{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T17:46:16Z","timestamp":1764783976323,"version":"3.37.3"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100004562","name":"Minist\u00e8re de l'Education Nationale, de l'Enseignement Superieur et de la Recherche","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004562","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1746-1","type":"journal-article","created":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T05:25:37Z","timestamp":1499750737000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["HLA-check: evaluating HLA data from SNP information"],"prefix":"10.1186","volume":"18","author":[{"given":"Marc","family":"Jeanmougin","sequence":"first","affiliation":[]},{"given":"Josselin","family":"Noirel","sequence":"additional","affiliation":[]},{"given":"C\u00e9dric","family":"Coulonges","sequence":"additional","affiliation":[]},{"given":"Jean-Fran\u00e7ois","family":"Zagury","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,7,11]]},"reference":[{"key":"1746_CR1","first-page":"11","volume":"1","author":"CA Janeway","year":"1997","unstructured":"Janeway CA, Travers P, Walport M, Shlomchik MJ. Immunobiology: the immune system in health and disease. Curr Biol. 1997; 1:11.","journal-title":"Curr Biol"},{"issue":"7","key":"1746_CR2","doi-asserted-by":"crossref","first-page":"453","DOI":"10.2174\/138920207783591690","volume":"8","author":"MJ Simmonds","year":"2007","unstructured":"Simmonds MJ, Gough SCL. The HLA region and autoimmune disease: associations and mechanisms of action. Curr Genomics. 2007; 8(7):453\u201365.","journal-title":"Curr Genomics"},{"issue":"4","key":"1746_CR3","doi-asserted-by":"crossref","first-page":"e1000024","DOI":"10.1371\/journal.pgen.1000024","volume":"4","author":"MM Fernando","year":"2008","unstructured":"Fernando MM, Stevens CR, Walsh EC, De Jager PL, Goyette P, Plenge RM, Rioux JD. Defining the role of the MHC in autoimmunity: a review and pooled analysis. PLoS Genet. 2008; 4(4):e1000024.","journal-title":"PLoS Genet"},{"issue":"1","key":"1746_CR4","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1146\/annurev.immunol.16.1.593","volume":"16","author":"AV Hill","year":"1998","unstructured":"Hill AV. The immunogenetics of human infectious diseases. Annu Rev Immunol. 1998; 16(1):593\u2013617.","journal-title":"Annu Rev Immunol"},{"issue":"2","key":"1746_CR5","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1128\/CMR.00048-08","volume":"22","author":"JM Blackwell","year":"2009","unstructured":"Blackwell JM, Jamieson SE, Burgner D. HLA and infectious diseases. Clin Microbiol Rev. 2009; 22(2):370\u201385.","journal-title":"Clin Microbiol Rev"},{"issue":"1","key":"1746_CR6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.blre.2012.10.001","volume":"27","author":"EW Petersdorf","year":"2013","unstructured":"Petersdorf EW. Genetics of graft-versus-host disease: the major histocompatibility complex. Blood Rev. 2013; 27(1):1\u201312.","journal-title":"Blood Rev"},{"issue":"D1","key":"1746_CR7","doi-asserted-by":"crossref","first-page":"D423","DOI":"10.1093\/nar\/gku1161","volume":"43","author":"J Robinson","year":"2015","unstructured":"Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SGE. The IPD and IMGT\/HLA database: allele variant databases. Nucleic Acids Res. 2015; 43(D1):D423-31.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"1746_CR8","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/hmg\/ddg066","volume":"12","author":"T Ahmad","year":"2003","unstructured":"Ahmad T, Neville M, Marshall SE, Armuzzi A, Mulcahy-Hawes K, Crawshaw J, Walton R. Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. Hum Mol Genet. 2003; 12(6):647\u201356.","journal-title":"Hum Mol Genet"},{"key":"1746_CR9","doi-asserted-by":"crossref","unstructured":"Delaneau O, Zagury JF. Haplotype inference. Data Production Anal Population Genomics: Methods Protoc. 2012;:177\u201396. http:\/\/www.springer.com\/in\/book\/9781617798696 .","DOI":"10.1007\/978-1-61779-870-2_11"},{"issue":"1","key":"1746_CR10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1399-0039.2012.01881.x","volume":"80","author":"H Erlich","year":"2012","unstructured":"Erlich H. HLA DNA typing: past, present, and future. Tissue antigens. 2012; 80(1):1\u201311.","journal-title":"Tissue antigens"},{"issue":"R1","key":"1746_CR11","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1093\/hmg\/dds384","volume":"21","author":"PI de Bakker","year":"2012","unstructured":"de Bakker PI, Raychaudhuri S. Interrogating the major histocompatibility complex with high-throughput genomics. Hum Mol Genet. 2012; 21(R1):R29\u201336.","journal-title":"Hum Mol Genet"},{"issue":"12","key":"1746_CR12","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1016\/j.humimm.2015.09.015","volume":"76","author":"N Cereb","year":"2015","unstructured":"Cereb N, Kim HR, Ryu J, Yang SY. Advances in DNA sequencing technologies for high resolution HLA typing. Human Immunol. 