Soumya Raychaudhuri

Summary

Publications

  1. pmc Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci
    Philip L De Jager
    Division of Molecular Immunology, Center for Neurologic Diseases, Department of Neurology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Nat Genet 41:776-82. 2009
  2. pmc A rare penetrant mutation in CFH confers high risk of age-related macular degeneration
    Soumya Raychaudhuri
    Division of Genetics, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Genet 43:1232-6. 2011
  3. pmc Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis
    Soumya Raychaudhuri
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 44:291-6. 2012
  4. pmc Recent advances in the genetics of rheumatoid arthritis
    Soumya Raychaudhuri
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Curr Opin Rheumatol 22:109-18. 2010
  5. pmc Mapping rare and common causal alleles for complex human diseases
    Soumya Raychaudhuri
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Cell 147:57-69. 2011
  6. pmc VIZ-GRAIL: visualizing functional connections across disease loci
    Soumya Raychaudhuri
    Divisions of Genetics and Rheumatology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Bioinformatics 27:1589-90. 2011
  7. pmc Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration
    Yi Yu
    Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Tufts University School of Medicine, 800 WashingtonStreet, No 450, Boston, MA 02111, USA
    Hum Mol Genet 20:3699-709. 2011
  8. pmc Heritability and genome-wide association study to assess genetic differences between advanced age-related macular degeneration subtypes
    Lucia Sobrin
    Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
    Ophthalmology 119:1874-85. 2012
  9. pmc Genetics of rheumatoid arthritis contributes to biology and drug discovery
    Yukinori Okada
    1 Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA 2 Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
    Nature 506:376-81. 2014
  10. pmc Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration
    Johanna M Seddon
    1 Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, Massachusetts, USA 2 Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, USA 3 Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
    Nat Genet 45:1366-70. 2013

