Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest.
Identifieur interne : 004688 ( Ncbi/Merge ); précédent : 004687; suivant : 004689Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest.
Auteurs : D J Pappas [États-Unis] ; A. Lizee [États-Unis] ; V. Paunic [États-Unis] ; K R Beutner [États-Unis] ; A. Motyer [Australie] ; D. Vukcevic [Australie] ; S. Leslie [Australie] ; J. Biesiada [États-Unis] ; J. Meller [États-Unis] ; K D Taylor [États-Unis] ; X. Zheng [États-Unis] ; L P Zhao [États-Unis] ; P-A Gourraud [États-Unis] ; J A Hollenbach [États-Unis] ; S J Mack [États-Unis] ; M. Maiers [États-Unis]Source :
- The pharmacogenomics journal [ 1473-1150 ] ; 2017.
Abstract
Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable improvement (+3.2%) for HLA-DRB1. As the HLA complex is highly relevant to the study of human health and disease, a standardized assessment of SNP-based HLA imputation methods is crucial for advancing genomic research. Considerable room remains for the improvement of HLA-B and especially HLA-DRB1 imputation methods, and no imputation method is as accurate as molecular genotyping. The application of large, ancestrally diverse HLA and SNP reference data sets and multiple imputation methods has the potential to make SNP-based HLA imputation methods a tractable option for determining HLA genotypes.The Pharmacogenomics Journal advance online publication, 25 April 2017; doi:10.1038/tpj.2017.7.
DOI: 10.1038/tpj.2017.7
PubMed: 28440342
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Lizee</name><affiliation wicri:level="2"><nlm:affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, University of California, San Francisco, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Paunic, V" sort="Paunic, V" uniqKey="Paunic V" first="V" last="Paunic">V. Paunic</name><affiliation wicri:level="2"><nlm:affiliation>Bioinformatics Research Department, National Marrow Donor Program, Minneapolis, MN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Research Department, National Marrow Donor Program, Minneapolis, MN</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author><author><name sortKey="Beutner, K R" sort="Beutner, K R" uniqKey="Beutner K" first="K R" last="Beutner">K R Beutner</name><affiliation wicri:level="2"><nlm:affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, University of California, San Francisco, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Motyer, A" sort="Motyer, A" uniqKey="Motyer A" first="A" last="Motyer">A. Motyer</name><affiliation wicri:level="4"><nlm:affiliation>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC</wicri:regionArea><orgName type="university">Université de Melbourne</orgName><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Vukcevic, D" sort="Vukcevic, D" uniqKey="Vukcevic D" first="D" last="Vukcevic">D. Vukcevic</name><affiliation wicri:level="4"><nlm:affiliation>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC</wicri:regionArea><orgName type="university">Université de Melbourne</orgName><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Leslie, S" sort="Leslie, S" uniqKey="Leslie S" first="S" last="Leslie">S. Leslie</name><affiliation wicri:level="4"><nlm:affiliation>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC</wicri:regionArea><orgName type="university">Université de Melbourne</orgName><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Biesiada, J" sort="Biesiada, J" uniqKey="Biesiada J" first="J" last="Biesiada">J. Biesiada</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center & Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center & Department of Environmental Health, University of Cincinnati, Cincinnati, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Meller, J" sort="Meller, J" uniqKey="Meller J" first="J" last="Meller">J. Meller</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center & Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center & Department of Environmental Health, University of Cincinnati, Cincinnati, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Taylor, K D" sort="Taylor, K D" uniqKey="Taylor K" first="K D" last="Taylor">K D Taylor</name><affiliation wicri:level="2"><nlm:affiliation>Los Angeles Biomedical Research Institute, Torrance, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Los Angeles Biomedical Research Institute, Torrance, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zheng, X" sort="Zheng, X" uniqKey="Zheng X" first="X" last="Zheng">X. Zheng</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biostatistics, University of Washington, Seattle, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biostatistics, University of Washington, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Zhao, L P" sort="Zhao, L P" uniqKey="Zhao L" first="L P" last="Zhao">L P Zhao</name><affiliation wicri:level="2"><nlm:affiliation>Fred Hutchinson Cancer Research Center, Seattle, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Fred Hutchinson Cancer Research Center, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Gourraud, P A" sort="Gourraud, P A" uniqKey="Gourraud P" first="P-A" last="Gourraud">P-A Gourraud</name><affiliation wicri:level="2"><nlm:affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, University of