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2. Neptune: an environment for the delivery of genomic medicine

Author

Eric, Venner, Yi, Victoria, Murdock, David, Kalla, Sara E., Wu, Tsung-Jung, Sabo, Aniko, Li, Shoudong, Meng, Qingchang, Tian, Xia, Murugan, Mullai, Cohen, Michelle, Kovar, Christie, Wei, Wei-Qi, Chung, Wendy K., Weng, Chunhua, Wiesner, Georgia L., Jarvik, Gail P., Muzny, Donna, Gibbs, Richard A., Abrams, Debra, Adunyah, Samuel E., Albertson-Junkans, Ladia, Almoguera, Berta, Ames, Darren C., Appelbaum, Paul, Aronson, Samuel, Aufox, Sharon, Babb, Lawrence J., Balasubramanian, Adithya, Bangash, Hana, Basford, Melissa, Bastarache, Lisa, Baxter, Samantha, Behr, Meckenzie, Benoit, Barbara, Bhoj, Elizabeth, Bielinski, Suzette J., Bland, Harris T., Blout, Carrie, Borthwick, Kenneth, Bottinger, Erwin P., Bowser, Mark, Brand, Harrison, Brilliant, Murray, Brodeur, Wendy, Caraballo, Pedro, Carrell, David, Carroll, Andrew, Castillo, Lisa, Castro, Victor, Chandanavelli, Gauthami, Chiang, Theodore, Chisholm, Rex L., Christensen, Kurt D., Chung, Wendy, Chute, Christopher G., City, Brittany, Cobb, Beth L., Connolly, John J., Crane, Paul, Crew, Katherine, Crosslin, David R., Dayal, Jyoti, De Andrade, Mariza, De la Cruz, Jessica, Denny, Josh C., Denson, Shawn, DeSmet, Tim, Dikilitas, Ozan, Dinsmore, Michael J., Dodge, Sheila, Dunlea, Phil, Edwards, Todd L., Eng, Christine M., Fasel, David, Fedotov, Alex, Feng, Qiping, Fleharty, Mark, Foster, Andrea, Freimuth, Robert, Friedrich, Christopher, Fullerton, Stephanie M., Funke, Birgit, Gabriel, Stacey, Gainer, Vivian, Gharavi, Ali, Glazer, Andrew M., Glessner, Joseph T., Goehringer, Jessica, Gordon, Adam S., Graham, Chet, Green, Robert C., Gundelach, Justin H., Hain, Heather S., Hakonarson, Hakon, Harden, Maegan V., Harley, John, Harr, Margaret, Hartzler, Andrea, Hayes, M. Geoffrey, Hebbring, Scott, Henrikson, Nora, Hershey, Andrew, Hoell, Christin, Holm, Ingrid, Howell, Kayla M., Hripcsak, George, Hu, Jianhong, Hynes, Elizabeth Duffy, Jayaseelan, Joy C., Jiang, Yunyun, Joo, Yoonjung Yoonie, Jose, Sheethal, Josyula, Navya Shilpa, Justice, Anne E., Kalra, Divya, Karlson, Elizabeth W., Keating, Brendan J., Kelly, Melissa A., Kenny, Eimear E., Key, Dustin, Kiryluk, Krzysztof, Kitchner, Terrie, Klanderman, Barbara, Klee, Eric, Kochan, David C., Korchina, Viktoriya, Kottyan, Leah, Kudalkar, Emily, Rahm, Alanna Kulchak, Kullo, Iftikhar J., Lammers, Philip, Larson, Eric B., Lebo, Matthew S., Leduc, Magalie, Lee, Ming Ta (Michael), Lennon, Niall J., Leppig, Kathleen A., Leslie, Nancy D., Li, Rongling, Liang, Wayne H., Lin, Chiao-Feng, Linder, Jodell E., Lindor, Noralane M., Lingren, Todd, Linneman, James G., Liu, Cong, Liu, Wen, Liu, Xiuping, Lynch, John, Lyon, Hayley, Macbeth, Alyssa, Mahadeshwar, Harshad, Mahanta, Lisa, Malin, Bradley, Manolio, Teri, Marasa, Maddalena, Marsolo, Keith, McGowan, Michelle L., McNally, Elizabeth, Meldrim, Jim, Mentch, Frank, Rasouly, Hila Milo, Mosley, Jonathan, Mukherjee, Shubhabrata, Mullen, Thomas E., Muniz, Jesse, Murdock, David R., Murphy, Shawn, Myers, Melanie F., Namjou, Bahram, Ni, Yizhao, Onofrio, Robert C., Obeng, Aniwaa Owusu, Person, Thomas N., Peterson, Josh F., Petukhova, Lynn, Pisieczko, Cassandra J., Pratap, Siddharth, Prows, Cynthia A., Puckelwartz, Megan J., Raj, Ritika, Ralston, James D., Ramaprasan, Arvind, Ramirez, Andrea, Rasmussen, Luke, Rasmussen-Torvik, Laura, Raychaudhuri, Soumya, Rehm, Heidi L., Ritchie, Marylyn D., Rives, Catherine, Riza, Beenish, Roden, Dan M., Rosenthal, Elisabeth A., Santani, Avni, Dan, Schaid, Scherer, Steven, Scott, Stuart, Scrol, Aaron, Sengupta, Soumitra, Shang, Ning, Sharma, Himanshu, Sharp, Richard R., Singh, Rajbir, Sleiman, Patrick M.A., Slowik, Kara, Smith, Joshua C., Smith, Maureen E., Smoot, Duane T., Smoller, Jordan W., Sohn, Sunghwan, Stanaway, Ian B., Starren, Justin, Stroud, Mary, Su, Jessica, Taylor, Casey Overby, Tolwinski, Kasia, Van Driest, Sara L., Vargas, Sean M., Varugheese, Matthew, Veenstra, David, Venner, Eric, Verbitsky, Miguel, Vicente, Gina, Wagner, Michael, Walker, Kimberly, Walunas, Theresa, Wang, Liwen, Wang, Qiaoyan, Weiss, Scott T., Wells, Quinn S., White, Peter S., Wiley, Ken L., Jr, Williams, Janet L., Williams, Marc S., Wilson, Michael W., Witkowski, Leora, Woods, Laura Allison, Woolf, Betty, Wynn, Julia, Yang, Yaping, Zhang, Ge, Zhang, Lan, and Zouk, Hana

Published
2021
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3. Erratum: A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling

Author

Li, Dong, Chang, Xiao, Connolly, John J, Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J, Robinson, Nora, Abrams, Debra, Li, Yun R, Bradfield, Jonathan P, Kim, Cecilia E, Li, Jin, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D, Thomas, Kelly A, Chiavacci, Rosetta M, Cone, Roger, Li, Bingshan, Sleiman, Patrick A, Eating Disorders Working Group of the Psychiatric Genomics Consortium, Price Foundation Collaborative Group, and Hakonarson, Hakon

Subjects
Biological Sciences, Mathematical Sciences, Genetics, Eating Disorders Working Group of the Psychiatric Genomics Consortium, Price Foundation Collaborative Group
Abstract

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.

Published
2017

4. A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling.

Author

Li, Dong, Chang, Xiao, Connolly, John J, Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J, Robinson, Nora, Abrams, Debra, Li, Yun R, Bradfield, Jonathan P, Kim, Cecilia E, Li, Jin, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D, Thomas, Kelly A, Chiavacci, Rosetta M, Cone, Roger, Li, Bingshan, Sleiman, Patrick A, Eating Disorders Working Group of the Psychiatric Genomics Consortium, Price Foundation Collaborative Group, and Hakonarson, Hakon

Subjects
Eating Disorders Working Group of the Psychiatric Genomics Consortium, Price Foundation Collaborative Group
Abstract

We conducted a genome-wide association study (GWAS) of anorexia nervosa (AN) using a stringently defined phenotype. Analysis of phenotypic variability led to the identification of a specific genetic risk factor that approached genome-wide significance (rs929626 in EBF1 (Early B-Cell Factor 1); P = 2.04 × 10-7; OR = 0.7; 95% confidence interval (CI) = 0.61-0.8) with independent replication (P = 0.04), suggesting a variant-mediated dysregulation of leptin signaling may play a role in AN. Multiple SNPs in LD with the variant support the nominal association. This demonstrates that although the clinical and etiologic heterogeneity of AN is universally recognized, further careful sub-typing of cases may provide more precise genomic signals. In this study, through a refinement of the phenotype spectrum of AN, we present a replicable GWAS signal that is nominally associated with AN, highlighting a potentially important candidate locus for further investigation.

