Browsing by Author "Plenge, Robert M."

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    • Analysis and Application of European Genetic Substructure Using 300 K SNP Information 

      Tian, Chao; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F; Plenge, Robert M. (Public Library of Science, 2008)
      European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest ...

    • Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records 

      Lin, Chen; Karlson, Elizabeth W.; Canhao, Helena; Miller, Timothy A.; Dligach, Dmitriy; Chen, Pei Jun; Perez, Raul Natanael Guzman; Shen, Yuanyan; Weinblatt, Michael E.; Shadick, Nancy A.; Plenge, Robert M.; Savova, Guergana K. (Public Library of Science, 2013)
      Objective: We aimed to mine the data in the Electronic Medical Record to automatically discover patients' Rheumatoid Arthritis disease activity at discrete rheumatology clinic visits. We cast the problem as a document ...

    • Brief Report: Identification of BACH2 and RAD51B as Rheumatoid Arthritis Susceptibility Loci in a Meta-Analysis of Genome-Wide Data 

      McAllister, Kate; Yarwood, Annie; Bowes, John; Orozco, Gisela; Viatte, Sebastian; Diogo, Dorothée; Hocking, Lynne J; Steer, Sophia; Wordsworth, Paul; Wilson, A G; Morgan, Ann W; Kremer, Joel M; Pappas, Dimitrios; Gregersen, Peter; Klareskog, Lars; Plenge, Robert; Barton, Anne; Greenberg, Jeffrey; Worthington, Jane; Eyre, Stephen (BlackWell Publishing Ltd, 2013)
      Objective: A recent high-density fine-mapping (ImmunoChip) study of genetic associations in rheumatoid arthritis (RA) identified 14 risk loci with validated genome-wide significance, as well as a number of loci showing ...

    • Data for Genetic Analysis Workshop (GAW) 15 Problem 2, Genetic Causes of Rheumatoid Arthritis and Associated Traits 

      Amos, Christopher I; Remmers, Elaine; Siminovitch, Katherine A; Seldin, Michael F; Criswell, Lindsey A; Lee, Annette T; John, Sally; Shephard, Neil D; Worthington, Jane; Cornelis, Francois; Begovich, Ann B; Dyer, Thomas D; Kastner, Daniel L; Gregersen, Peter K; Plenge, Robert M.; Chen, Wei Vivien (BioMed Central, 2007)
      For Genetic Analysis Workshop 15 Problem 2, we organized data from several ongoing studies designed to identify genetic and environmental risk factors for rheumatoid arthritis. Data were derived from the North American ...

    • Data for Genetic Analysis Workshop 16 Problem 1, Association Analysis of Rheumatoid Arthritis Data 

      Amos, Christopher I.; Chen, Wei Vivien; Seldin, Michael F.; Remmers, Elaine F.; Taylor, Kimberly E.; Criswell, Lindsey A.; Lee, Annette T.; Plenge, Robert M.; Kastner, Daniel L.; Gregersen, Peter K. (BioMed Central, 2009)
      For Genetic Analysis Workshop 16 Problem 1, we provided data for genome-wide association analysis of rheumatoid arthritis. Single-nucleotide polymorphism (SNP) genotype data were provided for 868 cases and 1194 controls ...

    • Defining the Role of the MHC in Autoimmunity: A Review and Pooled Analysis 

      Fernando, Michelle M. A.; Stevens, Christine R.; Walsh, Emily C.; De Jager, Philip Lawrence; Goyette, Philippe; Plenge, Robert M.; Vyse, Timothy J.; Rioux, John D. (Public Library of Science, 2008)
      The major histocompatibility complex (MHC) is one of the most extensively studied regions in the human genome because of the association of variants at this locus with autoimmune, infectious, and inflammatory diseases. ...

    • Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines 

      Yelensky, Roman; Bonakdar, Sasha; Wolfish, Cara S.; Cotsapas, Chris; Rivas, Manuel; Dermitzakis, Emmanouil T.; Choy, Edwin; Plenge, Robert M.; Saxena, Richa; De Jager, Philip Lawrence; Shaw, Stanley Yang; Slavik, Jacqueline Marie; Cahir-McFarland, Ellen D.; Kieff, Elliott D.; Hafler, David A.; Daly, Mark Joseph; Altshuler, David Matthew (Public Library of Science, 2008)
      Lymphoblastoid cell lines (LCLs), originally collected as renewable sources of DNA, are now being used as a model system to study genotype–phenotype relationships in human cells, including searches for QTLs influencing ...

    • Genetic polymorphisms in PTPN22, PADI-4, and CTLA-4 and risk for rheumatoid arthritis in two longitudinal cohort studies: evidence of gene-environment interactions with heavy cigarette smoking 

      Costenbader, Karen Harte; Chang, Shun-Chiao; De Vivo, Immaculata; Plenge, Robert M.; Karlson, Elizabeth Wood (BioMed Central, 2008)
      Introduction: PTPN22, PADI-4, and CTLA-4 have been associated with risk for rheumatoid arthritis (RA). We investigated whether polymorphisms in these genes were associated with RA in Caucasian women included in two large ...

    • Genetics of rheumatoid arthritis contributes to biology and drug discovery 

      Okada, Yukinori; Wu, Di; Trynka, Gosia; Raj, Towfique; Terao, Chikashi; Ikari, Katsunori; Kochi, Yuta; Ohmura, Koichiro; Suzuki, Akari; Yoshida, Shinji; Graham, Robert R.; Manoharan, Arun; Ortmann, Ward; Bhangale, Tushar; Denny, Joshua C.; Carroll, Robert J.; Eyler, Anne E.; Greenberg, Jeffrey D.; Kremer, Joel M.; Pappas, Dimitrios A.; Jiang, Lei; Yin, Jian; Ye, Lingying; Su, Ding-Feng; Yang, Jian; Xie, Gang; Keystone, Ed; Westra, Harm-Jan; Esko, Tõnu; Metspalu, Andres; Zhou, Xuezhong; Gupta, Namrata; Mirel, Daniel; Stahl, Eli A.; Diogo, Dorothée; Cui, Jing; Liao, Katherine; Guo, Michael H.; Myouzen, Keiko; Kawaguchi, Takahisa; Coenen, Marieke J.H.; van Riel, Piet L.C.M.; van de Laar, Mart A.F.J.; Guchelaar, Henk-Jan; Huizinga, Tom W.J.; Dieudé, Philippe; Mariette, Xavier; Bridges, S. Louis; Zhernakova, Alexandra; Toes, Rene E.M.; Tak, Paul P.; Miceli-Richard, Corinne; Bang, So-Young; Lee, Hye-Soon; Martin, Javier; Gonzalez-Gay, Miguel A.; Rodriguez-Rodriguez, Luis; Rantapää-Dahlqvist, Solbritt; Ärlestig, Lisbeth; Choi, Hyon K.; Kamatani, Yoichiro; Galan, Pilar; Lathrop, Mark; Eyre, Steve; Bowes, John; Barton, Anne; de Vries, Niek; Moreland, Larry W.; Criswell, Lindsey A.; Karlson, Elizabeth W.; Taniguchi, Atsuo; Yamada, Ryo; Kubo, Michiaki; Liu, Jun S.; Bae, Sang-Cheol; Worthington, Jane; Padyukov, Leonid; Klareskog, Lars; Gregersen, Peter K.; Raychaudhuri, Soumya; Stranger, Barbara E.; De Jager, Philip L.; Franke, Lude; Visscher, Peter M.; Brown, Matthew A.; Yamanaka, Hisashi; Mimori, Tsuneyo; Takahashi, Atsushi; Xu, Huji; Behrens, Timothy W.; Siminovitch, Katherine A.; Momohara, Shigeki; Matsuda, Fumihiko; Yamamoto, Kazuhiko; Plenge, Robert M. (2013)
      A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological datasets to provide insight into disease pathogenesis and guide drug ...

    • Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis 

      Cui, Jing; Stahl, Eli A.; Saevarsdottir, Saedis; Miceli, Corinne; Diogo, Dorothee; Trynka, Gosia; Raj, Towfique; Mirkov, Maša Umiċeviċ; Canhao, Helena; Ikari, Katsunori; Terao, Chikashi; Okada, Yukinori; Wedrén, Sara; Askling, Johan; Yamanaka, Hisashi; Momohara, Shigeki; Taniguchi, Atsuo; Ohmura, Koichiro; Matsuda, Fumihiko; Mimori, Tsuneyo; Gupta, Namrata; Kuchroo, Manik Razdan; Morgan, Ann W.; Isaacs, John D.; Wilson, Anthony G.; Hyrich, Kimme L.; Herenius, Marieke; Doorenspleet, Marieke E.; Tak, Paul-Peter; Crusius, J. Bart A.; van der Horst-Bruinsma, Irene E.; Wolbink, Gert Jan; van Riel, Piet L. C. M.; van de Laar, Mart; Guchelaar, Henk-Jan; Shadick, Nancy Ann; Allaart, Cornelia F.; Huizinga, Tom W. J.; Toes, Rene E. M.; Kimberly, Robert P.; Bridges, S. Louis; Criswell, Lindsey A.; Moreland, Larry W.; Fonseca, João Eurico; de Vries, Niek; Stranger, Barbara E.; De Jager, Philip Lawrence; Raychaudhuri, Soumya; Weinblatt, Michael Elliott; Gregersen, Peter K.; Mariette, Xavier; Barton, Anne; Padyukov, Leonid; Coenen, Marieke J. H.; Karlson, Elizabeth Wood; Plenge, Robert M. (Public Library of Science, 2013)
      Anti-tumor necrosis factor alpha (anti-TNF) biologic therapy is a widely used treatment for rheumatoid arthritis (RA). It is unknown why some RA patients fail to respond adequately to anti-TNF therapy, which limits the ...

    • GWAS in IMIDs 

      Plenge, Robert M. (BioMed Central, 2010)

    • High density genetic mapping identifies new susceptibility loci for rheumatoid arthritis 

      Eyre, Steve; Bowes, John; Diogo, Dorothée; Lee, Annette; Barton, Anne; Martin, Paul; Zhernakova, Alexandra; Stahl, Eli; Viatte, Sebastien; McAllister, Kate; Amos, Christopher I.; Padyukov, Leonid; Toes, Rene E.M.; Huizinga, Tom W.J.; Wijmenga, Cisca; Trynka, Gosia; Franke, Lude; Westra, Harm-Jan; Alfredsson, Lars; Hu, Xinli; Sandor, Cynthia; de Bakker, Paul I.W.; Davila, Sonia; Khor, Chiea Chuen; Heng, Khai Koon; Andrews, Robert; Edkins, Sarah; Hunt, Sarah E; Langford, Cordelia; Symmons, Deborah; Concannon, Pat; Onengut-Gumuscu, Suna; Rich, Stephen S; Deloukas, Panos; Gonzalez-Gay, Miguel A.; Rodriguez-Rodriguez, Luis; Ärlsetig, Lisbeth; Martin, Javier; Rantapää-Dahlqvist, Solbritt; Plenge, Robert; Raychaudhuri, Soumya; Klareskog, Lars; Gregersen, Peter K; Worthington, Jane (2012)
      Summary Using the Immunochip custom single nucleotide polymorphism (SNP) array, designed for dense genotyping of 186 genome wide association study (GWAS) confirmed loci we analysed 11,475 rheumatoid arthritis cases of ...

    • Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway 

      Li, Gang; Diogo, Dorothee; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth Jeffries; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip Lawrence; Siminovitch, Katherine A.; Zhernakova, Alexandra; Raychaudhuri, Soumya; Bowes, John; Eyre, Steve; Padyukov, Leonid; Gregersen, Peter K.; Worthington, Jane; Gupta, Namrata; Clemons, Paul A.; Stahl, Eli; Tolliday, Nicola; Plenge, Robert M. (Public Library of Science, 2013)
      Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. ...

    • Identification of the NF-κB activating protein-like locus as a risk locus for rheumatoid arthritis 

      Xie, Gang; Lu, Yue; Sun, Ye; Zhang, Steven Shiyang; Keystone, Edward Clark; Gregersen, Peter K; Plenge, Robert M; Amos, Christopher I; Siminovitch, Katherine A (BMJ Publishing Group, 2013)
      Objective: To fine-map the NF-κB activating protein-like (NKAPL) locus identified in a prior genome-wide study as a possible rheumatoid arthritis (RA) risk locus and thereby delineate additional variants with stronger ...

    • Improving Case Definition of Crohnʼs Disease and Ulcerative Colitis in Electronic Medical Records Using Natural Language Processing 

      Ananthakrishnan, Ashwin; Cai, Tianxi; Savova, Guergana; Cheng, Su-Chun; Chen, Pei; Guzman, Raul; Gainer, Vivian S.; Murphy, Shawn; Szolovits, Peter; Xia, Zongqi; Shaw, Stanley; Churchill, Susanne; Karlson, Elizabeth; Kohane, Isaac; Plenge, Robert M.; Liao, Katherine (Oxford University Press (OUP), 2013-06)
      Introduction Prior studies identifying patients with inflammatory bowel disease (IBD) utilizing administrative codes have yielded inconsistent results. Our objective was to develop a robust electronic medical record (EMR) ...

    • Informed Conditioning on Clinical Covariates Increases Power in Case-Control Association Studies 

      Zaitlen, Noah; Lindström, Sara; Pasaniuc, Bogdan; Cornelis, Marilyn; Genovese, Giulio; Pollack, Samuela; Barton, Anne; Bickeböller, Heike; Bowden, Donald W.; Eyre, Steve; Freedman, Barry I.; Friedman, David J.; Field, John K.; Groop, Leif; Haugen, Aage; Heinrich, Joachim; Henderson, Brian E.; Hicks, Pamela J.; Hocking, Lynne J.; Kolonel, Laurence N.; Landi, Maria Teresa; Langefeld, Carl D.; Le Marchand, Loic; Meister, Michael; Morgan, Ann W.; Raji, Olaide Y.; Risch, Angela; Rosenberger, Albert; Scherf, David; Steer, Sophia; Walshaw, Martin; Waters, Kevin M.; Wilson, Anthony G.; Wordsworth, Paul; Zienolddiny, Shanbeh; Tchetgen, Eric Tchetgen; Haiman, Christopher; Hunter, David J.; Plenge, Robert M.; Worthington, Jane; Christiani, David C.; Schaumberg, Debra Ann; Chasman, Daniel Ian; Altshuler, David Matthew; Voight, Benjamin; Kraft, Peter Elias; Patterson, Nick; Price, Alkes (Public Library of Science, 2012)
      Genetic case-control association studies often include data on clinical covariates, such as body mass index (BMI), smoking status, or age, that may modify the underlying genetic risk of case or control samples. For example, ...

    • Integration of Sequence Data from a Consanguineous Family with Genetic Data from an Outbred Population Identifies PLB1 as a Candidate Rheumatoid Arthritis Risk Gene 

