Publications by authors named "Soumya Raychaudhuri"

100Publications

Genome-wide Study Identifies Association between HLA-B55:01 and Self-Reported Penicillin Allergy.

Am J Hum Genet 2020 Aug 26. Epub 2020 Aug 26.

Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark; Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.

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http://dx.doi.org/10.1016/j.ajhg.2020.08.008DOI Listing
August 2020

HATK: HLA Analysis Toolkit.

Bioinformatics 2020 Jul 31. Epub 2020 Jul 31.

Department of Biomedical Sciences, Seoul National University College of Medicine.

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http://dx.doi.org/10.1093/bioinformatics/btaa684DOI Listing
July 2020

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares.

N Engl J Med 2020 07;383(3):218-228

From the Laboratory of Molecular Neuro-oncology, Rockefeller University (D.E.O., K.S., J.F., M.O.F., S.P., N.E.B., C.H., R.B.D.), the Hospital for Special Surgery (D.E.O.), and the Simons Foundation (O.G.T.) - all in New York; Rice University, Houston (V.Y.); Princeton University, Princeton, NJ (V.Y., O.G.T.); Howard Hughes Medical Institute, Chevy Chase, MD (N.E.B., R.B.D.); and the Divisions of Rheumatology and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, and the Broad Institute, Cambridge - both in Massachusetts (F.Z., S.R.).

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http://dx.doi.org/10.1056/NEJMoa2004114DOI Listing
July 2020

Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases.

Nat Genet 2020 07 8;52(7):669-679. Epub 2020 Jun 8.

Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

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http://dx.doi.org/10.1038/s41588-020-0640-3DOI Listing
July 2020

CUX1 and IκBζ (NFKBIZ) mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts.

Proc Natl Acad Sci U S A 2020 03 20;117(10):5532-5541. Epub 2020 Feb 20.

Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1912702117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071902PMC
March 2020

Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis.

Immunol Rev 2020 03 28;294(1):188-204. Epub 2019 Nov 28.

Center for Data Sciences, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1111/imr.12827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047592PMC
March 2020

Fast, sensitive and accurate integration of single-cell data with Harmony.

Nat Methods 2019 12 18;16(12):1289-1296. Epub 2019 Nov 18.

Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41592-019-0619-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884693PMC
December 2019

Distinct HLA Associations with Rheumatoid Arthritis Subsets Defined by Serological Subphenotype.

Am J Hum Genet 2019 Oct;105(4):880

Division of Rheumatology, Immunology, and Allergy Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, Oxford Road, Manchester M13 9PT, UK; Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297193035
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http://dx.doi.org/10.1016/j.ajhg.2019.09.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6817550PMC
October 2019

Distinct HLA Associations with Rheumatoid Arthritis Subsets Defined by Serological Subphenotype.

Am J Hum Genet 2019 09 29;105(3):616-624. Epub 2019 Aug 29.

Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, Oxford Road, Manchester M13 9PT, UK; Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731376PMC
September 2019

Multimodal single-cell approaches shed light on T cell heterogeneity.

Curr Opin Immunol 2019 12 17;61:17-25. Epub 2019 Aug 17.

Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.coi.2019.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901721PMC
December 2019

Benchmarker: An Unbiased, Association-Data-Driven Strategy to Evaluate Gene Prioritization Algorithms.

Am J Hum Genet 2019 06 2;104(6):1025-1039. Epub 2019 May 2.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.03.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556976PMC
June 2019

Genes with High Network Connectivity Are Enriched for Disease Heritability.

Am J Hum Genet 2019 05;104(5):896-913

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506868PMC
May 2019

IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors.

Am J Hum Genet 2019 05 18;104(5):879-895. Epub 2019 Apr 18.

Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA; Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297193010
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http://dx.doi.org/10.1016/j.ajhg.2019.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506796PMC
May 2019

Immunoprofiling comes of age.

Nat Med 2019 03;25(3):362-364

Broad Institute of Massachusetts Institute and Technology and Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41591-019-0387-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534817PMC
March 2019

Imputation-based analysis of alleles in the susceptibility to ankylosing spondylitis.

Ann Rheum Dis 2018 11 28;77(11):1691-1692. Epub 2018 Apr 28.

Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT) at Translational Research Institute, Brisbane, Queensland, Australia.

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http://ard.bmj.com/lookup/doi/10.1136/annrheumdis-2018-21341
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http://dx.doi.org/10.1136/annrheumdis-2018-213413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6716791PMC
November 2018

Review: Genetics and the Classification of Arthritis in Adults and Children.

Arthritis Rheumatol 2018 01 1;70(1):7-17. Epub 2017 Dec 1.

Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.

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http://doi.wiley.com/10.1002/art.40350
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http://dx.doi.org/10.1002/art.40350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805142PMC
January 2018

Functional genomics of stromal cells in chronic inflammatory diseases.

Curr Opin Rheumatol 2018 Jan;30(1):65-71

Center for Data Sciences, Brigham and Women's Hospital.

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http://dx.doi.org/10.1097/BOR.0000000000000455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890939PMC
January 2018

Leveraging blood and tissue CD4+ T cell heterogeneity at the single cell level to identify mechanisms of disease in rheumatoid arthritis.

Curr Opin Immunol 2017 Dec 6;49:27-36. Epub 2017 Sep 6.

Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; 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 Massachusetts Technical Institute and Harvard University, Cambridge, MA 02138, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK. Electronic address:

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http://dx.doi.org/10.1016/j.coi.2017.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705469PMC
December 2017

Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci.