Published
2017

6. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network

Author

Zouk, Hana, Venner, Eric, Lennon, Niall J., Muzny, Donna M., Abrams, Debra, Adunyah, Samuel, Albertson-Junkans, Ladia, Ames, Darren C., Appelbaum, Paul, Aronson, Samuel, Aufox, Sharon, Babb, Lawrence J., Balasubramanian, Adithya, Bangash, Hana, Basford, Melissa, Bastarache, Lisa, Baxter, Samantha, Behr, Meckenzie, Benoit, Barbara, Bhoj, Elizabeth, Bielinski, Suzette J., Bland, Harris T., Blout, Carrie, Borthwick, Kenneth, Bottinger, Erwin P., Bowser, Mark, Brand, Harrison, Brilliant, Murray, Brodeur, Wendy, Caraballo, Pedro, Carrell, David, Carroll, Andrew, Almoguera, Berta, Castillo, Lisa, Castro, Victor, Chandanavelli, Gauthami, Chiang, Theodore, Chisholm, Rex L., Christensen, Kurt D., Chung, Wendy, Chute, Christopher G., City, Brittany, Cobb, Beth L., Connolly, John J., Crane, Paul, Crew, Katherine, Crosslin, David, De Andrade, Mariza, De la Cruz, Jessica, Denson, Shawn, Denny, Josh, DeSmet, Tim, Dikilitas, Ozan, Friedrich, Christopher, Fullerton, Stephanie M., Funke, Birgit, Gabriel, Stacey, Gainer, Vivian, Gharavi, Ali, Glazer, Andrew M., Glessner, Joseph T., Goehringer, Jessica, Gordon, Adam S., Graham, Chet, Green, Robert C., Gundelach, Justin H., Dayal, Jyoti, Hain, Heather S., Hakonarson, Hakon, Harden, Maegan V., Harley, John, Harr, Margaret, Hartzler, Andrea, Hayes, M. Geoffrey, Hebbring, Scott, Henrikson, Nora, Hershey, Andrew, Hoell, Christin, Holm, Ingrid, Howell, Kayla M., Hripcsak, George, Hu, Jianhong, Jarvik, Gail P., Jayaseelan, Joy C., Jiang, Yunyun, Joo, Yoonjung Yoonie, Jose, Sheethal, Josyula, Navya Shilpa, Justice, Anne E., Kalla, Sara E., Kalra, Divya, Karlson, Elizabeth, Kelly, Melissa A., Keating, Brendan J., Kenny, Eimear E., Key, Dustin, Kiryluk, Krzysztof, Kitchner, Terrie, Klanderman, Barbara, Klee, Eric, Kochan, David C., Korchina, Viktoriya, Kottyan, Leah, Kovar, Christie, Kudalkar, Emily, Kullo, Iftikhar J., Lammers, Philip, Larson, Eric B., Lebo, Matthew S., Leduc, Magalie, Lee, Ming Ta (Michael), Leppig, Kathleen A., Leslie, Nancy D., Li, Rongling, Liang, Wayne H., Lin, Chiao-Feng, Linder, Jodell, Lindor, Noralane M., Lingren, Todd, Linneman, James G., Liu, Cong, Liu, Wen, Liu, Xiuping, Lynch, John, Lyon, Hayley, Macbeth, Alyssa, Mahadeshwar, Harshad, Mahanta, Lisa, Malin, Brad, Manolio, Teri, Marasa, Maddalena, Marsolo, Keith, Dinsmore, Michael J., Dodge, Sheila, Hynes, Elizabeth Duffy, Dunlea, Phil, Edwards, Todd L., Eng, Christine M., Fasel, David, Fedotov, Alex, Feng, Qiping, Fleharty, Mark, Foster, Andrea, Freimuth, Robert, McGowan, Michelle L., McNally, Elizabeth, Meldrim, Jim, Mentch, Frank, Mosley, Jonathan, Mukherjee, Shubhabrata, Mullen, Thomas E., Muniz, Jesse, Murdock, David R., Murphy, Shawn, Murugan, Mullai, Myers, Melanie F., Namjou, Bahram, Ni, Yizhao, Obeng, Aniwaa Owusu, Onofrio, Robert C., Taylor, Casey Overby, Person, Thomas N., Peterson, Josh F., Petukhova, Lynn, Pisieczko, Cassandra J., Pratap, Siddharth, Prows, Cynthia A., Puckelwartz, Megan J., Rahm, Alanna Kulchak, Raj, Ritika, Ralston, James D., Ramaprasan, Arvind, Ramirez, Andrea, Rasmussen, Luke, Rasmussen-Torvik, Laura, Rasouly, Hila Milo, Raychaudhuri, Soumya, Ritchie, Marylyn D., Rives, Catherine, Riza, Beenish, Roden, Dan, Rosenthal, Elisabeth A., Santani, Avni, Schaid, Dan, Scherer, Steven, Scott, Stuart, Scrol, Aaron, Sengupta, Soumitra, Shang, Ning, Sharma, Himanshu, Sharp, Richard R., Singh, Rajbir, Sleiman, Patrick M.A., Slowik, Kara, Smith, Joshua C., Smith, Maureen E., Smoller, Jordan W., Sohn, Sunghwan, Stanaway, Ian B., Starren, Justin, Stroud, Mary, Su, Jessica, Tolwinski, Kasia, Van Driest, Sara L., Vargas, Sean M., Varugheese, Matthew, Veenstra, David, Verbitsky, Miguel, Vicente, Gina, Wagner, Michael, Walker, Kimberly, Walunas, Theresa, Wang, Liwen, Wang, Qiaoyan, Wei, Wei-Qi, Weiss, Scott T., Wiesner, Georgia L., Wells, Quinn, Weng, Chunhua, White, Peter S., Wiley, Ken L., Jr., Williams, Janet L., Williams, Marc S., Wilson, Michael W., Witkowski, Leora, Woods, Laura Allison, Woolf, Betty, Wu, Tsung-Jung, Wynn, Julia, Yang, Yaping, Yi, Victoria, Zhang, Ge, Zhang, Lan, Rehm, Heidi L., and Gibbs, Richard A.

Published
2019
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7. 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 F. A., Sleiman, Patrick M. A., Li, Mingyao, Eichler, Evan E., and Hakonarson, Hakon

Published
2020
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9. Phenotype Specific Association of the TGFBR3 Locus with Nonsyndromic Cryptorchidism

Author

Barthold, Julia S., Wang, Yanping, Kolon, Thomas F., Kollin, Claude, Nordenskjöld, Agneta, Olivant Fisher, Alicia, Figueroa, T. Ernesto, BaniHani, Ahmad H., Hagerty, Jennifer A., Gonzalez, Ricardo, Noh, Paul H., Chiavacci, Rosetta M., Harden, Kisha R., Abrams, Debra J., Kim, Cecilia E., Mateson, Abigail B., Robbins, Alan K., Li, Jin, Akins, Robert E., Jr., Hakonarson, Hakon, and Devoto, Marcella

Published
2015
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10. COVID-19 in pediatrics: Genetic susceptibility

Author

Glessner, Joseph T., primary, Chang, Xiao, additional, Mentch, Frank, additional, Qu, Huiqi, additional, Abrams, Debra J., additional, Thomas, Alexandria, additional, Sleiman, Patrick M. A., additional, and Hakonarson, Hakon, additional

Published
2022
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11. Identification of Novel Loci Shared by Juvenile Idiopathic Arthritis Subtypes Through Integrative Genetic Analysis

Author

Li, Jin, primary, Li, Yun R., additional, Glessner, Joseph T., additional, Yang, Jie, additional, March, Michael E., additional, Kao, Charlly, additional, Vaccaro, Courtney N., additional, Bradfield, Jonathan P., additional, Li, Junyi, additional, Mentch, Frank D., additional, Qu, Hui‐Qi, additional, Qi, Xiaohui, additional, Chang, Xiao, additional, Hou, Cuiping, additional, Abrams, Debra J., additional, Qiu, Haijun, additional, Wei, Zhi, additional, Connolly, John J., additional, Wang, Fengxiang, additional, Snyder, James, additional, Flatø, Berit, additional, Thompson, Susan D., additional, Langefeld, Carl D., additional, Lie, Benedicte A., additional, Munro, Jane E., additional, Wise, Carol, additional, Sleiman, Patrick M. A., additional, and Hakonarson, Hakon, additional

Published
2022
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12. Additional file 1 of An electronic health record (EHR) phenotype algorithm to identify patients with attention deficit hyperactivity disorders (ADHD) and psychiatric comorbidities

Author

Slaby, Isabella, Hain, Heather S., Abrams, Debra, Mentch, Frank D., Glessner, Joseph T., Sleiman, Patrick M. A., and Hakonarson, Hakon

