A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response
Year: 2021
Type: article
Study design: Observational Study
Source: Nature Genetics
Authors: Yang Luo, Masahiro Kanai, Wanson Choi, Xinyi Li, Saori Sakaue, Kenichi Yamamoto, Kotaro Ogawa, Maria Gutierrez-Arcelus, Peter K. Gregersen, Philip E. Stuart, James T. Elder, Lukas Forer, Sebastian Schönherr, Christian Fuchsberger, Albert V. Smith, Jacques Fellay, Mary Carrington, David W. Haas, Xiuqing Guo, Nicholette D. Palmer, Yii-Der Ida Chen, Jerome I. Rotter, Kent D. Taylor, Stephen S. Rich, Adolfo Correa, James G. Wilson, Sekar Kathiresan, Michael H. Cho, Andres Metspalu, Tonu Esko, Yukinori Okada, Buhm Han, Namiko Abe, Gonçalo Abecasis, Francois Aguet, Christine Albert, Laura Almasy, Alvaro Alonso, Seth Ament, Peter Anderson, Pramod Anugu, Deborah Applebaum-Bowden, Kristin Ardlie, Dan Arking, Donna K. Arnett, Allison Ashley-Koch, Stella Aslibekyan, Tim Assimes, Paul Auer, Dimitrios Avramopoulos, Najib Ayas, Adithya Balasubramanian, John Barnard, Kathleen Barnes, R. Graham Barr, Emily Barron-Casella, Lucas Barwick, Terri Beaty, Gerald Beck, Diane Becker, Lewis Becker, Rebecca Beer, Amber Beitelshees, Emelia Benjamin, Takis Benos, Marcos Bezerra, Larry Bielak, Joshua Bis, Thomas Blackwell, John Blangero, Eric Boerwinkle, Donald W. Bowden, Russell Bowler, Jennifer Brody, Ulrich Broeckel, Jai Broome, Deborah Brown, Karen Bunting, Esteban Burchard, Carlos Bustamante, Erin Buth, Brian Cade, Jonathan Cardwell, Vincent Carey, Julie Carrier, Cara Carty, Richard Casaburi, Juan P. Casas Romero, James Casella, Peter Castaldi, Mark Chaffin, Christy Chang, Yi-Cheng Chang, Daniel Chasman, Sameer Chavan, Bo-Juen Chen, Wei-Min Chen, Seung Hoan Choi, Lee-Ming Chuang, Mina Chung, Ren-Hua Chung, Clary Clish, Suzy Comhair, Matthew Conomos, Elaine Cornell, Carolyn Crandall, James Crapo, L. Adrienne Cupples, Joanne Curran, Jeffrey Curtis, Brian Custer, Coleen Damcott, Dawood Darbar, Sean David, Colleen Davis, Michelle Daya, Mariza de Andrade, Lisa de las Fuentes, Paul de Vries, Michael DeBaun, Ranjan Deka, Dawn DeMeo, Scott Devine, Huyen Dinh, Harsha Doddapaneni, Qing Duan, Shannon Dugan-Perez, Ravi Duggirala, Jon Peter Durda, Susan K. Dutcher, Charles Eaton, Lynette Ekunwe, Adel El Boueiz, Patrick Ellinor, Leslie Emery, Serpil Erzurum, Charles Farber, Jesse Farek, Tasha Fingerlin, Matthew Flickinger, Myriam Fornage, Nora Franceschini, Chris Frazar, Mao Fu, Stephanie M. Fullerton, Lucinda Fulton, Stacey Gabriel, Weiniu Gan, Shanshan Gao, Yan Gao, Margery Gass, Heather Geiger, Bruce Gelb, Mark Geraci, Soren Germer, Robert Gerszten, Auyon Ghosh, Richard Gibbs, Chris Gignoux, Mark Gladwin, David Glahn, Stephanie Gogarten, Da-Wei Gong, Harald Goring, Sharon Graw, Kathryn J. Gray, Daniel Grine, Colin Gross, C. Charles Gu, Yue Guan, Namrata Gupta, David M. Haas, Jeff Haessler, Michael Hall, Yi Han, Patrick Hanly, Daniel Harris, Nicola L. Hawley, Jiang He, Ben Heavner, Susan Heckbert, Ryan Hernandez, David Herrington, Craig Hersh, Bertha Hidalgo, James Hixson, Brian Hobbs, John Hokanson, Elliott Hong, Karin Hoth, Chao Hsiung, Jianhong Hu, Yi-Jen Hung, Haley Huston, Chii Min Hwu, Marguerite Ryan Irvin, Rebecca Jackson, Deepti Jain, Cashell Jaquish, Jill Johnsen, Andrew Johnson, Craig Johnson, Rich Johnston, Kimberly Jones, Hyun Min Kang, Robert Kaplan, Sharon Kardia, Shannon Kelly, Eimear Kenny, Michael Kessler, Alyna Khan, Ziad Khan, Wonji Kim, John Kimoff, Greg Kinney, Barbara Konkle, Charles Kooperberg, Holly Kramer, Christoph Lange, Ethan Lange, Leslie Lange, Cathy Laurie, Cecelia Laurie, Meryl LeBoff, Jiwon Lee, Sandra Lee, Wen-Jane Lee, Jonathon LeFaive, David Levine, Dan Levy, Joshua Lewis, Xiaohui Li, Yun Li, Henry Lin, Honghuang