{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T19:15:18Z","timestamp":1772565318419,"version":"3.50.1"},"reference-count":64,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T00:00:00Z","timestamp":1772496000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-033578"],"award-info":[{"award-number":["INV-033578"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>\n                    India remains underrepresented in global genomic studies. We hypothesized that population-specific genetic variants contribute to COVID-19 severity and outcomes, and that the choice of reference panel during imputation impacts Genome-Wide Association Studies (GWAS) resolution. Integrating both global and indigenous reference panels may unravel unique and shared genetic associations that are otherwise missed during standard analyses. In this study, we aimed to perform a comparative GWAS using Indian population-specific (IndiGen) and global (1000 Genomes Project\/1KGenomes) reference panels to identify potential genetic loci associated with the COVID-19 differential severity and mortality among the Indian patients. Genomic DNA was extracted and genotyped from the patients who were stratified based on the clinical data capturing COVID-19 symptoms and clinical outcomes. Quality control, liftover, phasing and imputation were performed on the genotypic data. GWAS was performed separately for the severity and mortality phenotypes. Significant loci were functionally annotated using Linkage Disequilibrium (LD) analysis, eQTL mapping, and gene annotation tools. Comparative GWAS with 1KGenomes and IndiGen panels revealed both shared and unique loci. 1KGenomes identified protective variants near\n                    <jats:italic>MIR4432HG<\/jats:italic>\n                    involved in endothelial stability, while IndiGen uncovered risk variants with rs10096505 (\n                    <jats:italic>SFTPC\/BMP1<\/jats:italic>\n                    ) linked to alveolar collapse and fibrotic remodelling. rs9547631 was common to both panels for mortality, whereas IndiGen-specific risk variants (rs78554880, rs112982286, rs111390553, and rs79900659) were associated with immune dysregulation. Functional annotation of these loci pointed to key biologically plausible links to COVID-19 severity and fatal outcomes. Briefly, the use of an indigenous reference panel improved variant discovery and LD resolution, highlighting that population-specific signals are missed by the generic global datasets. Our findings underscore the importance of inclusive genomic resources for accurate association mapping in the underrepresented populations.\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0014020","type":"journal-article","created":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T18:30:52Z","timestamp":1772562652000},"page":"e0014020","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative GWAS using global and Indian Reference Panels reveals non-coding drivers of COVID-19 severity and mortality"],"prefix":"10.1371","volume":"20","author":[{"given":"Aastha","family":"Kaushik","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramakant","family":"Mohite","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ranjeet","family":"Maurya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bansidhar","family":"Tarai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandeep","family":"Budhiraja","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uzma","family":"Shamim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4404-8327","authenticated-orcid":true,"given":"Rajesh","family":"Pandey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,3,3]]},"reference":[{"issue":"10223","key":"pntd.0014020.ref001","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S0140-6736(20)30183-5","article-title":"Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China","volume":"395","author":"C Huang","year":"2020","journal-title":"Lancet"},{"issue":"3","key":"pntd.0014020.ref002","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0264785","article-title":"COVID-19 risk stratification and mortality prediction in hospitalized indian patients: harnessing clinical data for public health benefits","volume":"17","author":"S Alle","year":"2022","journal-title":"PLoS One"},{"issue":"1","key":"pntd.0014020.ref003","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1186\/s12889-020-09335-8","article-title":"Temporal dynamics in total excess mortality and COVID-19 deaths in Italian cities","volume":"20","author":"P Michelozzi","year":"2020","journal-title":"BMC Public Health"},{"issue":"3","key":"pntd.0014020.ref004","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/j.cmi.2020.10.020","article-title":"SARS-CoV-2 seroprevalence worldwide: a systematic review and meta-analysis","volume":"27","author":"A Rostami","year":"2021","journal-title":"Clin Microbiol Infect"},{"issue":"10229","key":"pntd.0014020.ref005","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/S0140-6736(20)30566-3","article-title":"Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study","volume":"395","author":"F