Subjects
mental disorders
Abstract

Additional file 1: Table S1. ADHD Inclusion/ Exclusion Table. ICD codes and direct terms of ADHD and ADD were used, as well as terms that were specific towards ADHD phenotypes and medications. Table S2. Anxiety Inclusion/ Exclusion Table. ICD codes and terms that were specific towards anxiety phenotypes and medications were used. Table S3. Autism Inclusion/ Exclusion Table. ICD Codes as well as terms that were specific towards autism phenotypes were used. Table S4. Conduct Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards conduct disorder phenotypes were used. Table S5. Oppositional Defiant Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards oppositional defiant disorder phenotypes were used. Table S6. Major Depressive Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards major depression phenotypes and medications were used. Diagnosis of major depressive disorder was present on at least two (2) distinct calendar days that are at least thirty (30) days apart and not more than one hundred and eighty (180) days apart. Table S7. Bipolar Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards bipolar disorder phenotypes and medications were used. Diagnosis of bipolar disorder was present on at least two (2) distinct calendar days that are at least thirty (30) days apart and not more than one hundred and eighty (180) days apart. Table S8. Schizophrenia and Psychoses Inclusion/ Exclusion Table. ICD codes and terms that were specific towards schizophrenia and psychoses phenotypes and medications were used. Table S9. Tic Disorders Inclusion/ Exclusion Table. ICD codes and terms that were specific towards tic disorder phenotypes were used. Table S10. Tourette Syndrome Inclusion/ Exclusion Table. ICD codes and terms that were specific towards Tourette syndrome phenotypes were used. Table S11. Intellectual Disability Inclusion/ Exclusion Table. ICD codes and terms that were specific towards intellectual disability phenotypes were used. Table S12. Learning Disability Inclusion/ Exclusion Table. ICD codes and terms that were specific towards learning disability phenotypes were used. Table S13. Case Exclusion Table. ICD codes and terms used for case exclusions. Table S14. Control Exclusion Table. ICD codes and terms used for control exclusions. Table S15. Control Syndromes Exclusion Table. ICD codes and terms used for control syndrome exclusions. Table S16. Psychiatric Conditions Prevalence in Extracted Subjects. Numbers and percent of psychiatric disorders and comorbidities in all cases and Psych Positive Cases. *has at least of the 10 psychiatric conditions (does not include learning disability or intellectual disability. Table S17. Validation of algorithms. Positive Predictive Values (PPV) of algorithms for each psychiatric disorders and comorbidity of ADHD measured.

Published
2022
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13. Pathway analysis supports association of nonsyndromic cryptorchidism with genetic loci linked to cytoskeleton-dependent functions

Author

Barthold, Julia Spencer, Wang, Yanping, Kolon, Thomas F., Kollin, Claude, Nordenskjöld, Agneta, Olivant Fisher, Alicia, Figueroa, T. Ernesto, BaniHani, Ahmad H., Hagerty, Jennifer A., Gonzaléz, Ricardo, Noh, Paul H., Chiavacci, Rosetta M., Harden, Kisha R., Abrams, Debra J., Kim, Cecilia E., Li, Jin, Hakonarson, Hakon, and Devoto, Marcella

Published
2015
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16. Association of Variants of the Interleukin-23 Receptor Gene With Susceptibility to Pediatric Crohn’s Disease

Author

Baldassano, Robert N., Bradfield, Jonathan P., Monos, Dimitri S., Kim, Cecilia E., Glessner, Joseph T., Casalunovo, Tracy, Frackelton, Edward C., Otieno, F. George, Kanterakis, Stathis, Shaner, Julie L., Smith, Ryan M., Eckert, Andrew W., Robinson, Luke J., Onyiah, Chioma C., Abrams, Debra J., Chiavacci, Rosetta M., Skraban, Robert, Devoto, Marcella, Grant, Struan F.A., and Hakonarson, Hakon

Published
2007
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18. Integrative Genetics Analysis of Juvenile Idiopathic Arthritis Identifies Novel Loci

Author

Li, Yun R., primary, Li, Jin, additional, Glessner, Joseph T., additional, Yang, Jie, additional, March, Michael E., additional, Kao, Charlly, additional, Bradfield, Jonathan P., additional, Li, Junyi, additional, Mentch, Frank D., additional, Qu, Huiqi, additional, Qi, Xiaohui, additional, Chang, Xiao, additional, Hou, Cuiping, additional, Abrams, Debra J., additional, Qiu, Haijun, additional, Wei, Zhi, additional, Connolly, John J., additional, Wang, Fengxiang, additional, Snyder, James, additional, Limou, Sophie, additional, Flatø, Berit, additional, Førr, Øystein, additional, Thompson, Susan D., additional, Langefeld, Carl D, additional, Glass, David N, additional, Becker, Mara L., additional, Perez, Elena, additional, Lie, Benedicte A., additional, Punaro, Marilynn, additional, Shivers, Debra K, additional, Ellis, Justine A., additional, Munro, Jane E., additional, Wise, Carol, additional, Sleiman, Patrick M.A., additional, and Hakonarson, Hakon, additional

Published
2020
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20. Association of the T300A non-synonymous variant of the ATG16L1 gene with susceptibility to paediatric Crohn’s disease

Author

Baldassano, Robert N, Bradfield, Jonathan P, Monos, Dimitri S, Kim, Cecilia E, Glessner, Joseph T, Casalunovo, Tracy, Frackelton, Edward C, Otieno, F George, Kanterakis, Stathis, Shaner, Julie L, Smith, Ryan M, Eckert, Andrew W, Robinson, Luke J, Onyiah, Chioma C, Abrams, Debra J, Chiavacci, Rosetta M, Skraban, Robert, Devoto, Marcella, Grant, Struan F A, and Hakonarson, Hakon

Published
2007

21. Above All, There Is a Voice.

Author

Abrams, Debra Josephson

Abstract

Describes the sensibilities and temperament that make a successful, daily writer. Questions why writers write. Attempts to define what it is that makes a writer write. (HB)

Published
1993

23. 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

24. Erratum: A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling (Scientific Reports (2017) 7 (3847) DOI: 10.1038/s41598-017-01674-8)

Author

Dong, Li, Chang, Xiao, Connolly, John J, Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J, Robinson, Nora, Abrams, Debra, Yun R, Li, Bradfield, Jonathan P, Kim, Cecilia E, Jin, Li, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D, Thomas, Kelly A, Chiavacci, Rosetta M, Cone, Roger, Bingshan, Li, Sleiman, Patrick A, Hakonarson, Hakon, and Tortorella, A

