PMID- 32681667
OWN - NLM
STAT- MEDLINE
DCOM- 20210531
LR  - 20221207
IS  - 1098-2272 (Electronic)
IS  - 0741-0395 (Print)
IS  - 0741-0395 (Linking)
VI  - 44
IP  - 7
DP  - 2020 Oct
TI  - SNP-HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting 
      MHC-centric analyses in genomics.
PG  - 733-740
LID - 10.1002/gepi.22334 [doi]
AB  - Genome-wide associations studies have repeatedly identified the major 
      histocompatibility complex genomic region (6p21.3) as key in immune pathologies. 
      Researchers have also aimed to extend the biological interpretation of 
      associations by focusing directly on human leukocyte antigen (HLA) polymorphisms 
      and their combination as haplotypes. To circumvent the effort and high costs of 
      HLA typing, statistical solutions have been developed to infer HLA alleles from 
      single-nucleotide polymorphism (SNP) genotyping data. Though HLA imputation 
      methods have been developed, no unified effort has yet been undertaken to share 
      large and diverse imputation models, or to improve methods. By training the HIBAG 
      software on SNP + HLA data generated by the Consortium on Asthma among 
      African-ancestry Populations in the Americas (CAAPA) to create reference panels, 
      we highlighted the importance of (a) the number of individuals in reference 
      panels, with a twofold increase in accuracy (from 10 to 100 individuals) and (b) 
      the number of SNPs, with a 1.5-fold increase in accuracy (from 500 to 24,504 
      SNPs). Results showed improved accuracy with CAAPA compared to the African 
      American models available in HIBAG, highlighting the need for precise 
      population-matching. The SNP-HLA Reference Consortium is an international 
      endeavor to gather data, enhance HLA imputation and broaden access to highly 
      accurate imputation models for the immunogenomics community.
CI  - (c) 2020 The Authors. Genetic Epidemiology published by Wiley Periodicals LLC.
FAU - Vince, Nicolas
AU  - Vince N
AUID- ORCID: 0000-0002-3767-6210
AD  - Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Universite 
      de Nantes, CHU Nantes, Inserm, Nantes, France.
FAU - Douillard, Venceslas
AU  - Douillard V
AUID- ORCID: 0000-0002-6762-4083
AD  - Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Universite 
      de Nantes, CHU Nantes, Inserm, Nantes, France.
FAU - Geffard, Estelle
AU  - Geffard E
AD  - Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Universite 
      de Nantes, CHU Nantes, Inserm, Nantes, France.
FAU - Meyer, Diogo
AU  - Meyer D
AD  - University of Sao Paulo, Sao Paulo, Brazil.
FAU - Castelli, Erick C
AU  - Castelli EC
AD  - UNESP-Universidade Estadual Paulista, Botucatu, Sao Paulo, Brazil.
FAU - Mack, Steven J
AU  - Mack SJ
AD  - Department of Pediatrics, University of California, San Francisco, UCSF Benioff 
      Children's Hospital Oakland, Oakland, California.
FAU - Limou, Sophie
AU  - Limou S
AD  - Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Universite 
      de Nantes, CHU Nantes, Inserm, Nantes, France.
AD  - Ecole Centrale de Nantes, Nantes, France.
FAU - Gourraud, Pierre-Antoine
AU  - Gourraud PA
AD  - Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Universite 
      de Nantes, CHU Nantes, Inserm, Nantes, France.
LA  - eng
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20200718
PL  - United States
TA  - Genet Epidemiol
JT  - Genetic epidemiology
JID - 8411723
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Black or African American/*genetics
MH  - Alleles
MH  - Asthma/genetics
MH  - Gene Frequency/genetics
MH  - Genome, Human/*genetics
MH  - Genomics
MH  - Genotype
MH  - HLA Antigens/*genetics
MH  - Haplotypes/genetics
MH  - Humans
MH  - Information Dissemination
MH  - Models, Genetic
MH  - Polymorphism, Single Nucleotide/*genetics
MH  - White People/genetics
PMC - PMC7540691
OTO - NOTNLM
OT  - HLA
OT  - SNP
OT  - consortium
OT  - imputation
COIS- The authors declare that there are no conflict of interests.
EDAT- 2020/07/19 06:00
MHDA- 2021/06/01 06:00
PMCR- 2020/10/07
CRDT- 2020/07/19 06:00
PHST- 2020/01/06 00:00 [received]
PHST- 2020/06/19 00:00 [revised]
PHST- 2020/07/03 00:00 [accepted]
PHST- 2020/07/19 06:00 [pubmed]
PHST- 2021/06/01 06:00 [medline]
PHST- 2020/07/19 06:00 [entrez]
PHST- 2020/10/07 00:00 [pmc-release]
AID - GEPI22334 [pii]
AID - 10.1002/gepi.22334 [doi]
PST - ppublish
SO  - Genet Epidemiol. 2020 Oct;44(7):733-740. doi: 10.1002/gepi.22334. Epub 2020 Jul 
      18.