2015; 76(12):923\u201327.","journal-title":"Human Immunol"},{"issue":"6","key":"1746_CR13","doi-asserted-by":"crossref","first-page":"e64683","DOI":"10.1371\/journal.pone.0064683","volume":"8","author":"X Jia","year":"2013","unstructured":"Jia X, Han B, Onengut-Gumuscu S, Chen WM, Concannon PJ, Rich SS, de Bakker PI. Imputing amino acid polymorphisms in human leukocyte antigens. PloS ONE. 2013; 8(6):e64683.","journal-title":"PloS ONE"},{"issue":"2","key":"1746_CR14","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1038\/tpj.2013.18","volume":"14","author":"X Zheng","year":"2014","unstructured":"Zheng X, Shen J, Cox C, Wakefield JC, Ehm MG, Nelson MR, Weir BS. HIBAG-HLA genotype imputation with attribute bagging. Pharmacogenomics J. 2014; 14(2):192.","journal-title":"Pharmacogenomics J"},{"issue":"7","key":"1746_CR15","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1093\/bioinformatics\/btr061","volume":"27","author":"AT Dilthey","year":"2011","unstructured":"Dilthey AT, Moutsianas L, Leslie S, McVean G. HLA* IMP-an integrated framework for imputing classical HLA alleles from SNP genotypes. Bioinformatics. 2011; 27(7):968\u201372.","journal-title":"Bioinformatics"},{"issue":"5","key":"1746_CR16","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1111\/tan.12343","volume":"83","author":"E Vlachopoulou","year":"2014","unstructured":"Vlachopoulou E, Lahtela E, Wennerstr\u00f6m A, Havulinna AS, Salo P, Perola M, Lokki ML. Evaluation of HLA\u2013DRB1 imputation using a Finnish dataset. Tissue Antigens. 2014; 83(5):350\u20135.","journal-title":"Tissue Antigens"},{"issue":"1 suppl","key":"1746_CR17","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1177\/1740774510373497","volume":"7","author":"JE Hilner","year":"2010","unstructured":"Hilner JE, Perdue LH, Sides EG, Pierce JJ, W\u00e4gner AM, Aldrich A, Akolkar B. Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC). Clinical Trials. 2010; 7(1 suppl):S5\u201332.","journal-title":"Clinical Trials"},{"key":"1746_CR18","doi-asserted-by":"crossref","unstructured":"Rich SS. Special Issue: Fine mapping of the MHC Region for Type 1 diabetes genes. Diabetes Obes Metab 11.s1. 2009. https:\/\/www.cabdirect.org\/cabdirect\/abstract\/20093046189 .","DOI":"10.1111\/j.1463-1326.2008.00996.x"},{"issue":"7","key":"1746_CR19","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1038\/ng.3312","volume":"47","author":"I Lappalainen","year":"2015","unstructured":"Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Saunders G, Laurent T. The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet. 2015; 47(7):692\u20135.","journal-title":"Nat Genet"},{"issue":"6","key":"1746_CR20","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1111\/j.1399-0039.2009.01245.x","volume":"73","author":"Y Xiao","year":"2009","unstructured":"Xiao Y, Lazaro AM, Masaberg C, Haagenson M, Vierra\u2013Green C, Spellman S, Hurley CK. Evaluating the potential impact of mismatches outside the antigen recognition site in unrelated hematopoietic stem cell transplantation: HLA\u2013DRB1* 1454 and DRB1* 140101. Tissue Antigens. 2009; 73(6):595\u20138.","journal-title":"Tissue Antigens"},{"key":"1746_CR21","doi-asserted-by":"crossref","unstructured":"1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015; 526(7571):68\u201374.","DOI":"10.1038\/nature15393"},{"issue":"2","key":"1746_CR22","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/nmeth.1785","volume":"9","author":"O Delaneau","year":"2012","unstructured":"Delaneau O, Marchini J, Zagury JF. A linear complexity phasing method for thousands of genomes. Nat Methods. 2012; 9(2):179\u201381.","journal-title":"Nat Methods"},{"issue":"8","key":"1746_CR23","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/ng.2354","volume":"44","author":"B Howie","year":"2012","unstructured":"Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 2012; 44(8):955\u201395.","journal-title":"Nat Genet"},{"key":"1746_CR24","doi-asserted-by":"crossref","unstructured":"1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015; 526(7571):68\u201374.","DOI":"10.1038\/nature15393"},{"issue":"10","key":"1746_CR25","doi-asserted-by":"crossref","first-page":"e1005151","DOI":"10.1371\/journal.pcbi.1005151","volume":"12","author":"AT Dilthey","year":"2016","unstructured":"Dilthey AT, Gourraud PA, Mentzer AJ, Cereb N, Iqbal Z, McVean G. High-Accuracy HLA type inference from whole-genome sequencing data using population reference graphs. PLoS Comput Biol. 2016; 12(10):e1005151.","journal-title":"PLoS Comput Biol"},{"key":"1746_CR26","doi-asserted-by":"crossref","unstructured":"Pappas DJ, Lizee A, Paunic V, Beutner KR, Motyer A, Vukcevic D, Zheng X. Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest. Pharmacogenomics J. 2017. http:\/\/dx.doi.org\/10.1038\/tpj.2017.7 . https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28440342.","DOI":"10.1038\/tpj.2017.7"},{"key":"1746_CR27","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1111\/j.1399-0039.2010.01466.x","volume":"75","author":"SGE Marsh","year":"2010","unstructured":"Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fern\u00e1ndez-Vina M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Mayr WR, Maiers M, M\u00fcller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system. Tissue Antigens. 2010; 75:291\u2013455.","journal-title":"Tissue Antigens"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1746-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,29]],"date-time":"2019-09-29T08:09:50Z","timestamp":1569744590000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1746-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,11]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1746"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1746-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2017,7,11]]},"article-number":"334"}}