{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:14:36Z","timestamp":1772172876855,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009059","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,4]],"date-time":"2022-03-04T00:00:00Z","timestamp":1646352000000}}],"reference-count":106,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T00:00:00Z","timestamp":1645488000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R56 AI151549 & R01 AI128775"],"award-info":[{"award-number":["R56 AI151549 & R01 AI128775"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 HG010297"],"award-info":[{"award-number":["R01 HG010297"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["2004262"],"award-info":[{"award-number":["2004262"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the\n                    <jats:italic>KIR3DL1\/S1<\/jats:italic>\n                    gene that has more than 200 diverse and divergent alleles. Determination of\n                    <jats:italic>KIR3DL1\/S1<\/jats:italic>\n                    genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing\n                    <jats:italic>KIR3DL1\/S1<\/jats:italic>\n                    alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping\n                    <jats:italic>KIR3DL1\/S1<\/jats:italic>\n                    alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles &gt;1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute\n                    <jats:italic>HLA<\/jats:italic>\n                    alleles also from whole-genome SNP data, PONG allows combinatorial diversity of\n                    <jats:italic>KIR3DL1\/S1<\/jats:italic>\n                    with\n                    <jats:italic>HLA-A<\/jats:italic>\n                    and\n                    <jats:italic>-B<\/jats:italic>\n                    to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009059","type":"journal-article","created":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T13:39:20Z","timestamp":1645537160000},"page":"e1009059","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1\/S1"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3386-8159","authenticated-orcid":true,"given":"Genelle F.","family":"Harrison","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0650-5830","authenticated-orcid":true,"given":"Laura Ann","family":"Leaton","sequence":"additional","affiliation":[]},{"given":"Erica A.","family":"Harrison","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9817-3043","authenticated-orcid":true,"given":"Katherine M.","family":"Kichula","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3917-9269","authenticated-orcid":true,"given":"Marte K.","family":"Viken","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7980-5420","authenticated-orcid":true,"given":"Jonathan","family":"Shortt","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9728-6567","authenticated-orcid":true,"given":"Christopher R.","family":"Gignoux","sequence":"additional","affiliation":[]},{"given":"Benedicte A.","family":"Lie","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7780-9586","authenticated-orcid":true,"given":"Damjan","family":"Vukcevic","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3511-3470","authenticated-orcid":true,"given":"Stephen","family":"Leslie","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8370-7703","authenticated-orcid":true,"given":"Paul J.","family":"Norman","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,2,22]]},"reference":[{"issue":"1","key":"pcbi.1009059.ref001","doi-asserted-by":"crossref","first-page":"11","DOI":"10.4049\/jimmunol.0902332","article-title":"Variable NK cell receptors exemplified by human KIR3DL1\/S1","volume":"187","author":"P Parham","year":"2011","journal-title":"The Journal of 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Stern","year":"2011","journal-title":"American journal of transplantation: official journal of the American Society of Transplantation and the American Society of Transplant Surgeons"},{"issue":"15","key":"pcbi.1009059.ref051","doi-asserted-by":"crossref","first-page":"3162","DOI":"10.1182\/blood-2009-08-236943","article-title":"Donor activating KIR3DS1 is associated with decreased acute GVHD in unrelated allogeneic hematopoietic stem cell transplantation","volume":"115","author":"JM Venstrom","year":"2010","journal-title":"Blood"},{"issue":"2","key":"pcbi.1009059.ref052","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1182\/blood-2008-01-132902","article-title":"The reactivity of Bw4+ HLA-B and HLA-A alleles with KIR3DL1: implications for patient and donor suitability for haploidentical stem cell transplantations","volume":"112","author":"BA 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immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1","volume":"128","author":"MP Martin","year":"2018","journal-title":"The Journal of clinical investigation"},{"issue":"1","key":"pcbi.1009059.ref071","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.ajhg.2007.09.001","article-title":"A