Authors:
Tin Aung Mineo Ozaki Mei Chin Lee Ursula Schlötzer-Schrehardt Gudmar Thorleifsson Takanori Mizoguchi Robert P Igo Aravind Haripriya Susan E Williams Yury S Astakhov Andrew C Orr Kathryn P Burdon Satoko Nakano Kazuhiko Mori Khaled Abu-Amero Michael Hauser Zheng Li Gopalakrishnan Prakadeeswari Jessica N Cooke Bailey Alina Popa Cherecheanu Jae H Kang Sarah Nelson Ken Hayashi Shin-Ichi Manabe Shigeyasu Kazama Tomasz Zarnowski Kenji Inoue Murat Irkec Miguel Coca-Prados Kazuhisa Sugiyama Irma Järvelä Patricio Schlottmann S Fabian Lerner Hasnaa Lamari Yildirim Nilgün Mukharram Bikbov Ki Ho Park Soon Cheol Cha Kenji Yamashiro Juan C Zenteno Jost B Jonas Rajesh S Kumar Shamira A Perera Anita S Y Chan Nino Kobakhidze Ronnie George Lingam Vijaya Tan Do Deepak P Edward Lourdes de Juan Marcos Mohammad Pakravan Sasan Moghimi Ryuichi Ideta Daniella Bach-Holm Per Kappelgaard Barbara Wirostko Samuel Thomas Daniel Gaston Karen Bedard Wenda L Greer Zhenglin Yang Xueyi Chen Lulin Huang Jinghong Sang Hongyan Jia Liyun Jia Chunyan Qiao Hui Zhang Xuyang Liu Bowen Zhao Ya-Xing Wang Liang Xu Stéphanie Leruez Pascal Reynier George Chichua Sergo Tabagari Steffen Uebe Matthias Zenkel Daniel Berner Georg Mossböck Nicole Weisschuh Ursula Hoja Ulrich-Christoph Welge-Luessen Christian Mardin Panayiota Founti Anthi Chatzikyriakidou Theofanis Pappas Eleftherios Anastasopoulos Alexandros Lambropoulos Arkasubhra Ghosh Rohit Shetty Natalia Porporato Vijayan Saravanan Rengaraj Venkatesh Chandrashekaran Shivkumar Narendran Kalpana Sripriya Sarangapani Mozhgan R Kanavi Afsaneh Naderi Beni Shahin Yazdani Alireza Lashay Homa Naderifar Nassim Khatibi Antonio Fea Carlo Lavia Laura Dallorto Teresa Rolle Paolo Frezzotti Daniela Paoli Erika Salvi Paolo Manunta Yosai Mori Kazunori Miyata Tomomi Higashide Etsuo Chihara Satoshi Ishiko Akitoshi Yoshida Masahide Yanagi Yoshiaki Kiuchi Tsutomu Ohashi Toshiya Sakurai Takako Sugimoto Hideki Chuman Makoto Aihara Masaru Inatani Masahiro Miyake Norimoto Gotoh Fumihiko Matsuda Nagahisa Yoshimura Yoko Ikeda Morio Ueno Chie Sotozono Jin Wook Jeoung Min Sagong Kyu Hyung Park Jeeyun Ahn Marisa Cruz-Aguilar Sidi M Ezzouhairi Abderrahman Rafei Yaan Fun Chong Xiao Yu Ng Shuang Ru Goh Yueming Chen Victor H K Yong Muhammad Imran Khan Olusola O Olawoye Adeyinka O Ashaye Idakwo Ugbede Adeola Onakoya Nkiru Kizor-Akaraiwe Chaiwat Teekhasaenee Yanin Suwan Wasu Supakontanasan Suhanya Okeke Nkechi J Uche Ifeoma Asimadu Humaira Ayub Farah Akhtar Ewa Kosior-Jarecka Urszula Lukasik Ignacio Lischinsky Vania Castro Rodolfo Perez Grossmann Gordana Sunaric Megevand Sylvain Roy Edward Dervan Eoin Silke Aparna Rao Priti Sahay Pablo Fornero Osvaldo Cuello Delia Sivori Tamara Zompa Richard A Mills Emmanuelle Souzeau Paul Mitchell Jie Jin Wang Alex W Hewitt Michael Coote Jonathan G Crowston Sergei Y Astakhov Eugeny L Akopov Anton Emelyanov Vera Vysochinskaya Gyulli Kazakbaeva Rinat Fayzrakhmanov Saleh A Al-Obeidan Ohoud Owaidhah Leyla Ali Aljasim Balram Chowbay Jia Nee Foo Raphael Q Soh Kar Seng Sim Zhicheng Xie Augustine W O Cheong Shi Qi Mok Hui Meng Soo Xiao Yin Chen Su Qin Peh Khai Koon Heng Rahat Husain Su-Ling Ho Axel M Hillmer Ching-Yu Cheng Francisco A Escudero-Domínguez Rogelio González-Sarmiento Frederico Martinon-Torres Antonio Salas Kessara Pathanapitoon Linda Hansapinyo Boonsong Wanichwecharugruang Naris Kitnarong Anavaj Sakuntabhai Hip X Nguyn Giang T T Nguyn Trình V Nguyn Werner Zenz Alexander Binder Daniela S Klobassa Martin L Hibberd Sonia Davila Stefan Herms Markus M Nöthen Susanne Moebus Robyn M Rautenbach Ari Ziskind Trevor R Carmichael Michele Ramsay Lydia Álvarez Montserrat García Héctor González-Iglesias Pedro P Rodríguez-Calvo Luis Fernández-Vega Cueto Çilingir Oguz Nevbahar Tamcelik Eray Atalay Bilge Batu Dilek Aktas Burcu Kasım M Roy Wilson Anne L Coleman Yutao Liu Pratap Challa Leon Herndon Rachel W Kuchtey John Kuchtey Karen Curtin Craig J Chaya Alan Crandall Linda M Zangwill Tien Yin Wong Masakazu Nakano Shigeru Kinoshita Anneke I den Hollander Eija Vesti John H Fingert Richard K Lee Arthur J Sit Bradford J Shingleton Ningli Wang Daniele Cusi Raheel Qamar Peter Kraft Margaret A Pericak-Vance Soumya Raychaudhuri Steffen Heegaard Tero Kivelä André Reis Friedrich E Kruse Robert N Weinreb Louis R Pasquale Jonathan L Haines Unnur Thorsteinsdottir Fridbert Jonasson R Rand Allingham Dan Milea Robert Ritch Toshiaki Kubota Kei Tashiro Eranga N Vithana Shazia Micheal Fotis Topouzis Jamie E Craig Michael Dubina Periasamy Sundaresan Kari Stefansson Janey L Wiggs Francesca Pasutto Chiea Chuen Khor

Nat Genet 2017 07 29;49(7):993-1004. Epub 2017 May 29.

Singapore Eye Research Institute, Singapore.

