A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response.
Alleles
Amino Acids
/ genetics
Gene Frequency
/ genetics
Genetic Variation
Genetics, Population
HIV Infections
/ genetics
HIV-1
/ genetics
HLA Antigens
/ genetics
Haplotypes
/ genetics
Host-Pathogen Interactions
/ genetics
Humans
Linkage Disequilibrium
/ genetics
Physical Chromosome Mapping
Reference Standards
Selection, Genetic
Viral Load
Journal
Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
received:
14
07
2020
accepted:
02
08
2021
entrez:
6
10
2021
pubmed:
7
10
2021
medline:
10
11
2021
Statut:
ppublish
Résumé
Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.
Identifiants
pubmed: 34611364
doi: 10.1038/s41588-021-00935-7
pii: 10.1038/s41588-021-00935-7
pmc: PMC8959399
mid: NIHMS1730054
doi:
Substances chimiques
Amino Acids
0
HLA Antigens
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1504-1516Subventions
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Investigateurs
Namiko Abe
(N)
Gonçalo Abecasis
(G)
Francois Aguet
(F)
Christine Albert
(C)
Laura Almasy
(L)
Alvaro Alonso
(A)
Seth Ament
(S)
Peter Anderson
(P)
Pramod Anugu
(P)
Deborah Applebaum-Bowden
(D)
Kristin Ardlie
(K)
None Dan Arking
Donna K Arnett
(DK)
Allison Ashley-Koch
(A)
Stella Aslibekyan
(S)
Tim Assimes
(T)
Paul Auer
(P)
Dimitrios Avramopoulos
(D)
Najib Ayas
(N)
Adithya Balasubramanian
(A)
John Barnard
(J)
Kathleen Barnes
(K)
R Graham Barr
(RG)
Emily Barron-Casella
(E)
Lucas Barwick
(L)
Terri Beaty
(T)
Gerald Beck
(G)
Diane Becker
(D)
Lewis Becker
(L)
Rebecca Beer
(R)
Amber Beitelshees
(A)
Emelia Benjamin
(E)
Takis Benos
(T)
Marcos Bezerra
(M)
Larry Bielak
(L)
Joshua Bis
(J)
Thomas Blackwell
(T)
John Blangero
(J)
Eric Boerwinkle
(E)
Donald W Bowden
(DW)
Russell Bowler
(R)
Jennifer Brody
(J)
Ulrich Broeckel
(U)
Jai Broome
(J)
Deborah Brown
(D)
Karen Bunting
(K)
Esteban Burchard
(E)
Carlos Bustamante
(C)
Erin Buth
(E)
Brian Cade
(B)
Jonathan Cardwell
(J)
Vincent Carey
(V)
Julie Carrier
(J)
Cara Carty
(C)
Richard Casaburi
(R)
Juan P Casas Romero
(JPC)
James Casella
(J)
Peter Castaldi
(P)
Mark Chaffin
(M)
Christy Chang
(C)
Yi-Cheng Chang
(YC)
Daniel Chasman
(D)
Sameer Chavan
(S)
Bo-Juen Chen
(BJ)
Wei-Min Chen
(WM)
Seung Hoan Choi
(SH)
Lee-Ming Chuang
(LM)
Mina Chung
(M)
Ren-Hua Chung
(RH)
Clary Clish
(C)
Suzy Comhair
(S)
Matthew Conomos
(M)
Elaine Cornell
(E)
Carolyn Crandall
(C)
James Crapo
(J)
L Adrienne Cupples
(LA)
Joanne Curran
(J)
Jeffrey Curtis
(J)
Brian Custer
(B)
Coleen Damcott
(C)
Dawood Darbar
(D)
Sean David
(S)
Colleen Davis
(C)
Michelle Daya
(M)
Mariza de Andrade
(M)
Lisa de Las Fuentes
(LL)
Paul de Vries
(P)
Michael DeBaun
(M)
Ranjan Deka
(R)
Dawn DeMeo