statistical method for predicting classical HLA alleles from SNP data","volume":"82","author":"S Leslie","year":"2008","journal-title":"American journal of human genetics"},{"issue":"2","key":"pcbi.1009059.ref072","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1002\/gepi.20549","article-title":"Predicting multiallelic genes using unphased and flanking single nucleotide polymorphisms","volume":"35","author":"SS Li","year":"2011","journal-title":"Genetic epidemiology"},{"issue":"2","key":"pcbi.1009059.ref073","doi-asserted-by":"crossref","first-page":"e1002877","DOI":"10.1371\/journal.pcbi.1002877","article-title":"Multi-population classical HLA type imputation","volume":"9","author":"A Dilthey","year":"2013","journal-title":"PLoS computational biology"},{"issue":"6","key":"pcbi.1009059.ref074","doi-asserted-by":"crossref","first-page":"e64683","DOI":"10.1371\/journal.pone.0064683","article-title":"Imputing amino acid polymorphisms in human leukocyte antigens.","volume":"8","author":"X Jia","year":"2013","journal-title":"PLoS One"},{"issue":"2","key":"pcbi.1009059.ref075","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1038\/tpj.2013.18","article-title":"HIBAG\u2014HLA genotype imputation with attribute bagging","volume":"14","author":"X Zheng","year":"2014","journal-title":"Pharmacogenomics J"},{"issue":"6","key":"pcbi.1009059.ref076","doi-asserted-by":"crossref","first-page":"2350","DOI":"10.1214\/aos\/1032181158","article-title":"Heuristics of instability and stabilization in model selection","volume":"24","author":"L. Breiman","year":"1996","journal-title":"Annals of Statistics"},{"issue":"8","key":"pcbi.1009059.ref077","doi-asserted-by":"crossref","first-page":"e1008904","DOI":"10.1371\/journal.pcbi.1008904","article-title":"High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING.","volume":"17","author":"WM Marin","year":"2021","journal-title":"PLoS computational biology"},{"issue":"7571","key":"pcbi.1009059.ref078","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"A Auton","year":"2015","journal-title":"Nature"},{"issue":"2","key":"pcbi.1009059.ref079","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.ajhg.2016.06.023","article-title":"Defining KIR and HLA class I genotypes at highest resolution via high-throughput sequencing","volume":"99","author":"PJ Norman","year":"2016","journal-title":"The American Journal of Human Genetics"},{"issue":"12","key":"pcbi.1009059.ref080","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1038\/ng.998","article-title":"Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease","volume":"43","author":"G Trynka","year":"2011","journal-title":"Nature genetics"},{"issue":"1","key":"pcbi.1009059.ref081","doi-asserted-by":"crossref","first-page":"5267","DOI":"10.1038\/s41598-020-62157-x","article-title":"Human Leukocyte Antigen alleles associated with Myalgic Encephalomyelitis\/Chronic Fatigue Syndrome (ME\/CFS).","volume":"10","author":"A Lande","year":"2020","journal-title":"Scientific reports."},{"issue":"3","key":"pcbi.1009059.ref082","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"S Purcell","year":"2007","journal-title":"American journal of human genetics"},{"key":"pcbi.1009059.ref083","doi-asserted-by":"crossref","first-page":"674778","DOI":"10.3389\/fimmu.2021.674778","article-title":"High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity","volume":"12","author":"LM Amorim","year":"2021","journal-title":"Front Immunol."},{"issue":"11","key":"pcbi.1009059.ref084","doi-asserted-by":"crossref","first-page":"e47491","DOI":"10.1371\/journal.pone.0047491","article-title":"Allele-level haplotype frequencies and pairwise linkage disequilibrium for 14 KIR loci in 506 European-American individuals","volume":"7","author":"C Vierra-Green","year":"2012","journal-title":"PLoS One"},{"issue":"10","key":"pcbi.1009059.ref085","doi-asserted-by":"crossref","first-page":"e0163973","DOI":"10.1371\/journal.pone.0163973","article-title":"Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes.","volume":"11","author":"C Vierra-Green","year":"2016","journal-title":"PLoS One."},{"key":"pcbi.1009059.ref086","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.3389\/fimmu.2018.02843","article-title":"Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations.","volume":"9","author":"I Wagner","year":"2018","journal-title":"Frontiers in immunology"},{"issue":"4","key":"pcbi.1009059.ref087","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/j.ajhg.2015.09.005","article-title":"Imputation of KIR Types from SNP Variation Data","volume":"97","author":"D Vukcevic","year":"2015","journal-title":"American journal of human genetics"},{"key":"pcbi.1009059.ref088","first-page":"563866","article-title":"Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.","author":"D Taliun","year":"2019","journal-title":"BioRxiv"},{"issue":"7","key":"pcbi.1009059.ref089","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/ng.3571","article-title":"Fast and accurate