Detail Information

Publications41

  1. pmc Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci
    Philip L De Jager
    Division of Molecular Immunology, Center for Neurologic Diseases, Department of Neurology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Nat Genet 41:776-82. 2009
    ....
  2. pmc A rare penetrant mutation in CFH confers high risk of age-related macular degeneration
    Soumya Raychaudhuri
    Division of Genetics, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Genet 43:1232-6. 2011
    ..This result suggests that loss-of-function alleles at CFH are likely to drive AMD risk. This finding represents one of the first instances in which a common complex disease variant has led to the discovery of a rare penetrant mutation...
  3. pmc Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis
    Soumya Raychaudhuri
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 44:291-6. 2012
    ..This study shows how imputation of functional variation from large reference panels can help fine map association signals in the MHC...
  4. pmc Recent advances in the genetics of rheumatoid arthritis
    Soumya Raychaudhuri
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Curr Opin Rheumatol 22:109-18. 2010
    ..To review the recently discovered genetic risk loci in rheumatoid arthritis (RA), the pathways they implicate, and the genetic architecture of RA...
  5. pmc Mapping rare and common causal alleles for complex human diseases
    Soumya Raychaudhuri
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Cell 147:57-69. 2011
    ....
  6. pmc VIZ-GRAIL: visualizing functional connections across disease loci
    Soumya Raychaudhuri
    Divisions of Genetics and Rheumatology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Bioinformatics 27:1589-90. 2011
    ..Here, we have implemented VIZ-GRAIL, a software tool to display those relationships and to depict the underlying biological patterns...
  7. pmc Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration
    Yi Yu
    Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Tufts University School of Medicine, 800 WashingtonStreet, No 450, Boston, MA 02111, USA
    Hum Mol Genet 20:3699-709. 2011
    ..The novel variants identified in this study suggest that angiogenesis (VEGFA) and extracellular collagen matrix (FRK/COL10A1) pathways contribute to the development of advanced AMD...
  8. pmc Heritability and genome-wide association study to assess genetic differences between advanced age-related macular degeneration subtypes
    Lucia Sobrin
    Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
    Ophthalmology 119:1874-85. 2012
    ....
  9. pmc Genetics of rheumatoid arthritis contributes to biology and drug discovery
    Yukinori Okada
    1 Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA 2 Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
    Nature 506:376-81. 2014
    ....
  10. pmc Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration
    Johanna M Seddon
    1 Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, Massachusetts, USA 2 Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, USA 3 Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
    Nat Genet 45:1366-70. 2013
    ..These results implicate loss of C3 protein regulation and excessive alternative complement activation in AMD pathogenesis, thus informing both the direction of effect and mechanistic underpinnings of this disorder...
  11. pmc Imputing amino acid polymorphisms in human leukocyte antigens
    Xiaoming Jia
    Harvard MIT Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
    PLoS ONE 8:e64683. 2013
    ..Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes...
  12. pmc Genome-wide association study and gene expression analysis identifies CD84 as a predictor of response to etanercept therapy in rheumatoid arthritis
    Jing Cui
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 9:e1003394. 2013
    ..These findings support a model in which CD84 genotypes and/or expression may serve as a useful biomarker for response to etanercept treatment in RA patients of European ancestry...
  13. pmc Use of a multiethnic approach to identify rheumatoid- arthritis-susceptibility loci, 1p36 and 17q12
    Fina A S Kurreeman
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, 02115, USA
    Am J Hum Genet 90:524-32. 2012
    ....
  14. pmc Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC)
    Benjamin M Neale
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Proc Natl Acad Sci U S A 107:7395-400. 2010
    ..Results implicate different biologic pathways than previously reported and provide new avenues for prevention and treatment of AMD...
  15. ncbi request reprint Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci
    Eli A Stahl
    Division of Rheumatology, Immunology and Allergy, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Genet 42:508-14. 2010
    ..An additional 11 SNPs replicated at P < 0.05, many of which are validated autoimmune risk alleles, suggesting that most represent genuine rheumatoid arthritis risk alleles...
  16. pmc Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis
    Dorothée Diogo
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 92:15-27. 2013
    ..Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA...
  17. ncbi request reprint Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes
    Towfique Raj
    Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women s Hospital, Boston, MA 02115, USA
    Science 344:519-23. 2014
    ..This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants. ..
  18. pmc Common risk alleles for inflammatory diseases are targets of recent positive selection
    Towfique Raj
    Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Am J Hum Genet 92:517-29. 2013
    ....
  19. pmc Fine mapping seronegative and seropositive rheumatoid arthritis to shared and distinct HLA alleles by adjusting for the effects of heterogeneity
    Buhm Han
    Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA
    Am J Hum Genet 94:522-32. 2014
    ..We expect that our approach might have broad applications in analyzing clinical conditions with heterogeneity at both major histocompatibility complex (MHC) and non-MHC regions...
  20. pmc Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls
    Katherine P Liao
    Division of Rheumatology, Immunology and Allergy, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Ann Rheum Dis 73:1170-5. 2014
    ..Our objective was to determine the association of established LDL and RA genetic alleles with LDL levels in RA cases compared with non-RA controls...
  21. pmc Rheumatoid arthritis risk allele PTPRC is also associated with response to anti-tumor necrosis factor alpha therapy
    Jing Cui
    Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Arthritis Rheum 62:1849-61. 2010
    ..The aim of the present study was to test established RA genetic risk factors to determine whether the same alleles also influence the response to anti-TNF therapy...
  22. pmc Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells
    Xinli Hu
    Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts, United States of America Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts, United States of America Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America Harvard Medical School, Boston, Massachusetts, United States of America Harvard MIT Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