Subjects
Multidisciplinary
Published
2017

25. A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling

Author

TN groep Adan, Brain, Circulatory Health, Translational Neuroscience, Genetica Groep Koeleman, Child Health, Onderzoek, Pathologie, AIOS Psychiatrie, Li, Dong, Chang, Xiao, Connolly, John J., Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J., Robinson, Nora, Abrams, Debra, Li, Yun R., Bradfield, Jonathan P., Kim, Cecilia E., Li, Jin, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D., Thomas, Kelly A., Chiavacci, Rosetta M., Cone, Roger, Li, Bingshan, Sleiman, Patrick A., Hakonarson, Hakon, Perica, Vesna Boraska, Franklin, Christopher S., Floyd, James A.B., Thornton, Laura M., Huckins, Laura M., Southam, Lorraine, Rayner, William N, Tachmazidou, Ioanna, Schmidt, Ulrike, Tozzi, Federica, Kiezebrink, Kirsty, Hebebrand, Johannes, Gorwood, Philip, Adan, Roger A.H., Kas, Martien J.H., Favaro, Angela, Santonastaso, Paolo, Fernánde-Aranda, Fernando, Gratacos, Monica, Rybakowski, Filip, Dmitrzak-Weglarz, Monika, Kaprio, Jaakko, Keski-Rahkonen, Anna, Raevuori-Helkamaa, Anu, Furth, Eric F.Van, Slof-Opt Landt, Margarita C.T., Hudson, James I., Reichborn-Kjennerud, Ted, Knudsen, Gun Peggy S., Monteleone, Palmiero, Karwautz, Andreas, Berrettini, Wade H., Schork, Nicholas J., Ando, Tetsuya, Inoko, Hidetoshi, Esko, Toñu, Fischer, Krista, Männik, Katrin, Metspalu, Andres, Baker, Jessica H., DeSocio, Janiece E., Hilliard, Christopher E., O'Toole, Julie K., Pantel, Jacques, Szatkiewicz, Jin P., Zerwas, Stephanie, Davis, Oliver S P, Helder, Sietske, Bühren, Katharina, Burghardt, Roland, De Zwaan, Martina, Egberts, Karin, Ehrlich, Stefan, Herpertz-Dahlmann, Beate, Herzog, Wolfgang, Imgart, Hartmut, Scherag, André, Zipfel, Stephan, Boni, Claudette, Ramoz, Nicolas, Versini, Audrey, Danner, Unna N., Hendriks, Judith, Koeleman, Bobby P.C., Ophoff, Roel A., Strengman, Eric, van Elburg, Annemarie A., Bruson, Alice, Clementi, Maurizio, Degortes, Daniela, Forzan, Monica, Tenconi, Elena, Docampo, Elisa, Escaramís, Geòrgia, Jiménez-Murcia, Susana, Lissowska, Jolanta, Rajewski, Andrzej, Szeszenia-Dabrowska, Neonila, Slopien, Agnieszka, Hauser, Joanna, Karhunen, Leila, Meulenbelt, Ingrid, Slagboom, P. Eline, Tortorella, Alfonso, Maj, Mario, Dedoussis, George, DIkeos, DImitris, Gonidakis, Fragiskos, Tziouvas, Konstantinos, Tsitsika, Artemis, Papezova, Hana, Slachtova, Lenka, Martaskova, Debora, Kennedy, James L., Levitan, Robert D., Yilmaz, Zeynep, Huemer, Julia, Koubek, Doris, Merl, Elisabeth, Wagner, Gudrun, Lichtenstein, Paul, Breen, Gerome, Cohen-Woods, Sarah, Farmer, Anne, McGuffin, Peter, Cichon, Sven, Giegling, Ina, Herms, Stefan, Rujescu, Dan, Schreiber, Stefan, Wichmann, H-Erich, Dina, Christian, Sladek, Rob, Gambaro, Giovanni, Soranzo, Nicole, Julia, Antonio, Marsal, Sara, Rabionet, Raquel, Gaborieau, Valerie, DIck, Danielle M., Palotie, Aarno, Ripatti, Samuli, Widén, Elisabeth, Andreassen, Ole A., Espeseth, Thomas, Lundervold, Astri J, Reinvang, Ivar, Steen, Vidar M., Le Hellard, Stephanie, Mattingsdal, Morten, Ntalla, Ioanna, Bencko, Vladimir, Foretova, Lenka, Janout, Vladimir, Navratilova, Marie, Gallinger, Steven, Pinto, Dalila, Scherer, Stephen W., Aschauer, Harald, Carlberg, Laura, Schosser, Alexandra, Alfredsson, Lars, Ding, Bo, Klareskog, Lars, Padyukov, Leonid, Finan, Chris, Kalsi, Gursharan, Roberts, Marion, Barrett, Jeff C., Estivill, Xavier, Hinney, Anke, Sullivan, Patrick F, Zeggini, Eleftheria, Bulik, Cynthia M., Brandt, Harry, Crawford, Steve, Crow, Scott, Fichter, Manfred M., Halmi, Katherine A., Johnson, Craig, Kaplan, Allan S., La Via, Maria C., Mitchell, James R., Strober, Michael, Rotondo, Alessandro, Treasure, Janet, Woodside, D. Blake, Keel, Pamela K., Klump, Kelly L., Lilenfeld, Lisa, Bergen, Andrew W., Kaye, Walter, Magistretti, Pierre, TN groep Adan, Brain, Circulatory Health, Translational Neuroscience, Genetica Groep Koeleman, Child Health, Onderzoek, Pathologie, AIOS Psychiatrie, Li, Dong, Chang, Xiao, Connolly, John J., Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J., Robinson, Nora, Abrams, Debra, Li, Yun R., Bradfield, Jonathan P., Kim, Cecilia E., Li, Jin, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D., Thomas, Kelly A., Chiavacci, Rosetta M., Cone, Roger, Li, Bingshan, Sleiman, Patrick A., Hakonarson, Hakon, Perica, Vesna Boraska, Franklin, Christopher S., Floyd, James A.B., Thornton, Laura M., Huckins, Laura M., Southam, Lorraine, Rayner, William N, Tachmazidou, Ioanna, Schmidt, Ulrike, Tozzi, Federica, Kiezebrink, Kirsty, Hebebrand, Johannes, Gorwood, Philip, Adan, Roger A.H., Kas, Martien J.H., Favaro, Angela, Santonastaso, Paolo, Fernánde-Aranda, Fernando, Gratacos, Monica, Rybakowski, Filip, Dmitrzak-Weglarz, Monika, Kaprio, Jaakko, Keski-Rahkonen, Anna, Raevuori-Helkamaa, Anu, Furth, Eric F.Van, Slof-Opt Landt, Margarita C.T., Hudson, James I., Reichborn-Kjennerud, Ted, Knudsen, Gun Peggy S., Monteleone, Palmiero, Karwautz, Andreas, Berrettini, Wade H., Schork, Nicholas J., Ando, Tetsuya, Inoko, Hidetoshi, Esko, Toñu, Fischer, Krista, Männik, Katrin, Metspalu, Andres, Baker, Jessica H., DeSocio, Janiece E., Hilliard, Christopher E., O'Toole, Julie K., Pantel, Jacques, Szatkiewicz, Jin P., Zerwas, Stephanie, Davis, Oliver S P, Helder, Sietske, Bühren, Katharina, Burghardt, Roland, De Zwaan, Martina, Egberts, Karin, Ehrlich, Stefan, Herpertz-Dahlmann, Beate, Herzog, Wolfgang, Imgart, Hartmut, Scherag, André, Zipfel, Stephan, Boni, Claudette, Ramoz, Nicolas, Versini, Audrey, Danner, Unna N., Hendriks, Judith, Koeleman, Bobby P.C., Ophoff, Roel A., Strengman, Eric, van Elburg, Annemarie A., Bruson, Alice, Clementi, Maurizio, Degortes, Daniela, Forzan, Monica, Tenconi, Elena, Docampo, Elisa, Escaramís, Geòrgia, Jiménez-Murcia, Susana, Lissowska, Jolanta, Rajewski, Andrzej, Szeszenia-Dabrowska, Neonila, Slopien, Agnieszka, Hauser, Joanna, Karhunen, Leila, Meulenbelt, Ingrid, Slagboom, P. Eline, Tortorella, Alfonso, Maj, Mario, Dedoussis, George, DIkeos, DImitris, Gonidakis, Fragiskos, Tziouvas, Konstantinos, Tsitsika, Artemis, Papezova, Hana, Slachtova, Lenka, Martaskova, Debora, Kennedy, James L., Levitan, Robert D., Yilmaz, Zeynep, Huemer, Julia, Koubek, Doris, Merl, Elisabeth, Wagner, Gudrun, Lichtenstein, Paul, Breen, Gerome, Cohen-Woods, Sarah, Farmer, Anne, McGuffin, Peter, Cichon, Sven, Giegling, Ina, Herms, Stefan, Rujescu, Dan, Schreiber, Stefan, Wichmann, H-Erich, Dina, Christian, Sladek, Rob, Gambaro, Giovanni, Soranzo, Nicole, Julia, Antonio, Marsal, Sara, Rabionet, Raquel, Gaborieau, Valerie, DIck, Danielle M., Palotie, Aarno, Ripatti, Samuli, Widén, Elisabeth, Andreassen, Ole A., Espeseth, Thomas, Lundervold, Astri J, Reinvang, Ivar, Steen, Vidar M., Le Hellard, Stephanie, Mattingsdal, Morten, Ntalla, Ioanna, Bencko, Vladimir, Foretova, Lenka, Janout, Vladimir, Navratilova, Marie, Gallinger, Steven, Pinto, Dalila, Scherer, Stephen W., Aschauer, Harald, Carlberg, Laura, Schosser, Alexandra, Alfredsson, Lars, Ding, Bo, Klareskog, Lars, Padyukov, Leonid, Finan, Chris, Kalsi, Gursharan, Roberts, Marion, Barrett, Jeff C., Estivill, Xavier, Hinney, Anke, Sullivan, Patrick F, Zeggini, Eleftheria, Bulik, Cynthia M., Brandt, Harry, Crawford, Steve, Crow, Scott, Fichter, Manfred M., Halmi, Katherine A., Johnson, Craig, Kaplan, Allan S., La Via, Maria C., Mitchell, James R., Strober, Michael, Rotondo, Alessandro, Treasure, Janet, Woodside, D. Blake, Keel, Pamela K., Klump, Kelly L., Lilenfeld, Lisa, Bergen, Andrew W., Kaye, Walter, and Magistretti, Pierre

Published
2017

26. Additional file 1: of Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

Author

Yanping Wang, Li, Jin, Kolon, Thomas, Fisher, Alicia Olivant, T. Figueroa, BaniHani, Ahmad, Hagerty, Jennifer, Gonzalez, Ricardo, Noh, Paul, Chiavacci, Rosetta, Harden, Kisha, Abrams, Debra, Stabley, Deborah, Kim, Cecilia, Sol-Church, Katia, Hakon Hakonarson, Devoto, Marcella, and Barthold, Julia