California, San Francisco, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Hollenbach, J A" sort="Hollenbach, J A" uniqKey="Hollenbach J" first="J A" last="Hollenbach">J A Hollenbach</name><affiliation wicri:level="2"><nlm:affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, University of California, San Francisco, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Mack, S J" sort="Mack, S J" uniqKey="Mack S" first="S J" last="Mack">S J Mack</name><affiliation wicri:level="2"><nlm:affiliation>Center for Genetics, Children's Hospital Research Institute, Oakland, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genetics, Children's Hospital Research Institute, Oakland, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Maiers, M" sort="Maiers, M" uniqKey="Maiers M" first="M" last="Maiers">M. Maiers</name><affiliation wicri:level="2"><nlm:affiliation>Bioinformatics Research Department, National Marrow Donor Program, Minneapolis, MN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics Research Department, National Marrow Donor Program, Minneapolis, MN</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author></analytic><series><title level="j">The pharmacogenomics journal</title><idno type="eISSN">1473-1150</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable improvement (+3.2%) for HLA-DRB1. As the HLA complex is highly relevant to the study of human health and disease, a standardized assessment of SNP-based HLA imputation methods is crucial for advancing genomic research. Considerable room remains for the improvement of HLA-B and especially HLA-DRB1 imputation methods, and no imputation method is as accurate as molecular genotyping. The application of large, ancestrally diverse HLA and SNP reference data sets and multiple imputation methods has the potential to make SNP-based HLA imputation methods a tractable option for determining HLA genotypes.The Pharmacogenomics Journal advance online publication, 25 April 2017; doi:10.1038/tpj.2017.7.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">28440342</PMID><DateCreated><Year>2017</Year><Month>04</Month><Day>25</Day></DateCreated><DateRevised><Year>2017</Year><Month>10</Month><Day>27</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1473-1150</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2017</Year><Month>Apr</Month><Day>25</Day></PubDate></JournalIssue><Title>The pharmacogenomics journal</Title><ISOAbbreviation>Pharmacogenomics J.</ISOAbbreviation></Journal><ArticleTitle>Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1038/tpj.2017.7</ELocationID><Abstract><AbstractText>Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable improvement (+3.2%) for HLA-DRB1. As the HLA complex is highly relevant to the study of human health and disease, a standardized assessment of SNP-based HLA imputation methods is crucial for advancing genomic research. Considerable room remains for the improvement of HLA-B and especially HLA-DRB1 imputation methods, and no imputation method is as accurate as molecular genotyping. The application of large, ancestrally diverse HLA and SNP reference data sets and multiple imputation methods has the potential to make SNP-based HLA imputation methods a tractable option for determining HLA genotypes.The Pharmacogenomics Journal advance online publication, 25 April 2017; doi:10.1038/tpj.2017.7.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pappas</LastName><ForeName>D J</ForeName><Initials>DJ</Initials><AffiliationInfo><Affiliation>Center for Genetics, Children's Hospital Research Institute, Oakland, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lizee</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paunic</LastName><ForeName>V</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Bioinformatics Research Department, National Marrow Donor Program, Minneapolis, MN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Beutner</LastName><ForeName>K R</ForeName><Initials>KR</Initials><AffiliationInfo><Affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Motyer</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Data Science, Murdoch Childrens Research Institute, Melbourne, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vukcevic</LastName><ForeName>D</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Data Science, Murdoch Childrens Research Institute, Melbourne, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leslie</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centre for Systems Genomics, Schools of Mathematics and Statistics, and BioSciences, The University of Melbourne, Melbourne, VIC, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Data Science, Murdoch Childrens Research Institute, Melbourne, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Biesiada</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center & Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meller</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center & Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>K D</ForeName><Initials>KD</Initials><AffiliationInfo><Affiliation>Los Angeles Biomedical Research Institute, Torrance, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>X</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Biostatistics, University