Lin, Xihong Lin, Simin Liu, Yongmei Liu, Yu Liu, Ruth J. F. Loos, Steven Lubitz, Kathryn Lunetta, James Luo, Ulysses Magalang, Michael Mahaney, Barry Make, Ani Manichaikul, Alisa Manning, JoAnn Manson, Lisa Martin, Melissa Marton, Susan Mathai, Rasika Mathias, Susanne May, Patrick McArdle, Merry-Lynn McDonald, Sean McFarland, Stephen McGarvey, Daniel McGoldrick, Caitlin McHugh, Becky McNeil, Hao Mei, James Meigs, Vipin Menon, Luisa Mestroni, Ginger Metcalf, Deborah A. Meyers, Emmanuel Mignot, Julie Mikulla, Nancy Min, Mollie Minear, Ryan L. Minster, Braxton D. Mitchell, Matt Moll, Zeineen Momin, May E. Montasser, Courtney Montgomery, Donna Muzny, Josyf C. Mychaleckyj, Girish Nadkarni, Rakhi Naik, Take Naseri, Pradeep Natarajan, Sergei Nekhai, Sarah C. Nelson, Bonnie Neltner, Caitlin Nessner, Deborah Nickerson, Osuji Nkechinyere, Kari North, Jeff O’Connell, Tim O’Connor, Heather Ochs-Balcom, Geoffrey Okwuonu, Allan Pack, David T. Paik, James Pankow, George Papanicolaou, Cora Parker, Gina Peloso, Juan Manuel Peralta, Marco Perez, James Perry, Ulrike Peters, Patricia Peyser, Lawrence S. Phillips, Jacob Pleiness, Toni Pollin, Wendy Post, Julia Powers Becker, Meher Preethi Boorgula, Michael Preuss, Bruce Psaty, Pankaj Qasba, Dandi Qiao, Zhaohui Qin, Nicholas Rafaels, Laura Raffield, Mahitha Rajendran, Vasan S. Ramachandran, D. C. Rao, Laura Rasmussen-Torvik, Aakrosh Ratan, Susan Redline, Robert Reed, Catherine Reeves, Elizabeth Regan, Alex Reiner, Muagututi’a Sefuiva Reupena, Ken Rice, Rebecca Robillard, Nicolas Robine, Dan Roden, Carolina Roselli, Ingo Ruczinski, Alexi Runnels, Pamela Russell, Sarah Ruuska, Kathleen Ryan, Ester Cerdeira Sabino, Danish Saleheen, Shabnam Salimi, Sejal Salvi, Steven Salzberg, Kevin Sandow, Vijay G. Sankaran, Jireh Santibanez, Karen Schwander, David Schwartz, Frank Sciurba, Christine Seidman, Jonathan Seidman, Frédéric Sériès, Vivien Sheehan, Stephanie L. Sherman, Amol Shetty, Aniket Shetty, Wayne Hui-Heng Sheu, M. Benjamin Shoemaker, Brian Silver, Edwin Silverman, Robert Skomro, Jennifer Smith, Josh Smith, Nicholas Smith, Tanja Smith, Sylvia Smoller, Beverly Snively, Michael Snyder, Tamar Sofer, Nona Sotoodehnia, Adrienne M. Stilp, Garrett Storm, Elizabeth Streeten, Jessica Lasky Su, Yun Ju Sung, Jody Sylvia, Adam Szpiro, Daniel Taliun, Hua Tang, Margaret Taub, Matthew Taylor, Simeon Taylor, Marilyn Telen, Timothy A. Thornton, Machiko Threlkeld, Lesley Tinker, David Tirschwell, Sarah Tishkoff, Hemant Tiwari, Catherine Tong, Russell Tracy, Michael Tsai, Dhananjay Vaidya, David Van Den Berg, Peter VandeHaar, Scott Vrieze, Tarik Walker, Robert Wallace, Avram Walts, Fei Fei Wang, Heming Wang, Jiongming Wang, Karol Watson, Jennifer Watt, Daniel E. Weeks, Joshua Weinstock, Bruce Weir, Scott T. Weiss, Lu-Chen Weng, Jennifer Wessel, Cristen Willer, Kayleen Williams, L. Keoki Williams, Carla Wilson, James Wilson, Lara Winterkorn, Quenna Wong, Joseph Wu, Huichun Xu, Lisa Yanek, Ivana Yang, Ketian Yu, Seyedeh Maryam Zekavat, Yingze Zhang, Snow Xueyan Zhao, Wei Zhao, Xiaofeng Zhu, Michael Zody, Sebastian Zoellner, Paul J. McLaren, Soumya Raychaudhuri
Institutions: Broad Institute, Brigham and Women's Hospital, Harvard University, Massachusetts General Hospital, Stanley Center for Psychiatric Research, The University of Osaka, Seoul National University, University of Chicago, Feinstein Institute for Medical Research, University of Michigan, Ann Arbor VA Medical Center, Innsbruck Medical University, Universität Innsbruck, Eurac Research, Institute for Biomedicine, Centre Hospitalier Universitaire Vaudois, École Polytechnique Fédérale de Lausanne, University of Lausanne, Ragon Institute of MGH, MIT and Harvard, Frederick National Laboratory for Cancer