Abstract

genome-wide significant genes/loci in gene-based association tests in each group. Listed all the genes/loci with genome-wide significance (pâ

Published
2016
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27. Additional file 3: of Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

Author

Yanping Wang, Li, Jin, Kolon, Thomas, Fisher, Alicia Olivant, T. Figueroa, BaniHani, Ahmad, Hagerty, Jennifer, Gonzalez, Ricardo, Noh, Paul, Chiavacci, Rosetta, Harden, Kisha, Abrams, Debra, Stabley, Deborah, Kim, Cecilia, Sol-Church, Katia, Hakon Hakonarson, Devoto, Marcella, and Barthold, Julia

Abstract

Array plot of Log R ration and B allele frequency for TARP and TONSL/TONSL-AS1. Showed the signal intensity plots of 2 CNVs in TARP and 1 CNV in TONSL/TONSL-AS1. The array plots did not pass visualization examination due to LRR close to 0, BAF cluster near 0.5, or both. (DOCX 141Â kb)

Published
2016
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28. Additional file 2: of Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

Author

Yanping Wang, Li, Jin, Kolon, Thomas, Fisher, Alicia Olivant, T. Figueroa, BaniHani, Ahmad, Hagerty, Jennifer, Gonzalez, Ricardo, Noh, Paul, Chiavacci, Rosetta, Harden, Kisha, Abrams, Debra, Stabley, Deborah, Kim, Cecilia, Sol-Church, Katia, Hakon Hakonarson, Devoto, Marcella, and Barthold, Julia

Abstract

genome-wide signficant genes/loci in meta-analysis. Listed all the genes/loci with genome-wide significant p-values (pâ

Published
2016
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29. Drug‐resistant epilepsy classified by a phenotyping algorithm associates with NTRK2.

Author

Almoguera, Berta, McGinnis, Emily, Abrams, Debra, Vazquez, Lyam, Cederquist, Anna, Sleiman, Patrick M., Dlugos, Dennis, Hakonarson, Hakon, Cagan, Andrew, Connolly, John, Gainer, Vivian S, Garifallou, James, Kaminski, Courtney, Lee, Yvonne C., Mafra, Fernanda, Mentch, Frank, Pellegrino, Renata, Qiu, Haijun, Snyder, James, and Tian, Lifeng

Subjects
EPILEPSY, ONTOGENY, CENTRAL nervous system, DRUG resistance, GENE families, PHARMACOGENOMICS
Abstract

Objective: Up to 40% of patients with epilepsy become drug resistant (DRE). Genetic factors are likely to play a role. While efforts have focused on the transporter and target hypotheses, neither of them fully explains the pan‐pharmacoresistance seen in DRE. Materials and methods: In this study, we developed and used a phenotyping algorithm for the identification of DRE, responders, and epilepsy‐free controls that were sequenced using a gene panel developed by the Pharmacogenomics Research Network (PGRN), which includes 82 genes involved in drug response. We tested the transporter hypothesis of DRE, the association between drug resistance and variants in the ATP‐binding cassette family of genes previously associated with DRE, and also investigated potential new genetic factors. Results: In the analysis of DRE vs controls, NTRK2 was significantly associated with DRE (rs76950094; P = 1.19 × 10−7 and gene‐based P‐value = 1.67 × 10−4). NTRK2 encodes TrkB, which is involved in the development and maturation of the central nervous system, and increased activation of TrkB signaling is suggested to promote epilepsy. Conclusion: Although the role of NTRK2 in DRE needs to be elucidated, these results support alternative mechanisms underlying DRE, complementary to the existing hypotheses, that should be evaluated. [ABSTRACT FROM AUTHOR]

Published
2019
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30. A Pilot Trial of Unmatched Human Placenta-Derived Stem Cells (HPDSCs) in Conjunction with Unrelated Cord Blood Transplantation (UCBT) in Children and Young Adults with Malignant and Non-Malignant Disease (IND 14949)

Author

Flower, Allyson M., primary, Nash, Michelle, additional, Minzer, Suzan, additional, Harrison, Lauren, additional, Pulsipher, Michael A, additional, Shi, Qiuhu, additional, Abrams, Debra, additional, Giller, Roger H., additional, Morris, Erin, additional, Militano, Olga, additional, Ayello, Janet, additional, Semidei-Pomales, Mildred, additional, Fabricatore, Sandra, additional, Zhang, Xiaokui, additional, Gurney, Jodi, additional, van de Ven, Carmella, additional, Abikoff, Cori M., additional, Hochberg, Jessica C., additional, Baxter-Lowe, Lee Ann, additional, and Cairo, Mitchell S., additional

Published
2016
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31. Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

Author

Wang, Yanping, primary, Li, Jin, additional, Kolon, Thomas F., additional, Olivant Fisher, Alicia, additional, Figueroa, T. Ernesto, additional, BaniHani, Ahmad H., additional, Hagerty, Jennifer A., additional, Gonzalez, Ricardo, additional, Noh, Paul H., additional, Chiavacci, Rosetta M., additional, Harden, Kisha R., additional, Abrams, Debra J., additional, Stabley, Deborah, additional, Kim, Cecilia E., additional, Sol-Church, Katia, additional, Hakonarson, Hakon, additional, Devoto, Marcella, additional, and Barthold, Julia Spencer, additional

Published
2016
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32. Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder

Author

Lingren, Todd, primary, Chen, Pei, additional, Bochenek, Joseph, additional, Doshi-Velez, Finale, additional, Manning-Courtney, Patty, additional, Bickel, Julie, additional, Wildenger Welchons, Leah, additional, Reinhold, Judy, additional, Bing, Nicole, additional, Ni, Yizhao, additional, Barbaresi, William, additional, Mentch, Frank, additional, Basford, Melissa, additional, Denny, Joshua, additional, Vazquez, Lyam, additional, Perry, Cassandra, additional, Namjou, Bahram, additional, Qiu, Haijun, additional, Connolly, John, additional, Abrams, Debra, additional, Holm, Ingrid A., additional, Cobb, Beth A., additional, Lingren, Nataline, additional, Solti, Imre, additional, Hakonarson, Hakon, additional, Kohane, Isaac S., additional, Harley, John, additional, and Savova, Guergana, additional

Published
2016
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33. A Pilot Trial of Unmatched Human Placental Derived Stem Cells (HPDSCs) in Conjunction with Unrelated Cord Blood Transplantation (UCBT) in Children and Young Adults with Malignant and Non-Malignant Disease (IND 14949)

Author

Nash, Michelle, primary, Harrison, Lauren, additional, Pulsipher, Michael A., additional, Shi, Qiuhu, additional, Abrams, Debra, additional, Giller, Roger, additional, Nickerson, Berkley, additional, Morris, Erin, additional, Militano, Olga, additional, Ayello, Janet, additional, Semidei-Pomales, Mildred, additional, Fabricatore, Sandra, additional, Zhang, Xiaokui, additional, Gurney, Jodi, additional, Herb, Stacy, additional, Sivalenka, Rajarajeswari, additional, van de Ven, Carmella, additional, El-Mallawany, Nader, additional, Abikoff, Cori, additional, Hochberg, Jessica, additional, Baxter Lowe, Lee-Ann, additional, and Cairo, Mitchell S., additional

Published
2016
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35. 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

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

Author

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

Published
2015
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37. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Author

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

Published
2015
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38. Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism.