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http://dx.doi.org/10.1038/ng.3875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685441PMC
July 2017

A rare coding allele in is protective for psoriatic arthritis.

Ann Rheum Dis 2017 Jul 13;76(7):1321-1324. Epub 2017 May 13.

Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1136/annrheumdis-2016-210592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5530346PMC
July 2017

52 Genetic Loci Influencing Myocardial Mass.

Authors:
Pim van der Harst Jessica van Setten Niek Verweij Georg Vogler Lude Franke Matthew T Maurano Xinchen Wang Irene Mateo Leach Mark Eijgelsheim Nona Sotoodehnia Caroline Hayward Rossella Sorice Osorio Meirelles Leo-Pekka Lyytikäinen Ozren Polašek Toshiko Tanaka Dan E Arking Sheila Ulivi Stella Trompet Martina Müller-Nurasyid Albert V Smith Marcus Dörr Kathleen F Kerr Jared W Magnani Fabiola Del Greco M Weihua Zhang Ilja M Nolte Claudia T Silva Sandosh Padmanabhan Vinicius Tragante Tõnu Esko Gonçalo R Abecasis Michiel E Adriaens Karl Andersen Phil Barnett Joshua C Bis Rolf Bodmer Brendan M Buckley Harry Campbell Megan V Cannon Aravinda Chakravarti Lin Y Chen Alessandro Delitala Richard B Devereux Pieter A Doevendans Anna F Dominiczak Luigi Ferrucci Ian Ford Christian Gieger Tamara B Harris Eric Haugen Matthias Heinig Dena G Hernandez Hans L Hillege Joel N Hirschhorn Albert Hofman Norbert Hubner Shih-Jen Hwang Annamaria Iorio Mika Kähönen Manolis Kellis Ivana Kolcic Ishminder K Kooner Jaspal S Kooner Jan A Kors Edward G Lakatta Kasper Lage Lenore J Launer Daniel Levy Alicia Lundby Peter W Macfarlane Dalit May Thomas Meitinger Andres Metspalu Stefania Nappo Silvia Naitza Shane Neph Alex S Nord Teresa Nutile Peter M Okin Jesper V Olsen Ben A Oostra Josef M Penninger Len A Pennacchio Tune H Pers Siegfried Perz Annette Peters Yigal M Pinto Arne Pfeufer Maria Grazia Pilia Peter P Pramstaller Bram P Prins Olli T Raitakari Soumya Raychaudhuri Ken M Rice Elizabeth J Rossin Jerome I Rotter Sebastian Schafer David Schlessinger Carsten O Schmidt Jobanpreet Sehmi Herman H W Silljé Gianfranco Sinagra Moritz F Sinner Kamil Slowikowski Elsayed Z Soliman Timothy D Spector Wilko Spiering John A Stamatoyannopoulos Ronald P Stolk Konstantin Strauch Sian-Tsung Tan Kirill V Tarasov Bosco Trinh Andre G Uitterlinden Malou van den Boogaard Cornelia M van Duijn Wiek H van Gilst Jorma S Viikari Peter M Visscher Veronique Vitart Uwe Völker Melanie Waldenberger Christian X Weichenberger Harm-Jan Westra Cisca Wijmenga Bruce H Wolffenbuttel Jian Yang Connie R Bezzina Patricia B Munroe Harold Snieder Alan F Wright Igor Rudan Laurie A Boyer Folkert W Asselbergs Dirk J van Veldhuisen Bruno H Stricker Bruce M Psaty Marina Ciullo Serena Sanna Terho Lehtimäki James F Wilson Stefania Bandinelli Alvaro Alonso Paolo Gasparini J Wouter Jukema Stefan Kääb Vilmundur Gudnason Stephan B Felix Susan R Heckbert Rudolf A de Boer Christopher Newton-Cheh Andrew A Hicks John C Chambers Yalda Jamshidi Axel Visel Vincent M Christoffels Aaron Isaacs Nilesh J Samani Paul I W de Bakker

J Am Coll Cardiol 2016 09;68(13):1435-1448

Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1016/j.jacc.2016.07.729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478167PMC
September 2016

Genome-Wide Association Studies Suggest Limited Immune Gene Enrichment in Schizophrenia Compared to 5 Autoimmune Diseases.