Research, National Cancer Institute, Massachusetts Institute of Technology, Meharry Medical College, Vanderbilt University Medical Center, The Lundquist Institute, Harbor–UCLA Medical Center, Wake Forest University Health Sciences, Wake Forest University, University of Virginia, University of Mississippi Medical Center, University of Tartu, New York Genome Center, Children's Hospital of Philadelphia, University of Pennsylvania, Emory University, University of Maryland, Baltimore, University of Washington, University of Mississippi, National Institutes of Health, Johns Hopkins University, University of Kentucky, Duke University, University of Alabama at Birmingham, Stanford University, University of Wisconsin–Milwaukee, Providence Health Care Research Institute, Baylor College of Medicine, Cleveland Clinic, University of Colorado Anschutz, Columbia University, Emmes (United States), National Heart, Lung, and Blood Institute, Boston University, University of Pittsburgh, The University of Texas Rio Grande Valley, The University of Texas Health Science Center at Houston, Atrium Health Wake Forest Baptist, National Jewish Health, Medical College of Wisconsin, University of California, San Francisco, University of Colorado Denver, Université de Montréal, Washington State University, University of California, Los Angeles, National Taiwan University, National Health Research Institutes, University of Vermont, Vitalant Research Institute, University of Illinois Chicago, Mayo Clinic, Washington University in St. Louis, Vanderbilt University, University of Cincinnati, University of North Carolina at Chapel Hill, Brown University, Fred Hutch Cancer Center, Icahn School of Medicine at Mount Sinai, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Mass General Brigham, Indiana University Indianapolis, University of Calgary, Yale University, Tulane University, University of Iowa, Tri-Service General Hospital, National Defense Medical Center, Bloodworks Northwest, Taichung Veterans General Hospital, Oklahoma State University Medical Center, Albert Einstein College of Medicine, McGill University, Loyola University Chicago, The Ohio State University, George Washington University, RTI International, University of Arizona, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Oklahoma Medical Research Foundation, Howard University, University at Buffalo, State University of New York, University of Minnesota, Northwestern University, University of Ottawa, Universidade de São Paulo, Université Laval, UMass Memorial Medical Center, University of Saskatchewan, University of Southern California, Henry Ford Health, Case Western Reserve University, Public Health Agency of Canada, University of Manitoba, University of Manchester, Arthritis UK
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Funders: U.S. Department of Health and Human Services, American Diabetes Association, Jackson State University, Wake Forest University, Frederick National Laboratory for Cancer Research, Mississippi State Department of Health, Northwell Health, National Institutes of Health, Japan Society for the Promotion of Science, National Institute on Aging, National Heart, Lung, and Blood Institute, National Human Genome Research Institute, National Cancer Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute of Environmental Health Sciences, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Center for Research Resources, National Center for Advancing Translational Sciences, National Institute on Minority Health and Health Disparities