Author

Yanping Wang, Jin Li, Kolon, Thomas F., Fisher, Alicia Olivant, Figueroa, T. Ernesto, BaniHani, Ahmad H., Hagerty, Jennifer A., Gonzalez, Ricardo, Noh, Paul H., Chiavacci, Rosetta M., Harden, Kisha R., Abrams, Debra J., Stabley, Deborah, Kim, Cecilia E., Sol-Church, Katia, Hakonarson, Hakon, Devoto, Marcella, and Barthold, Julia Spencer

Subjects
CRYPTORCHISM, DNA copy number variations, GENOMICS, CAUCASIAN race, GENITOURINARY diseases, HEALTH
Abstract

Background: Copy number variation (CNV) is a potential contributing factor to many genetic diseases. Here we investigated the potential association of CNV with nonsyndromic cryptorchidism, the most common male congenital genitourinary defect, in a Caucasian population. Methods: Genome wide genotyping were performed in 559 cases and 1772 controls (Group 1) using Illumina HumanHap550 v1, HumanHap550 v3 or Human610-Quad platforms and in 353 cases and 1149 controls (Group 2) using the Illumina Human OmniExpress 12v1 or Human OmniExpress 12v1-1. Signal intensity data including log R ratio (LRR) and B allele frequency (BAF) for each single nucleotide polymorphism (SNP) were used for CNV detection using PennCNV software. After sample quality control, gene- and CNV-based association tests were performed using cleaned data from Group 1 (493 cases and 1586 controls) and Group 2 (307 cases and 1102 controls) using ParseCNV software. Meta-analysis was performed using gene-based test results as input to identify significant genes, and CNVs in or around significant genes were identified in CNV-based association test results. Called CNVs passing quality control and signal intensity visualization examination were considered for validation using TaqMan CNV assays and QuantStudio® 3D Digital PCR System. Results: The meta-analysis identified 373 genome wide significant (p < 5 X 10-4) genes/loci including 49 genes/loci with deletions and 324 with duplications. Among them, 17 genes with deletion and 1 gene with duplication were identified in CNV-based association results in both Group 1 and Group 2. Only 2 genes (NUCB2 and UPF2) containing deletions passed CNV quality control in both groups and signal intensity visualization examination, but laboratory validation failed to verify these deletions. Conclusions: Our data do not support that structural variation is a major cause of nonsyndromic cryptorchidism. [ABSTRACT FROM AUTHOR]

Published
2016
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40. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease

Author

Kugathasan, Subra, primary, Baldassano, Robert N, additional, Bradfield, Jonathan P, additional, Sleiman, Patrick M A, additional, Imielinski, Marcin, additional, Guthery, Stephen L, additional, Cucchiara, Salvatore, additional, Kim, Cecilia E, additional, Frackelton, Edward C, additional, Annaiah, Kiran, additional, Glessner, Joseph T, additional, Santa, Erin, additional, Willson, Tara, additional, Eckert, Andrew W, additional, Bonkowski, Erin, additional, Shaner, Julie L, additional, Smith, Ryan M, additional, Otieno, F George, additional, Peterson, Nicholas, additional, Abrams, Debra J, additional, Chiavacci, Rosetta M, additional, Grundmeier, Robert, additional, Mamula, Petar, additional, Tomer, Gitit, additional, Piccoli, David A, additional, Monos, Dimitri S, additional, Annese, Vito, additional, Denson, Lee A, additional, Grant, Struan F A, additional, and Hakonarson, Hakon, additional

Published
2008
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43. ▪Association of Variants of the Interleukin-23 Receptor Gene With Susceptibility to Pediatric Crohn’s Disease.

Author

Baldassano, Robert N., Bradfield, Jonathan P., Monos, Dimitri S., Kim, Cecilia E., Glessner, Joseph T., Casalunovo, Tracy, Frackelton, Edward C., Otieno, F. George, Kanterakis, Stathis, Shaner, Julie L., Smith, Ryan M., Eckert, Andrew W., Robinson, Luke J., Onyiah, Chioma C., Abrams, Debra J., Chiavacci, Rosetta M., Skraban, Robert, Devoto, Marcella, Grant, Struan F.A., and Hakonarson, Hakon

Subjects
INTERLEUKINS, CROHN'S disease, JUVENILE diseases, STATISTICAL hypothesis testing
Abstract

Background & Aims: Recently an association was shown between the single nucleotide polymorphism (SNP), rs11209026, within the interleukin-23 receptor (IL23R) locus and Crohn’s disease (CD) as a consequence of a genome-wide association study of this disease in adults. We examined the effects of this and other previously reported SNPs at this locus with respect to CD in children. Methods: By using data from our ongoing genome-wide association study in our cohort of 142 pediatric CD patients and 281 matched controls, we investigated the association of the previously reported SNPs at the IL23R locus with the childhood form of this disease. Results: By using the Fisher exact test, the minor allele frequency of rs11209026 in the patients was 1.75%, whereas it was 6.61% in the controls, yielding a protective odds ratio (OR) of 0.25 (95% confidence interval, 0.10–0.65; 1-sided P = 9.2 × 10−4). Furthermore, of all the SNPs previously reported, rs11209026 was associated the most strongly. A subsequent family based association test (which is more resistant to population stratification) with 65 sets of trios derived from our initial patient cohort yielded significant association with rs11209026 in a transmission disequilibrium test (1-sided P = .0017). In contrast, no association was detected to the caspase-recruitment domain 15 gene for the inflammatory bowel disease phenotype. Conclusions: The OR of the IL23R variant in our pediatric study is highly comparable with that reported previously in a non-Jewish adult inflammatory bowel disease case-control cohort (OR, 0.26). As such, variants in the IL23R gene confer a similar magnitude of risk of CD to children as for their adult counterparts. [Copyright &y& Elsevier]

Published
2007
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44. Ain't I a Runner?

Author

Abrams, Debra Josephson

Abstract

The article discusses the author's experience training for the 2004 Marine Corps Marathon. She pledged to raise money for a local cancer center in honor of her mother who died from breast cancer. A month before her marathon debut she suffered painful injuries and sought advice from seasoned female runners. She finished her first marathon in five hours, 57 minutes. She says she can't wait to run her next marathon.

Published
2007

45. Association of the T300A non- synonymous variant of the ATG16L1 gene with susceptibility to paediatric Crohn's disease.

Author

Boldassano, Robert N., Bradfield, Jonathan P., Manos, Dimitri S., Kim, Cecilia E., Glessner, Joseph T., Casalunovo, Tracy, Frackelton, Edward C., Otieno, F. George, Kanterakis, Stathis, Shaner, Julie L., Smith, Ryan M., Eckert, Andrew W., Robinson, Luke J., Onyiah, Chioma C., Abrams, Debra J., Chiavacci, Rosetta M., Skraban, Robert, Devoto, Marcella, Grant, Struaan F. A., and Hakonarson, Hakon

Subjects
LETTERS to the editor, CROHN'S disease
Abstract

A letter to the editor which offers information about the association of the T300A non-synonymous variant of the ATG16L1 gene with susceptibility to pediatric Crohn's disease is presented.

Published
2007
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46. A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling

Author

Dong, Li, Chang, Xiao, Connolly, John J., Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J., Robinson, Nora, Abrams, Debra, Yun R., Li, Bradfield, Jonathan P., Kim, Cecilia E., Jin, Li, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D., Thomas, Kelly A., Chiavacci, Rosetta M., Cone, Roger, Bingshan, Li, Sleiman, Patrick A., Hakonarson, Hakon, Perica, Vesna Boraska, Franklin, Christopher S., Floyd, James A. B., Thornton, Laura M., Huckins, Laura M., Southam, Lorraine, Rayner, N. William, Tachmazidou, Ioanna, Schmidt, Ulrike, Tozzi, Federica, Kiezebrink, Kirsty, Hebebrand, Johannes, Gorwood, Philip, Adan, Roger A. H., Kas, Martien J. H., Favaro, Angela, Santonastaso, Paolo, Fernánde Aranda, Fernando, Gratacos, Monica, Rybakowski, Filip, Dmitrzak Weglarz, Monika, Kaprio, Jaakko, Keski Rahkonen, Anna, Raevuori Helkamaa, Anu, Furth, Eric F. Van, Slof Opt Landt, Margarita C. T., Hudson, James I., Reichborn Kjennerud, Ted, Knudsen, Gun Peggy S., Monteleone, Palmiero, Karwautz, Andreas, Berrettini, Wade H., Schork, Nicholas J., Ando, Tetsuya, Inoko, Hidetoshi, Esko, Toã±u, Fischer, Krista, Mã¤nnik, Katrin, Metspalu, Andres, Baker, Jessica H., Desocio, Janiece E., Hilliard, Christopher E., O'Toole, Julie K., Pantel, Jacques, Szatkiewicz, Jin P., Zerwas, Stephanie, Davis, Oliver S. P., Helder, Sietske, Bã¼hren, Katharina, Burghardt, Roland, De Zwaan, Martina, Egberts, Karin, Ehrlich, Stefan, Herpertz Dahlmann, Beate, Herzog, Wolfgang, Imgart, Hartmut, Scherag, Andrã, Zipfel, Stephan, Boni, Claudette, Ramoz, Nicolas, Versini, Audrey, Danner, Unna N., Hendriks, Judith, Koeleman, Bobby P. C., Ophoff, Roel A., Strengman, Eric, Van Elburg, Annemarie A., Bruson, Alice, Clementi, Maurizio, Degortes, Daniela, Forzan, Monica, Tenconi, Elena, Docampo, Elisa, Escaramã­s, Geã²rgia, Jiménez Murcia, Susana, Lissowska, Jolanta, Rajewski, Andrzej, Szeszenia Dabrowska, Neonila, Slopien, Agnieszka, Hauser, Joanna, Karhunen, Leila, Meulenbelt, Ingrid, Slagboom, P. Eline, Tortorella, Alfonso Antonio Vincenzo, Maj, Mario, Dedoussis, George, Dikeos, Dimitris, Gonidakis, Fragiskos, Tziouvas, Konstantinos, Tsitsika, Artemis, Papezova, Hana, Slachtova, Lenka, Martaskova, Debora, Kennedy, James L., Levitan, Robert D., Yilmaz, Zeynep, Huemer, Julia, Koubek, Doris, Merl, Elisabeth, Wagner, Gudrun, Lichtenstein, Paul, Breen, Gerome, Cohen Woods, Sarah, Farmer, Anne, Mcguffin, Peter, Cichon, Sven, Giegling, Ina, Herms, Stefan, Rujescu, Dan, Schreiber, Stefan, Wichmann, H. Erich, Dina, Christian, Sladek, Rob, Gambaro, Giovanni, Soranzo, Nicole, Julia, Antonio, Marsal, Sara, Rabionet, Raquel, Gaborieau, Valerie, Dick, Danielle M., Palotie, Aarno, Ripatti, Samuli, Widã©n, Elisabeth, Andreassen, Ole A., Espeseth, Thomas, Lundervold, Astri, Reinvang, Ivar, Steen, Vidar M., Le Hellard, Stephanie, Mattingsdal, Morten, Ntalla, Ioanna, Bencko, Vladimir, Foretova, Lenka, Janout, Vladimir, Navratilova, Marie, Gallinger, Steven, Pinto, Dalila, Scherer, Stephen W., Aschauer, Harald, Carlberg, Laura, Schosser, Alexandra, Alfredsson, Lars, Ding, Bo, Klareskog, Lars, Padyukov, Leonid, Finan, Chris, Kalsi, Gursharan, Roberts, Marion, Barrett, Jeff C., Estivill, Xavier, Hinney, Anke, Sullivan, Patrick F., Zeggini, Eleftheria, Bulik, Cynthia M., Brandt, Harry, Crawford, Steve, Crow, Scott, Fichter, Manfred M., Halmi, Katherine A., Johnson, Craig, Kaplan, Allan S., La Via, Maria C., Mitchell, James, Strober, Michael, Rotondo, Alessandro, Treasure, Janet, Woodside, D. Blake, Keel, Pamela K., Klump, Kelly L., Lilenfeld, Lisa, Bergen, Andrew W., Kaye, Walter, Magistretti, Pierre, Universitat de Barcelona, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Department of Public Health, Clinicum, Samuli Olli Ripatti / Principal Investigator, Biostatistics Helsinki, HUS Children and Adolescents, Complex Disease Genetics, Genomics of Neurological and Neuropsychiatric Disorders, Genetic Epidemiology, Kas lab, School of Medicine / Clinical Nutrition, Li, Dong, Chang, Xiao, Connolly, John J., Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J., Robinson, Nora, Abrams, Debra, Li, Yun R., Bradfield, Jonathan P., Kim, Cecilia E., Li, Jin, Wang, Fengxiang, Snyder, Jame, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D., Thomas, Kelly A., Chiavacci, Rosetta M., Cone, Roger, Li, Bingshan, Sleiman, Patrick A., Hakonarson, Hakon, Perica, Vesna Boraska, Franklin, Christopher S., Floyd, James A. B., Thornton, Laura M., Huckins, Laura M., Southam, Lorraine, Rayner, N. William, Tachmazidou, Ioanna, Schmidt, Ulrike, Tozzi, Federica, Kiezebrink, Kirsty, Hebebrand, Johanne, Gorwood, Philip, Adan, Roger A. H., Kas, Martien J. H., Favaro, Angela, Santonastaso, Paolo, Fernánde-Aranda, Fernando, Gratacos, Monica, Rybakowski, Filip, Dmitrzak-Weglarz, Monika, Kaprio, Jaakko, Keski-Rahkonen, Anna, Raevuori-Helkamaa, Anu, Furth, Eric F. Van, Slof-Opt Landt, Margarita C. T., Hudson, James I., Reichborn-Kjennerud, Ted, Knudsen, Gun Peggy S., Monteleone, Palmiero, Karwautz, Andrea, Berrettini, Wade H., Schork, Nicholas J., Ando, Tetsuya, Inoko, Hidetoshi, Esko, Toã±u, Fischer, Krista, Mã¤nnik, Katrin, Metspalu, Andre, Baker, Jessica H., Desocio, Janiece E., Hilliard, Christopher E., O'Toole, Julie K., Pantel, Jacque, Szatkiewicz, Jin P., Zerwas, Stephanie, Davis, Oliver S. P., Helder, Sietske, Bã¼hren, Katharina, Burghardt, Roland, De Zwaan, Martina, Egberts, Karin, Ehrlich, Stefan, Herpertz-Dahlmann, Beate, Herzog, Wolfgang, Imgart, Hartmut, Scherag, Andrã©, Zipfel, Stephan, Boni, Claudette, Ramoz, Nicola, Versini, Audrey, Danner, Unna N., Hendriks, Judith, Koeleman, Bobby P. C., Ophoff, Roel A., Strengman, Eric, Van Elburg, Annemarie A., Bruson, Alice, Clementi, Maurizio, Degortes, Daniela, Forzan, Monica, Tenconi, Elena, Docampo, Elisa, Escaramã­s, Geã²rgia, Jiménez-Murcia, Susana, Lissowska, Jolanta, Rajewski, Andrzej, Szeszenia-Dabrowska, Neonila, Slopien, Agnieszka, Hauser, Joanna, Karhunen, Leila, Meulenbelt, Ingrid, Slagboom, P. Eline, Tortorella, Alfonso, Maj, Mario, Dedoussis, George, Dikeos, Dimitri, Gonidakis, Fragisko, Tziouvas, Konstantino, Tsitsika, Artemi, Papezova, Hana, Slachtova, Lenka, Martaskova, Debora, Kennedy, James L., Levitan, Robert D., Yilmaz, Zeynep, Huemer, Julia, Koubek, Dori, Merl, Elisabeth, Wagner, Gudrun, Lichtenstein, Paul, Breen, Gerome, Cohen-Woods, Sarah, Farmer, Anne, Mcguffin, Peter, Cichon, Sven, Giegling, Ina, Herms, Stefan, Rujescu, Dan, Schreiber, Stefan, Wichmann, H-Erich, Dina, Christian, Sladek, Rob, Gambaro, Giovanni, Soranzo, Nicole, Julia, Antonio, Marsal, Sara, Rabionet, Raquel, Gaborieau, Valerie, Dick, Danielle M., Palotie, Aarno, Ripatti, Samuli, Widã©n, Elisabeth, Andreassen, Ole A., Espeseth, Thoma, Lundervold, Astri, Reinvang, Ivar, Steen, Vidar M., Le Hellard, Stephanie, Mattingsdal, Morten, Ntalla, Ioanna, Bencko, Vladimir, Foretova, Lenka, Janout, Vladimir, Navratilova, Marie, Gallinger, Steven, Pinto, Dalila, Scherer, Stephen W., Aschauer, Harald, Carlberg, Laura, Schosser, Alexandra, Alfredsson, Lar, Ding, Bo, Klareskog, Lar, Padyukov, Leonid, Finan, Chri, Kalsi, Gursharan, Roberts, Marion, Barrett, Jeff C., Estivill, Xavier, Hinney, Anke, Sullivan, Patrick F., Zeggini, Eleftheria, Bulik, Cynthia M., Brandt, Harry, Crawford, Steve, Crow, Scott, Fichter, Manfred M., Halmi, Katherine A., Johnson, Craig, Kaplan, Allan S., La Via, Maria C., Mitchell, Jame, Strober, Michael, Rotondo, Alessandro, Treasure, Janet, Woodside, D. Blake, Keel, Pamela K., Klump, Kelly L., Lilenfeld, Lisa, Bergen, Andrew W., Kaye, Walter, Magistretti, Pierre, Guo, Yiran [0000-0002-6549-8589], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Leptin signaling, Eating Disorders, Medizin, Genome-wide association study, CHILDREN, VARIANTS, Bioinformatics, 3124 Neurology and psychiatry, 0302 clinical medicine, B-CELL-FACTOR, Eating Disorders Working Group of the Psychiatric Genomics Consortium, 2.1 Biological and endogenous factors, Aetiology, Genetics, Multidisciplinary, Anorèxia nerviosa, Genomics, Phenotype, Price Foundation Collaborative Group, 3142 Public health care science, environmental and occupational health, Anorexia, Eating disorders, Mental Health, Behavioural genetics, Medicine, Erratum, GENETICS, Science, Locus (genetics), Single-nucleotide polymorphism, Biology, PRESSURE, PARAMETERS, 03 medical and health sciences, medicine, Journal Article, General, EBF1, Prevention, Human Genome, EATING-DISORDERS, Settore MED/13 - ENDOCRINOLOGIA, OBSESSIVE-COMPULSIVE DISORDER, Anorexia nervosa, medicine.disease, Confidence interval, 030227 psychiatry, Genòmica, 030104 developmental biology, Risk factors
Abstract