Schizophr Bull 2016 09 30;42(5):1176-84. Epub 2016 May 30.

Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Lancaster Medical School and Data Science Institute, Lancaster University, Lancaster, UK;

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https://academic.oup.com/schizophreniabulletin/article-looku
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http://dx.doi.org/10.1093/schbul/sbw059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988748PMC
September 2016

Recent Advances in Defining the Genetic Basis of Rheumatoid Arthritis.

Annu Rev Genomics Hum Genet 2016 08 23;17:273-301. Epub 2016 May 23.

Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York 11030; email:

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http://dx.doi.org/10.1146/annurev-genom-090314-045919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727201PMC
August 2016

Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation.

Authors:
Alexander Gusev Huwenbo Shi Gleb Kichaev Mark Pomerantz Fugen Li Henry W Long Sue A Ingles Rick A Kittles Sara S Strom Benjamin A Rybicki Barbara Nemesure William B Isaacs Wei Zheng Curtis A Pettaway Edward D Yeboah Yao Tettey Richard B Biritwum Andrew A Adjei Evelyn Tay Ann Truelove Shelley Niwa Anand P Chokkalingam Esther M John Adam B Murphy Lisa B Signorello John Carpten M Cristina Leske Suh-Yuh Wu Anslem J M Hennis Christine Neslund-Dudas Ann W Hsing Lisa Chu Phyllis J Goodman Eric A Klein John S Witte Graham Casey Sam Kaggwa Michael B Cook Daniel O Stram William J Blot Rosalind A Eeles Douglas Easton Zsofia Kote-Jarai Ali Amin Al Olama Sara Benlloch Kenneth Muir Graham G Giles Melissa C Southey Liesel M Fitzgerald Henrik Gronberg Fredrik Wiklund Markus Aly Brian E Henderson Johanna Schleutker Tiina Wahlfors Teuvo L J Tammela Børge G Nordestgaard Tim J Key Ruth C Travis David E Neal Jenny L Donovan Freddie C Hamdy Paul Pharoah Nora Pashayan Kay-Tee Khaw Janet L Stanford Stephen N Thibodeau Shannon K McDonnell Daniel J Schaid Christiane Maier Walther Vogel Manuel Luedeke Kathleen Herkommer Adam S Kibel Cezary Cybulski Dominika Wokolorczyk Wojciech Kluzniak Lisa Cannon-Albright Craig Teerlink Hermann Brenner Aida K Dieffenbach Volker Arndt Jong Y Park Thomas A Sellers Hui-Yi Lin Chavdar Slavov Radka Kaneva Vanio Mitev Jyotsna Batra Amanda Spurdle Judith A Clements Manuel R Teixeira Hardev Pandha Agnieszka Michael Paula Paulo Sofia Maia Andrzej Kierzek David V Conti Demetrius Albanes Christine Berg Sonja I Berndt Daniele Campa E David Crawford W Ryan Diver Susan M Gapstur J Michael Gaziano Edward Giovannucci Robert Hoover David J Hunter Mattias Johansson Peter Kraft Loic Le Marchand Sara Lindström Carmen Navarro Kim Overvad Elio Riboli Afshan Siddiq Victoria L Stevens Dimitrios Trichopoulos Paolo Vineis Meredith Yeager Gosia Trynka Soumya Raychaudhuri Frederick R Schumacher Alkes L Price Matthew L Freedman Christopher A Haiman Bogdan Pasaniuc

Nat Commun 2016 Apr 7;7:10979. Epub 2016 Apr 7.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1038/ncomms10979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829663PMC
April 2016

A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping.

Hum Mol Genet 2016 05 21;25(9):1857-66. Epub 2016 Feb 21.

Division of Genetics, Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA and Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.

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http://dx.doi.org/10.1093/hmg/ddw049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986332PMC
May 2016

Autoimmune diseases - connecting risk alleles with molecular traits of the immune system.

Nat Rev Genet 2016 Mar 15;17(3):160-74. Epub 2016 Feb 15.

Division of Genetics, and Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nrg.2015.33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896831PMC
March 2016

Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease.