Awards: ADULT AIDS CLINICAL TRIALS UNIT (AACTU), G1017297203, G1028935811, G1032411263, G1050281965, G1068660208, G1093951984, G1118287939, G1125781002, G1150504664, G1156594538, G1158968046, Multi-Ethnic Study of Atherosclerosis (MESA) Study, G1169301292, G1182793083, G119332616, G1201304535, G1203176964, G1214792496, G1225594167, G1261793039, G1269631540, G1276754516, G1294553593, G1295889178, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY-FIELD CENTER, G1324971107, G1342903740, G1386795942, G1409423729, G1412221515, G1446319095, G145303395, G1483344193, G1497137905, G1508998135, G1516086731, Stanford AIDS Clinical Trials Unit, G152041249, G1522144118, G1539384734, G1540916838, G1558725192, G1593133010, G1624947793, G1640378483, G1665045980, G16708505, G1678638035, G1686417863, UCLA Clinical and Translational Science Institute, G1711244518, G1730507467, G1740741465, G17630474, G1803853571, G183157880, G1844704720, G185513119, G1865158448, G1880761000, G1922428914, G1939689254, G1972444143, G1978423557, G1979271746, G1983464145, G2059393314, SUBCLINICAL CARDIOVASCULAR DISEASE COORDINATING CENTER, G2093356446, G2095596736, G2095942735, G2127051194, G2130928551, G2135258891, G2144938473, G215709867, G2215790005, G2221742881, G2241242742, G22458031, G2248434558, G2262782284, G2268686290, G2316258288, G232264632, G232810045, G2334180555, G2370685347, G2394140265, G2415573643, G2417647834, G2474977437, G2501702145, G2539633428, G2545476352, G2548217053, G2553282249, G2553732570, G2577056464, G2580996367, Vanderbilt CTU SARS-CoV-2 Supplement, G2644038179, G265762973, G2663518188, G2691056019, G2722674331, G2726417417, G2736197438, Identification of Psoriatic Arthritis Genes, G2737559749, G2760875884, G2779429302, G2809357584, G2833553957, G2837638605, G283874107, G284047611, G290884426, G291913881, ADULT AIDS CLINICAL TRIALS UNIT, Genetic Epidemiology of Cerebrovascular Disease and Cognition in Diabetes, G296458788, G297113894, G2989067737, G303055330, G3031339626, G3057025668, G3093995152, G3106377335, G3142995538, G3161396180, G3179975197, G324457968, G3252259982, G3256118428, UCLA Clinical and Translational Science Institute, G3392891757, G3410090833, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY--FIELD CENTER, G343705321, G3441327761, G3483687112, Linkage Analysis of Familial Psoriasis, G3501419682, G350245564, G3503792436, G3549415863, G3556086929, G3568487487, G3570589137, G3595232572, G3627259325, G3647016462, GBV-C effects on CD4 activation and expansion, G3668973775, G3676546685, G3687594596, G3692229207, Metabolic factors that control the spectrum of human tuberculosis, G370977179, G375632836, G377726100, UW Clinical HIV Integrated Research Program, G3809606526, G386607036, G3873853564, G3903846675, G390975780, G3922356, ADULT THERAPEUTIC CLINICAL TRIALS PROGRAM FOR AIDS, G3990748671, G399481048, G4036023366, G4086346382, G4086764833, G4099673573, Harvard Medical School Vaccine Clinical Trials Unit, G4118980254, G4147193711, G4186273061, G4293135095, G4296038422, G4296437920, G4309390892, G4338596594, G4400189231, Whole Genome Association Analysis of the Diabetes Heart Study, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY-ULTRASOUND, G4471225931, G4486601323, G4512137732, G4521137762, G4553935269, G4563812999, G457330776, G4585269469, G4590187187, G4649361189, G4693579409, G4711807797, G47192932, G475936976, Functional Genomics of Psoriasis, G4827249719, G483408255, G4887378724, G488872913, G4894370356, G4897018079, G492229355, G4986157935, G4988656331, University of Pittsburgh Clinical Trials Unit, G50080621, G5031627105, G5046654427, G5058294782, G5075046117, G5088122703, G5108002584, G5125637173, G5140077856, G514410172, Pharmacogenomics of HIV Therapy, ADULT THERAPEUTIC CLINICAL TRIALS PROGRAM IN AIDS, Integrated University of Puerto Rico Clinical Trials Unit, G5253921404, G5254636657, G5268332287, G5342184217, Re-annotation