Now showing items 21-30 of 30

    • 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 ...
    • A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases 

      Han, Buhm; Pouget, Jennie G.; Slowikowski, Kamil; Stahl, Eli; Lee, Cue Hyunkyu; Diogo, Dorothee; Hu, Xinli; Park, Yu Rang; Kim, Eunji; Gregersen, Peter K.; Dahlqvist, Solbritt Rantapää; Worthington, Jane; Martin, Javier; Eyre, Steve; Klareskog, Lars; Huizinga, Tom; Chen, Wei-Min; Onengut-Gumuscu, Suna; Rich, Stephen S.; Wray, Naomi R.; Raychaudhuri, Soumya (2016)
      There is growing evidence of shared risk alleles between complex traits (pleiotropy), including autoimmune and neuropsychiatric diseases. This might be due to sharing between all individuals (whole-group pleiotropy), or a ...
    • Partitioning heritability by functional annotation using genome-wide association summary statistics 

      Finucane, Hilary K.; Bulik-Sullivan, Brendan; Gusev, Alexander; Trynka, Gosia; Reshef, Yakir; Loh, Po-Ru; Anttila, Verneri; Xu, Han; Zang, Chongzhi; Farh, Kyle; Ripke, Stephan; Day, Felix R.; Consortium, ReproGen; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R. B.; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark; Patterson, Nick; Neale, Benjamin M.; Price, Alkes L. (2015)
      Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here, we analyze a broad set of functional elements, including cell-type-specific ...
    • Pathologically Expanded Peripheral T Helper Cell Subset Drives B Cells in Rheumatoid Arthritis 

      Rao, Deepak; Gurish, Michael F.; Marshall, Jennifer L.; Slowikowski, Kamil; Fonseka, Chamith Y.; Liu, Yanyan; Donlin, Laura T.; Henderson, Lauren; Wei, Kevin; Mizoguchi, Fumitaka; Teslovich, Nikola; Weinblatt, Michael; Massarotti, Elena; Coblyn, Jonathan; Helfgott, Simon; Lee, Yvonne C.; Todd, Derrick; Bykerk, Vivian P.; Goodman, Susan M.; Pernis, Alessandra B.; Ivashkiv, Lionel B.; Karlson, Elizabeth; Nigrovic, Peter; Filer, Andrew; Buckley, Christopher D.; Lederer, James; Raychaudhuri, Soumya; Brenner, Michael (Springer Science and Business Media LLC, 2017-02-02)
      CD4+ T cells are central mediators of autoimmune pathology; however, defining their key effector functions in specific autoimmune diseases remains challenging. Pathogenic CD4+ T cells within affected tissues may be identified ...
    • A positively selected FBN1 missense variant reduces height in Peruvian individuals 

      Asgari, Samira; Luo, Yang; Akbari, Ali; Belbin, Gillian M.; Li, Xinyi; Harris, Daniel N.; Selig, Martin; Bartell, Eric; Calderon, Roger; Slowikowski, Kamil; Contreras, Carmen; Yataco, Rosa; Galea, Jerome; Jimenez, Judith; Coit, Julia; Farroñay, Chandel; Nazarian, Rosalynn; O’Connor, Timothy D.; Dietz, Harry C.; Hirschhorn, Joel; Guio, Heinner; Lecca, Leonid; Kenny, Eimear E.; Freeman, Esther E.; Murray, Megan B.; Raychaudhuri, Soumya; Murray (Springer Science and Business Media LLC, 2020-05-13)
      On average, the Peruvian population is among the shortest in the world1. Here we show that Native American ancestry is associated with reduced height in an ethnically diverse group of Peruvians, and identify a novel, ...
    • 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 ...
    • Single-cell eQTL models reveal dynamic T cell state dependence of disease loci 

      Nathan, Aparna; Asgari, Samira; Ishigaki, Kazuyoshi; Valencia, Cristian; Amariuta, Tiffany; Luo, Yang; Beynor, Jessica; Baglaenko, Yuriy; Suliman, Sara; Price, Alkes; Lecca, Leonid; Murray, Megan; Moddy, D Branch; Raychaudhuri, Soumya (Springer Science and Business Media LLC, 2022-05-11)
      Non-coding genetic variants may cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by gene-regulation differences across fluid functional cell ...
    • SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci 

      Slowikowski, Kamil; Hu, Xinli; Raychaudhuri, Soumya (Oxford University Press, 2014)
      Summary: We created a fast, robust and general C++ implementation of a single-nucleotide polymorphism (SNP) set enrichment algorithm to identify cell types, tissues and pathways affected by risk loci. It tests trait-associated ...
    • TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits 

      Diogo, Dorothée; Bastarache, Lisa; Liao, Katherine P.; Graham, Robert R.; Fulton, Robert S.; Greenberg, Jeffrey D.; Eyre, Steve; Bowes, John; Cui, Jing; Lee, Annette; Pappas, Dimitrios A.; Kremer, Joel M.; Barton, Anne; Coenen, Marieke J. H.; Franke, Barbara; Kiemeney, Lambertus A.; Mariette, Xavier; Richard-Miceli, Corrine; Canhão, Helena; Fonseca, João E.; de Vries, Niek; Tak, Paul P.; Crusius, J. Bart A.; Nurmohamed, Michael T.; Kurreeman, Fina; Mikuls, Ted R.; Okada, Yukinori; Stahl, Eli A.; Larson, David E.; Deluca, Tracie L.; O'Laughlin, Michelle; Fronick, Catrina C.; Fulton, Lucinda L.; Kosoy, Roman; Ransom, Michael; Bhangale, Tushar R.; Ortmann, Ward; Cagan, Andrew; Gainer, Vivian; Karlson, Elizabeth W.; Kohane, Isaac; Murphy, Shawn N.; Martin, Javier; Zhernakova, Alexandra; Klareskog, Lars; Padyukov, Leonid; Worthington, Jane; Mardis, Elaine R.; Seldin, Michael F.; Gregersen, Peter K.; Behrens, Timothy; Raychaudhuri, Soumya; Denny, Joshua C.; Plenge, Robert M. (Public Library of Science, 2015)
      Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves ...
    • Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases 

      Lenz, Tobias L.; Deutsch, Aaron J.; Han, Buhm; Hu, Xinli; Okada, Yukinori; Eyre, Stephen; Knapp, Michael; Zhernakova, Alexandra; Huizinga, Tom W.J.; Abecasis, Goncalo; Becker, Jessica; Boeckxstaens, Guy E.; Chen, Wei-Min; Franke, Andre; Gladman, Dafna D.; Gockel, Ines; Gutierrez-Achury, Javier; Martin, Javier; Nair, Rajan P.; Nöthen, Markus M.; Onengut-Gumuscu, Suna; Rahman, Proton; Rantapää-Dahlqvist, Solbritt; Stuart, Philip E.; Tsoi, Lam C.; Van Heel, David A.; Worthington, Jane; Wouters, Mira M.; Klareskog, Lars; Elder, James T.; Gregersen, Peter K.; Schumacher, Johannes; Rich, Stephen S.; Wijmenga, Cisca; Sunyaev, Shamil R.; de Bakker, Paul I.W.; Raychaudhuri, Soumya (2015)
      Human leukocyte antigen (HLA) genes confer strong risk for autoimmune diseases on a log-additive scale. Here we speculated that differences in autoantigen binding repertoires between a heterozygote’s two expressed HLA ...