PLoS Genet 2015 Oct 28;11(10):e1005622. Epub 2015 Oct 28.

Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America; Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Charles Bronfman Institute for Personalized Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Center for Statistical Genetics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Zena and Michael A. Weiner Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625039PMC
October 2015

Tissue-Specific Enrichment of Lymphoma Risk Loci in Regulatory Elements.

PLoS One 2015 30;10(9):e0139360. Epub 2015 Sep 30.

Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America; Program in Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America; Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139360PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589387PMC
June 2016

Loci associated with N-glycosylation of human IgG are not associated with rheumatoid arthritis: a Mendelian randomisation study.

Ann Rheum Dis 2016 Jan 17;75(1):317-20. Epub 2015 Sep 17.

Faculty of Medical and Human Sciences, Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1136/annrheumdis-2014-207210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717396PMC
January 2016

New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis.

Authors:
S Hong Lee Enda M Byrne Christina M Hultman Anna Kähler Anna A E Vinkhuyzen Stephan Ripke Ole A Andreassen Thomas Frisell Alexander Gusev Xinli Hu Robert Karlsson Vasilis X Mantzioris John J McGrath Divya Mehta Eli A Stahl Qiongyi Zhao Kenneth S Kendler Patrick F Sullivan Alkes L Price Michael O'Donovan Yukinori Okada Bryan J Mowry Soumya Raychaudhuri Naomi R Wray William Byerley Wiepke Cahn Rita M Cantor Sven Cichon Paul Cormican David Curtis Srdjan Djurovic Valentina Escott-Price Pablo V Gejman Lyudmila Georgieva Ina Giegling Thomas F Hansen Andrés Ingason Yunjung Kim Bettina Konte Phil H Lee Andrew McIntosh Andrew McQuillin Derek W Morris Markus M Nöthen Colm O'Dushlaine Ann Olincy Line Olsen Carlos N Pato Michele T Pato Benjamin S Pickard Danielle Posthuma Henrik B Rasmussen Marcella Rietschel Dan Rujescu Thomas G Schulze Jeremy M Silverman Srinivasa Thirumalai Thomas Werge Ingrid Agartz Farooq Amin Maria H Azevedo Nicholas Bass Donald W Black Douglas H R Blackwood Richard Bruggeman Nancy G Buccola Khalid Choudhury Robert C Cloninger Aiden Corvin Nicholas Craddock Mark J Daly Susmita Datta Gary J Donohoe Jubao Duan Frank Dudbridge Ayman Fanous Robert Freedman Nelson B Freimer Marion Friedl Michael Gill Hugh Gurling Lieuwe De Haan Marian L Hamshere Annette M Hartmann Peter A Holmans René S Kahn Matthew C Keller Elaine Kenny George K Kirov Lydia Krabbendam Robert Krasucki Jacob Lawrence Todd Lencz Douglas F Levinson Jeffrey A Lieberman Dan-Yu Lin Don H Linszen Patrik K E Magnusson Wolfgang Maier Anil K Malhotra Manuel Mattheisen Morten Mattingsdal Steven A McCarroll Helena Medeiros Ingrid Melle Vihra Milanova Inez Myin-Germeys Benjamin M Neale Roel A Ophoff Michael J Owen Jonathan Pimm Shaun M Purcell Vinay Puri Digby J Quested Lizzy Rossin Douglas Ruderfer Alan R Sanders Jianxin Shi Pamela Sklar David St Clair T Scott Stroup Jim Van Os Peter M Visscher Durk Wiersma Stanley Zammit S Louis Bridges Hyon K Choi Marieke J H Coenen Niek de Vries Philippe Dieud Jeffrey D Greenberg Tom W J Huizinga Leonid Padyukov Katherine A Siminovitch Paul P Tak Jane Worthington Philip L De Jager Joshua C Denny Peter K Gregersen Lars Klareskog Xavier Mariette Robert M Plenge Mart van Laar Piet van Riel

Int J Epidemiol 2015 Oct;44(5):1706-21

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http://dx.doi.org/10.1093/ije/dyv136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881824PMC
October 2015

Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk.

Nat Genet 2015 Aug 13;47(8):898-905. Epub 2015 Jul 13.