of Washington, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>L P</ForeName><Initials>LP</Initials><AffiliationInfo><Affiliation>Fred Hutchinson Cancer Research Center, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gourraud</LastName><ForeName>P-A</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>ATIP-Avenir Team UMR Inserm, 1064, Nantes, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Nantes University Hospital Department of Public Health, Nantes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hollenbach</LastName><ForeName>J A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Department of Neurology, University of California, San Francisco, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mack</LastName><ForeName>S J</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>Center for Genetics, Children's Hospital Research Institute, Oakland, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Maiers</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Bioinformatics Research Department, National Marrow Donor Program, Minneapolis, MN, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 NS049477</GrantID><Acronym>NS</Acronym><Agency>NINDS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P01 GM099568</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 NS076492</GrantID><Acronym>NS</Acronym><Agency>NINDS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U01 AI067068</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 NS046297</GrantID><Acronym>NS</Acronym><Agency>NINDS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM109030</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U19 AI067152</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Pharmacogenomics J</MedlineTA><NlmUniqueID>101083949</NlmUniqueID><ISSNLinking>1470-269X</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Hum Mol Genet. 2012 Oct 15;21(R1):R29-36</RefSource><PMID Version="1">22976473</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bone Marrow Transplant. 2014 Jun;49(6):850-1</RefSource><PMID Version="1">24566707</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Science. 2002 Apr 12;296(5566):261-2</RefSource><PMID Version="1">11954565</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Rev Genet. 2005 Feb;6(2):95-108</RefSource><PMID Version="1">15716906</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Rev Genet. 2013 Sep;14(9):661-73</RefSource><PMID Version="1">23917628</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Trends Genet. 2012 Oct;28(10):480-6</RefSource><PMID Version="1">22867968</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Tissue Antigens. 2005 Aug;66(2):114-24</RefSource><PMID Version="1">16029431</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Int J Immunogenet. 2016 Dec;43(6):369-375</RefSource><PMID Version="1">27774761</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2012 Nov 1;491(7422):56-65</RefSource><PMID Version="1">23128226</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Immunol. 1992 Jan 1;148(1):249-58</RefSource><PMID Version="1">1727870</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Immunol. 1989 Jun 1;142(11):4041-5</RefSource><PMID Version="1">2785571</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2013 Jun 06;8(6):e64683</RefSource><PMID Version="1">23762245</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Hum Immunol. 2008 Jul;69(7):443-64</RefSource><PMID Version="1">18638659</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Pharmacogenomics. 2012 Aug;13(11):1285-306</RefSource><PMID Version="1">22920398</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Pharmacogenomics J. 2015 Dec;15(6):530-7</RefSource><PMID Version="1">25707395</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Hum Mol Genet. 2014 Aug 15;23(16):4443-51</RefSource><PMID Version="1">24698974</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2014 Jan;42(Database issue):D1001-6</RefSource><PMID Version="1">24316577</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Rev Genet. 2008 May;9(5):356-69</RefSource><PMID Version="1">18398418</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2014 Jul 02;9(7):e97282</RefSource><PMID Version="1">24988075</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2013 Jan;41(Database issue):D1222-7</RefSource><PMID Version="1">23080122</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS Genet. 2006 Jan;2(1):e9</RefSource><PMID Version="1">16440057</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Hum Genet. 2008 Jan;82(1):48-56</RefSource><PMID Version="1">18179884</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Hum Genet. 2013 Nov 7;93(5):984-93</RefSource><PMID Version="1">24183452</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2011 Aug 1;27(15):2156-8</RefSource><PMID Version="1">21653522</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Eur J Immunogenet. 1991 Feb-Apr;18(1-2):33-55</RefSource><PMID Version="1">2069944</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):4134-9</RefSource><PMID Version="1">15743917</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Tissue Antigens. 