of large-scale human genome data by integration of statistical genetics and operations research, The University of Rochester Clinical and Translational Science Institute, G5431849782, ADULT ACTG CENTRAL GROUP, G5456679025, G5469398932, G547379174, G5478822001, G5484367322, G5527220128, G5543592212, G555405467, Seattle Vaccine Trials Unit, G5586061334, G5588634031, Center for Clinical and Translational Research, G5605591545, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY--FIELD CENTER, Genetics of Bone and Vascular Calcium in Type 2 Diabetes, G5646160752, G5647179126, G5653954166, G5654179670, G5654328532, G5737582129, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY--FIELD CENTER, G5787256936, G579045871, UCSD Department of Medicine HIV/AIDS Clinical Trials Unit, G5868276417, G5888954722, G5961507559, G596908699, Case AIDS Clinical Trials Unit, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY, G6095866717, G611940047, G6156766399, G6166306658, Philadelphia IMPAACT Clinical Trials Unit, G6186512954, G6270489734, G6359107525, G637127232, Institute for Clinical and Translational Research, G6422850347, Metabolomics of Neurocognitive Risk for Dementia in Diabetes, G650174051, G6514094751, G652183828, G6541715359, G6571475356, UNC Clinical and Translational Science Award, G6615853387, G6624517043, G66341962, G6643580741, University of Cincinnati AIDS Clinical Trials Unit- UC ACTU, G6687940712, G6742279884, G6798586005, G6812155733, G681742546, Epidemiology of cardiovascular disease in diabetes, G6856766826, G6896646558, G690901646, G6949607825, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY, G7032370290, Genetic and Genomic Dissection of Psoriatic Arthritis, G7091571603, G713258703, G7166352866, G7172347143, G7176072369, Partners Healthcare Systems/Harvard Medical School/Boston Medical Center AIDS CTU, G7249398899, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY--FIELD CENTER, G7401883790, G7433273234, G7462069030, G7526106616, G7559525041, General Clinical Research Center, G7656630962, The Vanderbilt Institute for Clinical and Translational Research (VICTR), G7807354757, G7845680141, G78770644, G7907723076, G7914201511, G7924587209, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY--EBCT READING, Clinical and Translational Science Award, G813915034, G8145863542, G818071322, G818308888, G8267425417, General Clinical Research Center, G830266829, G8330951150, G833338434, Studies of Rare Genetic Variation in the Isolated Population of Sardinia, G841832496, G842756795, G8444803071, G8487837538, HIV/AIDS Clinical Trials Unit, G8554689160, SUBCLINICAL CARDIOVASCULAR DISEASE STUDY-FIELD CENTER, Subclinical CVD in African American Type 2 Diabetics, G857487509, G8637122261, Institute of Human Virology Clinical Trials Unit, G87163782, G8751278327, G8761005068, G878552033, G8811786671, G8852914737, G89699440, Penn prevention clinical trials unit, G9000000101, G9000004549, G9000004784, G9000005043, G9000006353, G9000017360, G9000019818, G9000021980, G9000023087, G9000025517, G9000031392, G9000033427, G9000038353, G9000038858, G9000055512, G9000062084, G9000063950, G9000065698, Tennessee Center for AIDS Research (TN-CFAR), G9000102603, G9000126704, G9000140433, G9000166311, G9000170215, G9000176728, G9000177955, G9000193433, G9000212843, G9000246407, G9000270193, G9000293488, G9000313355, G9000326552, AIDS Clinical Trial Group Laboratory Center, Columbia Collaborative HIV/AIDS Clinical Trials Unit, University of North Carolina Global HIV Prevention and Treatment Clinical Trials Unit, Training Grant in Cancer Biology, G90079629, G911141979, G91260997, G926868656, G932915660, G936311976, G94668252, G957732833, G961682679, G991334795
OpenAlex ID: W3203889005