    PLoS Genet 10:e1004404. 2014
    ..Our study underscores the power of examining molecular phenotypes in relevant cells and conditions for understanding pathogenic mechanisms of disease variants. ..
  23. pmc Fast pairwise IBD association testing in genome-wide association studies
    Buhm Han
    Division of Genetics, Brigham and Women s Hospital and Division of Rheumatology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA, Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, Computer Science Department, University of California, Los Angeles, CA 90095, USA, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 30:206-13. 2014
    ....
  24. pmc Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells
    Xinli Hu
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115
    Proc Natl Acad Sci U S A 110:19030-5. 2013
    ....
  25. pmc Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway
    Gang Li
    Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    PLoS Genet 9:e1003487. 2013
    ..Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in complex traits such as RA...
  26. pmc The PRL -1149 G/T polymorphism and rheumatoid arthritis susceptibility
    Yvonne C Lee
    Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Arthritis Rheum 60:1250-4. 2009
    ..The aim of this study was to determine the role of the PRL -1149 G/T polymorphism (rs1341239) in rheumatoid arthritis (RA) susceptibility...
  27. pmc Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records
    Fina Kurreeman
    Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
    Am J Hum Genet 88:57-69. 2011
    ....
  28. pmc Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk
    Soumya Raychaudhuri
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Genet 41:1313-8. 2009
    ..0008 replication, P = 4 x 10(-6) overall) and FCGR2A (rs12746613, P = 0.0022 replication, P = 2 x 10(-5) overall). Many of these loci are also associated to other immunologic diseases...
  29. pmc Integrating autoimmune risk loci with gene-expression data identifies specific pathogenic immune cell subsets
    Xinli Hu
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 89:496-506. 2011
    ..Our approach has application in other phenotypes, outside of autoimmunity, where many loci have been discovered and high-quality cell-type-specific gene expression is available...
  30. pmc Quantifying missing heritability at known GWAS loci
    Alexander Gusev
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS Genet 9:e1003993. 2013
    ..These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture...
  31. pmc Chromatin marks identify critical cell types for fine mapping complex trait variants
    Gosia Trynka
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 45:124-30. 2013
    ..003) and the liver (P = 0.003), and 14 SNPs for neuropsychiatric disease in neuronal tissues (P = 0.007). We show how cell type-specific H3K4me3 peaks can inform the fine mapping of associated SNPs to identify causal variation...
  32. ncbi request reprint Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
    Eli A Stahl
    Division of Rheumatology Immunology and Allergy, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Genet 44:483-9. 2012
    ..These analyses suggest that GWAS will continue to be highly productive for the discovery of additional susceptibility loci for common diseases...
  33. pmc Practical aspects of imputation-driven meta-analysis of genome-wide association studies
    Paul I W de Bakker
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School Partners Healthcare Systems Center for Genetics and Genomics, Boston, MA 02115, USA
    Hum Mol Genet 17:R122-8. 2008
    ..As many groups are forming collaborations to engage in these efforts, this review collects a series of guidelines, practical detail and learned experiences from a variety of individuals who have contributed to the subject...
  34. pmc Leveraging human genetics to develop future therapeutic strategies in rheumatoid arthritis
    Robert M Plenge
    Division of Rheumatology, Immunology and Allergy, Brigham and Women s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Suite 168, Boston, MA 02115, USA
    Rheum Dis Clin North Am 36:259-70. 2010
    ....
  35. pmc Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene
    Yukinori Okada
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Tokyo, Japan Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
    PLoS ONE 9:e87645. 2014
    ..049 for C-alpha test and P = 0.055 for SKAT). Together, these data suggest that PLB1 is a candidate risk gene for RA. Future studies to characterize the full spectrum of genetic risk in the PLB1 genetic locus are warranted...
  36. pmc Rheumatoid arthritis. Evidence for a genetic component to disease severity in RA
    Eli A Stahl
    Divisions of Rheumatology and Genetics, Department of Medicine, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Nat Rev Rheumatol 8:312-3. 2012
    ..But given clinical heterogeneity in RA, can we predict who will develop severe disease? Substantial heritability of erosive progression rates has now been identified, but better prognostic biomarkers remain wanting...
  37. pmc Electronic medical records for discovery research in rheumatoid arthritis
    Katherine P Liao
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Arthritis Care Res (Hoboken) 62:1120-7. 2010
    ..We assessed whether a classification algorithm incorporating narrative EMR data (typed physician notes) more accurately classifies subjects with rheumatoid arthritis (RA) compared with an algorithm using codified EMR data alone...
  38. pmc Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders
    Elaine T Lim
    Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
    Neuron 77:235-42. 2013
    ..Taken together, these results provide compelling evidence that rare autosomal and X chromosome complete gene knockouts are important inherited risk factors for ASD...
  39. pmc Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
    Elizabeth K Speliotes
    Metabolism Initiative and Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
    Nat Genet 42:937-48. 2010
    ..Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation...
  40. pmc Using chromatin marks to interpret and localize genetic associations to complex human traits and diseases
    Gosia Trynka
    Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA Division of Rheumatology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA Partners Center for Personalized Genetic Medicine, Boston, MA, USA
    Curr Opin Genet Dev 23:635-41. 2013
    ..We discuss the efforts to integrate common trait-associated variants with genomic annotations. Finally, we highlight some caveats of these approaches and outline future directions for improvement. ..
  41. pmc The Lin28/let-7 axis regulates glucose metabolism
    Hao Zhu
    Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children s Hospital Boston and Dana Farber Cancer Institute, Boston, MA, USA
    Cell 147:81-94. 2011
    ..These data establish the Lin28/let-7 pathway as a central regulator of mammalian glucose metabolism...