Michael E, Sleiman,Patrick MA, Hakonarson,Hakon, March,Michael E, Sleiman,Patrick MA, and Hakonarson,Hakon

Abstract

Michael E March,1 Patrick MA Sleiman,1 Hakon Hakonarson1,2 1Center for Applied Genomics, Abramson Research Center of the Joseph Stokes Jr Research Institute, The Children's Hospital of Philadelphia, 2Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, USA Abstract: As complex common diseases, asthma and allergic diseases are caused by the interaction of multiple genetic variants with a variety of environmental factors. Candidate-gene studies have examined the involvement of a very large list of genes in asthma and allergy, demonstrating a role for more than 100 loci. These studies have elucidated several themes in the biology and pathogenesis of these diseases. A small number of genes have been associated with asthma or allergy through traditional linkage analyses. The publication of the first asthma-focused genome-wide association (GWA) study in 2007 has been followed by nearly 30 reports of GWA studies targeting asthma, allergy, or associated phenotypes and quantitative traits. GWA studies have confirmed several candidate genes and have identified new, unsuspected, and occasionally uncharacterized genes as asthma susceptibility loci. Issues of results replication persist, complicating interpretation and making conclusions difficult to draw, and much of the heritability of these diseases remains undiscovered. In the coming years studies of complex diseases like asthma and allergy will probably involve the use of high-throughput next-generation sequencing, which will bring a tremendous influx of new information as well as new problems in dealing with vast datasets. Keywords: genome-wide association study, high-throughput next-generation sequencing, allergy, environmental irritant, allergen

Published
2013

15. Multi-ethnic genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis

Author

Paternoster, Lavinia, Standl, Marie, Waage, Johannes, Baurecht, Hansjörg, Hotze, Melanie, Strachan, David P, Curtin, John A, Bønnelykke, Klaus, Tian, Chao, Takahashi, Atsushi, Esparza-Gordillo, Jorge, Alves, Alexessander Couto, Thyssen, Jacob P, den Dekker, Herman T, Ferreira, Manuel A, Altmaier, Elisabeth, Sleiman, Patrick MA, Xiao, Feng Li, Gonzalez, Juan R, Marenholz, Ingo, Kalb, Birgit, Yanes, Maria Pino, Xu, Cheng-Jian, Carstensen, Lisbeth, Groen-Blokhuis, Maria M, Venturini, Cristina, Pennell, Craig E, Barton, Sheila J, Levin, Albert M, Curjuric, Ivan, Bustamante, Mariona, Kreiner-Møller, Eskil, Lockett, Gabrielle A, Bacelis, Jonas, Bunyavanich, Supinda, Myers, Rachel A, Matanovic, Anja, Kumar, Ashish, Tung, Joyce Y, Hirota, Tomomitsu, Kubo, Michiaki, McArdle, Wendy L, Henderson, A J, Kemp, John P, Zheng, Jie, Smith, George Davey, Rüschendorf, Franz, Bauerfeind, Anja, Lee-Kirsch, Min Ae, Arnold, Andreas, Homuth, Georg, Schmidt, Carsten O, Mangold, Elisabeth, Cichon, Sven, Keil, Thomas, Rodríguez, Elke, Peters, Annette, Franke, Andre, Lieb, Wolfgang, Novak, Natalija, Fölster-Holst, Regina, Horikoshi, Momoko, Pekkanen, Juha, Sebert, Sylvain, Husemoen, Lise L, Grarup, Niels, de Jongste, Johan C, Rivadeneira, Fernando, Hofman, Albert, Jaddoe, Vincent WV, Pasmans, Suzanne GMA, Elbert, Niels J, Uitterlinden, André G, Marks, Guy B, Thompson, Philip J, Matheson, Melanie C, Robertson, Colin F, Ried, Janina S, Li, Jin, Zuo, Xian Bo, Zheng, Xiao Dong, Yin, Xian Yong, Sun, Liang Dan, McAleer, Maeve A, O'Regan, Grainne M, Fahy, Caoimhe MR, Campbell, Linda E, Macek, Milan, Kurek, Michael, Hu, Donglei, Eng, Celeste, Postma, Dirkje S, Feenstra, Bjarke, Geller, Frank, Hottenga, Jouke Jan, Middeldorp, Christel M, Hysi, Pirro, Bataille, Veronique, Spector, Tim, Tiesler, Carla MT, Thiering, Elisabeth, Pahukasahasram, Badri, Yang, James J, Imboden, Medea, Huntsman, Scott, Vilor-Tejedor, Natàlia, Relton, Caroline L, Myhre, Ronny, Nystad, Wenche, Custovic, Adnan, Weiss, Scott T, Meyers, Deborah A, Söderhäll, Cilla, Melén, Erik, Ober, Carole, Raby, Benjamin A, Simpson, Angela, Jacobsson, Bo, Holloway, John W, Bisgaard, Hans, Sunyer, Jordi, Hensch, Nicole M Probst, Williams, L Keoki, Godfrey, Keith M, Wang, Carol A, Boomsma, Dorret I, Melbye, Mads, Koppelman, Gerard H, Jarvis, Deborah, McLean, WH Irwin, Irvine, Alan D, Zhang, Xue Jun, Hakonarson, Hakon, Gieger, Christian, Burchard, Esteban G, Martin, Nicholas G, Duijts, Liesbeth, Linneberg, Allan, Jarvelin, Marjo-Riitta, Noethen, Markus M, Lau, Susanne, Hübner, Norbert, Lee, Young-Ae, Tamari, Mayumi, Hinds, David A, Glass, Daniel, Brown, Sara J, Heinrich, Joachim, Evans, David M, and Weidinger, Stephan

Abstract

Genetic association studies have identified 21 loci associated with atopic dermatitis risk predominantly in populations of European ancestry. To identify further susceptibility loci for this common complex skin disease, we performed a meta-analysis of >15 million genetic variants in 21,399 cases and 95,464 controls from populations of European, African, Japanese and Latino ancestry, followed by replication in 32,059 cases and 228,628 controls from 18 studies. We identified 10 novel risk loci, bringing the total number of known atopic dermatitis risk loci to 31 (with novel secondary signals at 4 of these). Notably, the new loci include candidate genes with roles in regulation of innate host defenses and T-cell function, underscoring the important contribution of (auto-)immune mechanisms to atopic dermatitis pathogenesis.

Published
2015
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16. Genetic polymorphisms and associated susceptibility to asthma.

Author

March ME, Sleiman PM, and Hakonarson H

Abstract

As complex common diseases, asthma and allergic diseases are caused by the interaction of multiple genetic variants with a variety of environmental factors. Candidate-gene studies have examined the involvement of a very large list of genes in asthma and allergy, demonstrating a role for more than 100 loci. These studies have elucidated several themes in the biology and pathogenesis of these diseases. A small number of genes have been associated with asthma or allergy through traditional linkage analyses. The publication of the first asthma-focused genome-wide association (GWA) study in 2007 has been followed by nearly 30 reports of GWA studies targeting asthma, allergy, or associated phenotypes and quantitative traits. GWA studies have confirmed several candidate genes and have identified new, unsuspected, and occasionally uncharacterized genes as asthma susceptibility loci. Issues of results replication persist, complicating interpretation and making conclusions difficult to draw, and much of the heritability of these diseases remains undiscovered. In the coming years studies of complex diseases like asthma and allergy will probably involve the use of high-throughput next-generation sequencing, which will bring a tremendous influx of new information as well as new problems in dealing with vast datasets.

Published
2013
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