(D)
Scott Devine
(S)
Huyen Dinh
(H)
Harsha Doddapaneni
(H)
Qing Duan
(Q)
Shannon Dugan-Perez
(S)
Ravi Duggirala
(R)
Jon Peter Durda
(JP)
Susan K Dutcher
(SK)
Charles Eaton
(C)
Lynette Ekunwe
(L)
Adel El Boueiz
(AE)
Patrick Ellinor
(P)
Leslie Emery
(L)
Serpil Erzurum
(S)
Charles Farber
(C)
Jesse Farek
(J)
Tasha Fingerlin
(T)
Matthew Flickinger
(M)
Myriam Fornage
(M)
Nora Franceschini
(N)
Chris Frazar
(C)
Mao Fu
(M)
Stephanie M Fullerton
(SM)
Lucinda Fulton
(L)
Stacey Gabriel
(S)
Weiniu Gan
(W)
Shanshan Gao
(S)
Yan Gao
(Y)
Margery Gass
(M)
Heather Geiger
(H)
Bruce Gelb
(B)
Mark Geraci
(M)
Soren Germer
(S)
Robert Gerszten
(R)
Auyon Ghosh
(A)
Richard Gibbs
(R)
Chris Gignoux
(C)
Mark Gladwin
(M)
David Glahn
(D)
Stephanie Gogarten
(S)
Da-Wei Gong
(DW)
Harald Goring
(H)
Sharon Graw
(S)
Kathryn J Gray
(KJ)
Daniel Grine
(D)
Colin Gross
(C)
C Charles Gu
(CC)
Yue Guan
(Y)
Namrata Gupta
(N)
David M Haas
(DM)
Jeff Haessler
(J)
Michael Hall
(M)
Yi Han
(Y)
Patrick Hanly
(P)
Daniel Harris
(D)
Nicola L Hawley
(NL)
Jiang He
(J)
Ben Heavner
(B)
Susan Heckbert
(S)
Ryan Hernandez
(R)
David Herrington
(D)
Craig Hersh
(C)
Bertha Hidalgo
(B)
James Hixson
(J)
Brian Hobbs
(B)
John Hokanson
(J)
Elliott Hong
(E)
Karin Hoth
(K)
Chao Agnes Hsiung
(CA)
Jianhong Hu
(J)
Yi-Jen Hung
(YJ)
Haley Huston
(H)
Chii Min Hwu
(CM)
Marguerite Ryan Irvin
(MR)
Rebecca Jackson
(R)
Deepti Jain
(D)
Cashell Jaquish
(C)
Jill Johnsen
(J)
Andrew Johnson
(A)
Craig Johnson
(C)
Rich Johnston
(R)
Kimberly Jones
(K)
Hyun Min Kang
(HM)
Robert Kaplan
(R)
Sharon Kardia
(S)
Shannon Kelly
(S)
Eimear Kenny
(E)
Michael Kessler
(M)
Alyna Khan
(A)
Ziad Khan
(Z)
Wonji Kim
(W)
John Kimoff
(J)
Greg Kinney
(G)
Barbara Konkle
(B)
Charles Kooperberg
(C)
Holly Kramer
(H)
Christoph Lange
(C)
Ethan Lange
(E)
Leslie Lange
(L)
Cathy Laurie
(C)
Cecelia Laurie
(C)
Meryl LeBoff
(M)
Jiwon Lee
(J)
Sandra Lee
(S)
Wen-Jane Lee
(WJ)
Jonathon LeFaive
(J)
David Levine
(D)
None Dan Levy
Joshua Lewis
(J)
Xiaohui Li
(X)
Yun Li
(Y)
Henry Lin
(H)
Honghuang Lin
(H)
Xihong Lin
(X)
Simin Liu
(S)
Yongmei Liu
(Y)
Yu Liu
(Y)
Ruth J F Loos
(RJF)
Steven Lubitz
(S)
Kathryn Lunetta
(K)
James Luo
(J)
Ulysses Magalang
(U)
Michael Mahaney
(M)
Barry Make
(B)
Ani Manichaikul
(A)
Alisa Manning
(A)
JoAnn Manson
(J)
Lisa Martin
(L)
Melissa Marton
(M)
Susan Mathai
(S)
Rasika Mathias
(R)
Susanne May
(S)
Patrick McArdle
(P)
Merry-Lynn McDonald
(ML)
Sean McFarland
(S)
Stephen McGarvey
(S)
Daniel McGoldrick
(D)
Caitlin McHugh
(C)
Becky McNeil
(B)
Hao Mei
(H)
James Meigs
(J)
Vipin Menon
(V)
Luisa Mestroni
(L)
Ginger Metcalf
(G)
Deborah A Meyers
(DA)
Emmanuel Mignot
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