      Okada, Yukinori; Diogo, Dorothee; Greenberg, Jeffrey D.; Mouassess, Faten; Achkar, Walid A. L.; Fulton, Robert S.; Denny, Joshua C.; Gupta, Namrata; Mirel, Daniel; Gabriel, Stacy; Li, Gang; Kremer, Joel M.; Pappas, Dimitrios A.; Carroll, Robert J.; Eyler, Anne E.; Trynka, Gosia; Stahl, Eli A.; Cui, Jing; Saxena, Richa; Coenen, Marieke J. H.; Guchelaar, Henk-Jan; Huizinga, Tom W. J.; Dieudé, Philippe; Mariette, Xavier; Barton, Anne; Canhão, Helena; Fonseca, João E.; de Vries, Niek; Tak, Paul P.; Moreland, Larry W.; Bridges, S. Louis; Miceli-Richard, Corinne; Choi, Hyon K.; Kamatani, Yoichiro; Galan, Pilar; Lathrop, Mark; Raj, Towfique; De Jager, Philip L.; Raychaudhuri, Soumya; Worthington, Jane; Padyukov, Leonid; Klareskog, Lars; Siminovitch, Katherine A.; Gregersen, Peter K.; Mardis, Elaine R.; Arayssi, Thurayya; Kazkaz, Layla A.; Plenge, Robert M. (Public Library of Science, 2014)
      Integrating genetic data from families with highly penetrant forms of disease together with genetic data from outbred populations represents a promising strategy to uncover the complete frequency spectrum of risk alleles ...

    • Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci 

      Zhernakova, Alexandra; Stahl, Eli A.; Trynka, Gosia; Festen, Eleanora A.; Franke, Lude; Westra, Harm-Jan; Fehrmann, Rudolf S. N.; Kurreeman, Fina A. S.; Thomson, Brian; Gupta, Namrata; Romanos, Jihane; McManus, Ross; Ryan, Anthony W.; Turner, Graham; Brouwer, Elisabeth; Posthumus, Marcel D.; Remmers, Elaine F.; Tucci, Francesca; Toes, Rene; Grandone, Elvira; Mazzilli, Maria Cristina; Rybak, Anna; Cukrowska, Bozena; Coenen, Marieke J. H.; Radstake, Timothy R. D. J.; van Riel, Piet L. C. M.; Li, Yonghong; Gregersen, Peter K.; Worthington, Jane; Siminovitch, Katherine A.; Klareskog, Lars; Huizinga, Tom W. J.; Wijmenga, Cisca; Raychaudhuri, Soumya; de Bakker, Paul I Wen; Plenge, Robert M. (Public Library of Science, 2011)
      Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease (CD) and rheumatoid arthritis (RA), but the extent of this sharing has not been systematically explored. Previous studies demonstrate ...

    • Modeling Disease Severity in Multiple Sclerosis Using Electronic Health Records 

      Xia, Zongqi; Secor, Elizabeth; Chibnik, Lori B.; Bove, Riley M.; Cheng, Suchun; Chitnis, Tanuja; Cagan, Andrew; Gainer, Vivian S.; Chen, Pei J.; Liao, Katherine P.; Shaw, Stanley Y.; Ananthakrishnan, Ashwin N.; Szolovits, Peter; Weiner, Howard L.; Karlson, Elizabeth W.; Murphy, Shawn N.; Savova, Guergana K.; Cai, Tianxi; Churchill, Susanne E.; Plenge, Robert M.; Kohane, Isaac S.; De Jager, Philip L. (Public Library of Science, 2013)
      Objective: To optimally leverage the scalability and unique features of the electronic health records (EHR) for research that would ultimately improve patient care, we need to accurately identify patients and extract ...

    • Quantifying Missing Heritability at Known GWAS Loci 

      Gusev, Alexander; Bhatia, Gaurav; Zaitlen, Noah; Vilhjalmsson, Bjarni J.; Diogo, Dorothée; Stahl, Eli A.; Gregersen, Peter K.; Worthington, Jane; Klareskog, Lars; Raychaudhuri, Soumya; Plenge, Robert M.; Pasaniuc, Bogdan; Price, Alkes L. (Public Library of Science, 2013)
      Recent work has shown that much of the missing heritability of complex traits can be resolved by estimates of heritability explained by all genotyped SNPs. However, it is currently unknown how much heritability is missing ...