We conducted a genome-wide association study (GWAS) of anorexia nervosa (AN) using a stringently defined phenotype. Analysis of phenotypic variability led to the identification of a specific genetic risk factor that approached genome-wide significance (rs929626 in EBF1 (Early B-Cell Factor 1); P = 2.04 × 10−7; OR = 0.7; 95% confidence interval (CI) = 0.61–0.8) with independent replication (P = 0.04), suggesting a variant-mediated dysregulation of leptin signaling may play a role in AN. Multiple SNPs in LD with the variant support the nominal association. This demonstrates that although the clinical and etiologic heterogeneity of AN is universally recognized, further careful sub-typing of cases may provide more precise genomic signals. In this study, through a refinement of the phenotype spectrum of AN, we present a replicable GWAS signal that is nominally associated with AN, highlighting a potentially important candidate locus for further investigation., published version, peerReviewed

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47. Erratum: A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling

Author

Li, Dong, Chang, Xiao, Connolly, John J., Tian, Lifeng, Liu, Yichuan, Bhoj, Elizabeth J., Robinson, Nora, Abrams, Debra, Li, Yun R., Bradfield, Jonathan P., Kim, Cecilia E., Li, Jin, Wang, Fengxiang, Snyder, James, Lemma, Maria, Hou, Cuiping, Wei, Zhi, Guo, Yiran, Qiu, Haijun, Mentch, Frank D., Thomas, Kelly A., Chiavacci, Rosetta M., Cone, Roger, Li, Bingshan, Sleiman, Patrick A., Eating Disorders Working Group Of The Psychiatric Genomics Consortium, Price Foundation Collaborative Group, Hakonarson, Hakon, Boraska Perica, Vesna, Franklin, Christopher S., Floyd, James A B., Thornton, Laura M., Huckins, Laura M., Southam, Lorraine, Rayner, N William, Tachmazidou, Ioanna, Klump, Kelly L., Treasure, Janet, Schmidt, Ulrike, Tozzi, Federica, Kiezebrink, Kirsty, Hebebrand, Johannes, Gorwood, Philip, Adan, Roger A H., Kas, Martien J H., Favaro, Angela, Santonastaso, Paolo, Fernánde-Aranda, Fernando, Gratacos, Monica, Rybakowski, Filip, Dmitrzak-Weglarz, Monika, Kaprio, Jaakko, Keski-Rahkonen, Anna, Raevuori-Helkamaa, Anu, Van Furth, Eric F., Slof-Op't Landt, Margarita C T., Hudson, James I., Reichborn-Kjennerud, Ted, Knudsen, Gun Peggy S., Monteleone, Palmiero, Kaplan, Allan S., Karwautz, Andreas, Berrettini, Wade H., Schork, Nicholas J., Ando, Tetsuya, Inoko, Hidetoshi, Esko, Tõnu, Fischer, Krista, Männik, Katrin, Metspalu, Andres, Baker, Jessica H., DeSocio, Janiece E., Hilliard, Christopher E., O'Toole, Julie K., Pantel, Jacques, Szatkiewicz, Jin P., Zerwas, Stephanie, Davis, Oliver S P., Helder, Sietske, Bühren, Katharina, Burghardt, Roland, De Zwaan, Martina, Egberts, Karin, Ehrlich, Stefan, Herpertz-Dahlmann, Beate, Herzog, Wolfgang, Imgart, Hartmut, Scherag, André, Zipfel, Stephan, Boni, Claudette, Ramoz, Nicolas, Versini, Audrey, Danner, Unna N., Hendriks, Judith, Koeleman, Bobby P C., Ophoff, Roel A., Strengman, Eric, Van Elburg, Annemarie A., Bruson, Alice, Clementi, Maurizio, Degortes, Daniela, Forzan, Monica, Tenconi, Elena, Docampo, Elisa, Escaramís, Geòrgia, Jiménez-Murcia, Susana, Lissowska, Jolanta, Rajewski, Andrzej, Szeszenia-Dabrowska, Neonila, Slopien, Agnieszka, Hauser, Joanna, Karhunen, Leila, Meulenbelt, Ingrid, Slagboom, P Eline, Tortorella, Alfonso, Maj, Mario, Dedoussis, George, Dikeos, Dimitris, Gonidakis, Fragiskos, Tziouvas, Konstantinos, Tsitsika, Artemis, Papezova, Hana, Slachtova, Lenka, Martaskova, Debora, Kennedy, James L., Levitan, Robert D., Yilmaz, Zeynep, Huemer, Julia, Koubek, Doris, Merl, Elisabeth, Wagner, Gudrun, Lichtenstein, Paul, Breen, Gerome, Cohen-Woods, Sarah, Farmer, Anne, McGuffin, Peter, Cichon, Sven, Giegling, Ina, Herms, Stefan, Dan Rujescu, Schreiber, Stefan, Wichmann, H-Erich, Dina, Christian, Sladek, Rob, Gambaro, Giovanni, Soranzo, Nicole, Julia, Antonio, Marsal, Sara, Rabionet, Raquel, Gaborieau, Valerie, Dick, Danielle M., Palotie, Aarno, Ripatti, Samuli, Widén, Elisabeth, Andreassen, Ole A., Espeseth, Thomas, Lundervold, Astri, Reinvang, Ivar, Steen, Vidar M., Le Hellard, Stephanie, Mattingsdal, Morten, Ntalla, Ioanna, Bencko, Vladimir, Foretova, Lenka, Janout, Vladimir, Navratilova, Marie, Gallinger, Steven, Pinto, Dalila, Scherer, Stephen W., Aschauer, Harald, Carlberg, Laura, Schosser, Alexandra, Alfredsson, Lars, Ding, Bo, Klareskog, Lars, Padyukov, Leonid, Finan, Chris, Kalsi, Gursharan, Roberts, Marion, Barrett, Jeff C., Estivill, Xavier, Hinney, Anke, Sullivan, Patrick F., Zeggini, Eleftheria, Bulik, Cynthia M., Brandt, Harry, Crawford, Steve, Crow, Scott, Fichter, Manfred M., Halmi, Katherine A., Johnson, Craig, La Via, Maria C., Mitchell, James, Strober, Michael, Rotondo, Alessandro, Woodside, D Blake, Keel, Pamela K., Lilenfeld, Lisa, Bergen, Andrew W., Berrettini, Wade, Kaye, Walter, and Magistretti, Pierre

Subjects
3. Good health
Abstract

Scientific reports 7(1), 8379 (2017). doi:10.1038/s41598-017-06409-3, Published by Nature Publishing Group, London

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

Author

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

Subjects
Male, Adolescent, Population, European Continental Ancestry Group, General Physics and Astronomy, Genome-wide association study, Biology, Major histocompatibility complex, Inflammatory bowel disease, Autoimmune Disease, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, White People, Article, Autoimmune Diseases, 03 medical and health sciences, Physics and Astronomy (all), 0302 clinical medicine, medicine, Humans, Genetic Predisposition to Disease, Age of Onset, education, Child, 030304 developmental biology, 030203 arthritis & rheumatology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Biochemistry, Genetics and Molecular Biology (all), Chemistry (all), Case-control study, General Chemistry, Heritability, medicine.disease, 3. Good health, Rheumatoid arthritis, Case-Control Studies, Child, Preschool, biology.protein, Female, Age of onset, Case-Control Studie, Genome-Wide Association Study, Human
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-h2). SNP-h2 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-h2 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., Autoimmune diseases are genetically complex disorders that affect up to 10% of the Western population. Here Li et al. quantify the heritability of a range of autoimmune diseases in the largest paediatric cohort examined to date, illustrating that genetic and non-genetic components variably contribute to the susceptibility of each disease.

Published
2015
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50. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Author

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

Subjects
Candidate gene, Population, Quantitative Trait Loci, Single-nucleotide polymorphism, Genome-wide association study, Quantitative trait locus, Autoimmune Disease, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Autoimmune Diseases, Risk Factors, Humans, Medicine, education, Child, Genetic association, Genetics, education.field_of_study, Biochemistry, Genetics and Molecular Biology (all), business.industry, Risk Factor, Medicine (all), General Medicine, Genetic architecture, Expression quantitative trait loci, Immunology, business, Genome-Wide Association Study, Human
Abstract

Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases.

Published
2015
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