1] Department of Medicine, Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, Massachusetts, USA. [2] Department of Medicine, Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [3] Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA. [4] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [5] Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1038/ng.3353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930791PMC
August 2015

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci.

Am J Hum Genet 2015 Jul;97(1):139-52

Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute of Inflammation and Repair, University of Manchester, Manchester M13 9PT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.05.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572568PMC
July 2015

Immune cell profiling to guide therapeutic decisions in rheumatic diseases.

Nat Rev Rheumatol 2015 Sep 2;11(9):541-51. Epub 2015 Jun 2.

Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, New Research Building (NRB), 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

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http://dx.doi.org/10.1038/nrrheum.2015.71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898649PMC
September 2015

Accurate and fast multiple-testing correction in eQTL studies.

Am J Hum Genet 2015 Jun 28;96(6):857-68. Epub 2015 May 28.

Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Republic of Korea; Department of Medicine, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457958PMC
June 2015

Do Genetic Susceptibility Variants Associate with Disease Severity in Early Active Rheumatoid Arthritis?

J Rheumatol 2015 Jul 15;42(7):1131-40. Epub 2015 May 15.

From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof

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http://www.jrheum.org/cgi/doi/10.3899/jrheum.141211
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http://dx.doi.org/10.3899/jrheum.141211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714044PMC
July 2015

Association of HLA-DRB1 haplotypes with rheumatoid arthritis severity, mortality, and treatment response.

JAMA 2015 Apr;313(16):1645-56

Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, England2NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manches.

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http://dx.doi.org/10.1001/jama.2015.3435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928097PMC
April 2015

Fine mapping in the MHC region accounts for 18% additional genetic risk for celiac disease.

Nat Genet 2015 Jun 20;47(6):577-8. Epub 2015 Apr 20.

1] Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.

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http://www.nature.com/articles/ng.3268
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http://dx.doi.org/10.1038/ng.3268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449296PMC
June 2015

TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits.

PLoS One 2015 7;10(4):e0122271. Epub 2015 Apr 7.

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.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122271PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388675PMC
March 2016

Rare genetic variants in the CFI gene are associated with advanced age-related macular degeneration and commonly result in reduced serum factor I levels.

Hum Mol Genet 2015 Jul 18;24(13):3861-70. Epub 2015 Mar 18.

Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA, Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA and Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, USA

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http://dx.doi.org/10.1093/hmg/ddv091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459386PMC
July 2015

Familial aggregation of arthritis-related diseases in seropositive and seronegative rheumatoid arthritis: a register-based case-control study in Sweden.

Ann Rheum Dis 2016 Jan 12;75(1):183-9. Epub 2014 Dec 12.

Clinical Epidemiology Unit, Department of Medicine, Karolinska Institutet, Solna, Sweden Rheumatology Unit, Department of Medicine, Karolinska Institutet, Solna, Sweden.

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http://dx.doi.org/10.1136/annrheumdis-2014-206133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465879PMC
January 2016

A role for noncoding variation in schizophrenia.

Cell Rep 2014 Nov 6;9(4):1417-29. Epub 2014 Nov 6.

Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(14)00869-9.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471400869
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http://dx.doi.org/10.1016/j.celrep.2014.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255904PMC
November 2014

A novel test for recessive contributions to complex diseases implicates Bardet-Biedl syndrome gene BBS10 in idiopathic type 2 diabetes and obesity.

Am J Hum Genet 2014 Nov 16;95(5):509-20. Epub 2014 Oct 16.

Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297140039
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http://dx.doi.org/10.1016/j.ajhg.2014.09.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4225638PMC
November 2014

Variation at HLA-DRB1 is associated with resistance to enteric fever.

Nat Genet 2014 Dec 10;46(12):1333-6. Epub 2014 Nov 10.

1] Genome Institute of Singapore, Singapore. [2] Singapore Eye Research Institute, Singapore. [3] Saw Swee Hock School of Public Health, National University of Singapore, Singapore. [4] Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. [5] Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

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http://dx.doi.org/10.1038/ng.3143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099079PMC
December 2014

Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes.

Am J Hum Genet 2014 Aug 31;95(2):162-72. Epub 2014 Jul 31.

Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, University of Manchester, Manchester M13 9PT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129407PMC
August 2014