long-range phasing in a UK Biobank cohort","volume":"48","author":"P-R Loh","year":"2016","journal-title":"Nature genetics"},{"issue":"12","key":"pcbi.1009059.ref090","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/hmg\/ddy443","article-title":"Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles","volume":"28","author":"F Degenhardt","year":"2019","journal-title":"Human molecular genetics"},{"issue":"4","key":"pcbi.1009059.ref091","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1034\/j.1399-0039.2000.560403.x","article-title":"Development of a PCR-SSOP approach capable of defining the natural killer cell inhibitory receptor (KIR) gene sequence repertoires","volume":"56","author":"KA Crum","year":"2000","journal-title":"Tissue antigens"},{"issue":"5","key":"pcbi.1009059.ref092","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1101\/gr.085738.108","article-title":"Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes","volume":"19","author":"PJ Norman","year":"2009","journal-title":"Genome research"},{"issue":"7762","key":"pcbi.1009059.ref093","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/s41586-019-1310-4","article-title":"Genetic analyses of diverse populations improves discovery for complex traits","volume":"570","author":"GL Wojcik","year":"2019","journal-title":"Nature"},{"key":"pcbi.1009059.ref094","author":"RC Team","year":"2013","journal-title":"R: A language and environment for statistical computing"},{"issue":"12","key":"pcbi.1009059.ref095","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1016\/j.exphem.2015.08.004","article-title":"Killer immunoglobulin-like receptors can predict TKI treatment-free remission in chronic myeloid leukemia patients","volume":"43","author":"G Caocci","year":"2015","journal-title":"Exp Hematol"},{"key":"pcbi.1009059.ref096","doi-asserted-by":"crossref","first-page":"675","DOI":"10.3389\/fimmu.2017.00675","article-title":"HLA-Bw4-I-80 Isoform Differentially Influences Clinical Outcome As Compared to HLA-Bw4-T-80 and HLA-A-Bw4 Isoforms in Rituximab or Dinutuximab-Based Cancer Immunotherapy.","volume":"8","author":"AK Erbe","year":"2017","journal-title":"Frontiers in immunology"},{"issue":"12","key":"pcbi.1009059.ref097","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1182\/blood-2010-03-273706","article-title":"Interaction between KIR3DS1 and HLA-Bw4 predicts for progression-free survival after autologous stem cell transplantation in patients with multiple myeloma","volume":"116","author":"IH Gabriel","year":"2010","journal-title":"Blood"},{"issue":"4","key":"pcbi.1009059.ref098","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/ng934","article-title":"Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS","volume":"31","author":"MP Martin","year":"2002","journal-title":"Nat Genet"},{"issue":"6","key":"pcbi.1009059.ref099","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1002\/eji.201546236","article-title":"Hematopoietic stem cell transplantation: Improving alloreactive Bw4 donor selection by genotyping codon 86 of KIR3DL1\/S1","volume":"46","author":"C Alicata","year":"2016","journal-title":"European journal of immunology"},{"issue":"11","key":"pcbi.1009059.ref100","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1016\/j.bbmt.2009.06.015","article-title":"Donor KIR3DL1\/3DS1 gene and recipient Bw4 KIR ligand as prognostic markers for outcome in unrelated hematopoietic stem cell transplantation.","volume":"15","author":"K Gagne","year":"2009","journal-title":"Biology of blood and marrow transplantation: journal of the American Society for Blood and Marrow Transplantation"},{"issue":"6","key":"pcbi.1009059.ref101","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1158\/2326-6066.CIR-17-0462","article-title":"Allelic Polymorphisms of KIRs and HLAs Predict Favorable Responses to Tyrosine Kinase Inhibitors in CML","volume":"6","author":"H Ureshino","year":"2018","journal-title":"Cancer immunology research"},{"issue":"4","key":"pcbi.1009059.ref102","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1002\/art.27332","article-title":"Association of the KIR3DS1* 013 and KIR3DL1* 004 alleles with susceptibility to ankylosing spondylitis","volume":"62","author":"R D\u00edaz-Pe\u00f1a","year":"2010","journal-title":"Arthritis & 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Mostovoy","year":"2020","journal-title":"bioRxiv"},{"issue":"7","key":"pcbi.1009059.ref106","doi-asserted-by":"crossref","first-page":"2003","DOI":"10.1182\/bloodadvances.2020002701","article-title":"Prospective KIR genotype evaluation of hematopoietic cell donors is feasible with potential to benefit patients with AML","volume":"5","author":"BC Shaffer","year":"2021","journal-title":"Blood advances"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1009059","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,4]],"date-time":"2022-03-04T00:00:00Z","timestamp":1646352000000}}],"container-title":["PLOS Computational 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