2010 Apr;75(4):291-455</RefSource><PMID Version="1">20356336</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>N Engl J Med. 2011 Mar 24;364(12):1134-43</RefSource><PMID Version="1">21428769</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2010 Feb 15;26(4):445-55</RefSource><PMID Version="1">20053841</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2014 Jan 29;15:81</RefSource><PMID Version="1">24476119</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genet Epidemiol. 2011 Feb;35(2):85-92</RefSource><PMID Version="1">21254215</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2006 Oct;38(10):1166-72</RefSource><PMID Version="1">16998491</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Front Biosci. 1998 Jul 27;3:d739-45</RefSource><PMID Version="1">9675159</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genet. 2014 Jun 16;15:72</RefSource><PMID Version="1">24935557</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Adv Immunol. 2016;129:175-249</RefSource><PMID Version="1">26791860</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2005 Nov;15(11):1592-3</RefSource><PMID Version="1">16251469</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genet. 2011 Apr 25;12:39</RefSource><PMID Version="1">21518453</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Lancet. 2002 Mar 2;359(9308):727-32</RefSource><PMID Version="1">11888582</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Int J Immunogenet. 2008 Jun;35(3):179-92</RefSource><PMID Version="1">18397301</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Tissue Antigens. 2012 Jul;80(1):1-11</RefSource><PMID Version="1">22651253</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS Comput Biol. 2013;9(2):e1002877</RefSource><PMID Version="1">23459081</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Pharmacogenomics J. 2014 Apr;14(2):192-200</RefSource><PMID Version="1">23712092</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2011 Apr 1;27(7):968-72</RefSource><PMID Version="1">21300701</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS Genet. 2008 Apr 25;4(4):e1000024</RefSource><PMID Version="1">18437207</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Tissue Antigens. 2014 May;83(5):350-5</RefSource><PMID Version="1">24666112</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4180-5</RefSource><PMID Version="1">15024131</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Tissue Antigens. 2013 Apr;81(4):194-203</RefSource><PMID Version="1">23510415</PMID></CommentsCorrections></CommentsCorrectionsList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>06</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>12</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>02</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="pmc-release"><Year>2018</Year><Month>10</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>4</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28440342</ArticleId><ArticleId IdType="pii">tpj20177</ArticleId><ArticleId IdType="doi">10.1038/tpj.2017.7</ArticleId><ArticleId IdType="pmc">PMC5656547</ArticleId><ArticleId IdType="mid">NIHMS879450</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>États-Unis</li></country><region><li>Californie</li><li>Minnesota</li><li>Ohio</li><li>Victoria (État)</li><li>Washington (État)</li></region><settlement><li>Melbourne</li><li>Seattle</li></settlement><orgName><li>Université de Melbourne</li><li>Université de Washington</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Pappas, D J" sort="Pappas, D J" uniqKey="Pappas D" first="D J" last="Pappas">D J Pappas</name></region><name sortKey="Beutner, K R" sort="Beutner, K R" uniqKey="Beutner K" first="K R" last="Beutner">K R Beutner</name><name sortKey="Biesiada, J" sort="Biesiada, J" uniqKey="Biesiada J" first="J" last="Biesiada">J. Biesiada</name><name sortKey="Gourraud, P A" sort="Gourraud, P A" uniqKey="Gourraud P" first="P-A" last="Gourraud">P-A Gourraud</name><name sortKey="Hollenbach, J A" sort="Hollenbach, J A" uniqKey="Hollenbach J" first="J A" last="Hollenbach">J A Hollenbach</name><name sortKey="Lizee, A" sort="Lizee, A" uniqKey="Lizee A" first="A" last="Lizee">A. Lizee</name><name sortKey="Mack, S J" sort="Mack, S J" uniqKey="Mack S" first="S J" last="Mack">S J Mack</name><name sortKey="Maiers, M" sort="Maiers, M" uniqKey="Maiers M" first="M" last="Maiers">M. Maiers</name><name sortKey="Meller, J" sort="Meller, J" uniqKey="Meller J" first="J" last="Meller">J. Meller</name><name sortKey="Paunic, V" sort="Paunic, V" uniqKey="Paunic V" first="V" last="Paunic">V. Paunic</name><name sortKey="Taylor, K D" sort="Taylor, K D" uniqKey="Taylor K" first="K D" last="Taylor">K D Taylor</name><name sortKey="Zhao, L P" sort="Zhao, L P" uniqKey="Zhao L" first="L P" last="Zhao">L P Zhao</name><name sortKey="Zheng, X" sort="Zheng, X" uniqKey="Zheng X" first="X" last="Zheng">X. Zheng</name></country><country name="Australie"><region name="Victoria (État)"><name sortKey="Motyer, A" sort="Motyer, A" uniqKey="Motyer A" first="A" last="Motyer">A. Motyer</name></region><name sortKey="Leslie, S" sort="Leslie, S" uniqKey="Leslie S" first="S" last="Leslie">S. Leslie</name><name sortKey="Vukcevic, D" sort="Vukcevic, D" uniqKey="Vukcevic D" first="D" last="Vukcevic">D. Vukcevic</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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