Zhou","year":"2020","journal-title":"Lancet"},{"issue":"1","key":"pntd.0014020.ref006","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1186\/s12916-020-01640-8","article-title":"Ethnic and socioeconomic differences in SARS-CoV-2 infection: prospective cohort study using UK Biobank","volume":"18","author":"CL Niedzwiedz","year":"2020","journal-title":"BMC Med"},{"key":"pntd.0014020.ref007","doi-asserted-by":"crossref","first-page":"103629","DOI":"10.1016\/j.ebiom.2021.103629","article-title":"Host genetic factors determining COVID-19 susceptibility and severity","volume":"72","author":"TP Velavan","year":"2021","journal-title":"EBioMedicine"},{"key":"pntd.0014020.ref008","doi-asserted-by":"crossref","first-page":"105426","DOI":"10.1016\/j.meegid.2023.105426","article-title":"Genetic susceptibility to severe COVID-19","volume":"110","author":"C Cappadona","year":"2023","journal-title":"Infect Genet Evol"},{"issue":"6","key":"pntd.0014020.ref009","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/s41588-021-00854-7","article-title":"Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity","volume":"53","author":"JF Shelton","year":"2021","journal-title":"Nat Genet"},{"issue":"4","key":"pntd.0014020.ref010","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/s41588-021-01006-7","article-title":"Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease","volume":"54","author":"JE Horowitz","year":"2022","journal-title":"Nat Genet"},{"issue":"7848","key":"pntd.0014020.ref011","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/s41586-020-03065-y","article-title":"Genetic mechanisms of critical illness in COVID-19","volume":"591","author":"E Pairo-Castineira","year":"2021","journal-title":"Nature"},{"issue":"1","key":"pntd.0014020.ref012","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1038\/s41421-021-00318-6","article-title":"Genome-wide association study of COVID-19 severity among the Chinese population","volume":"7","author":"Y Li","year":"2021","journal-title":"Cell Discov"},{"key":"pntd.0014020.ref013","doi-asserted-by":"crossref","first-page":"103695","DOI":"10.1016\/j.ebiom.2021.103695","article-title":"Genome-wide association study of hospitalized COVID-19 patients in the United Arab Emirates","volume":"74","author":"M Mousa","year":"2021","journal-title":"EBioMedicine"},{"key":"pntd.0014020.ref014","doi-asserted-by":"crossref","first-page":"714185","DOI":"10.3389\/fgene.2021.714185","article-title":"Genetic risk prediction of COVID-19 susceptibility and severity in the indian population","volume":"12","author":"P Prakrithi","year":"2021","journal-title":"Front Genet"},{"issue":"1","key":"pntd.0014020.ref015","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s40246-024-00584-x","article-title":"Correction: association of the C allele of rs479200 in the EGLN1 gene with COVID-19 severity in Indian population: a novel finding","volume":"18","author":"R Harit","year":"2024","journal-title":"Hum Genomics"},{"key":"pntd.0014020.ref016","doi-asserted-by":"crossref","first-page":"105206","DOI":"10.1016\/j.meegid.2022.105206","article-title":"Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 case fatality rate among Indian populations","volume":"98","author":"RK Pandey","year":"2022","journal-title":"Infect Genet Evol"},{"issue":"1","key":"pntd.0014020.ref017","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/s43042-022-00344-3","article-title":"Implication of single nucleotide polymorphisms in Interleukin-10 gene (rs1800896 and rs1800872) with severity of COVID-19","volume":"23","author":"S Rizvi","year":"2022","journal-title":"Egypt J Med Hum Genet"},{"issue":"4","key":"pntd.0014020.ref018","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/s41588-025-02153-x","article-title":"Mapping genetic diversity with the GenomeIndia project","volume":"57","author":"C Bhattacharyya","year":"2025","journal-title":"Nat Genet"},{"issue":"11","key":"pntd.0014020.ref019","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2010-11-11-r113","article-title":"Genetic diversity in India and the inference of Eurasian population expansion","volume":"11","author":"J Xing","year":"2010","journal-title":"Genome Biol"},{"issue":"1","key":"pntd.0014020.ref020","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/s41435-021-00150-8","article-title":"COVID-19: Impact on linguistic and genetic isolates of India","volume":"23","author":"PP Singh","year":"2021","journal-title":"Genes Immun"},{"issue":"4","key":"pntd.0014020.ref021","doi-asserted-by":"crossref","first-page":"110399","DOI":"10.1016\/j.ygeno.2022.110399","article-title":"First report on genome wide association study in western Indian population reveals host genetic factors for COVID-19 severity and outcome","volume":"114","author":"R Pandit","year":"2022","journal-title":"Genomics"},{"issue":"6","key":"pntd.0014020.ref022","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010243","article-title":"Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals","volume":"18","author":"R Tournebize","year":"2022","journal-title":"PLoS Genet"},{"issue":"1","key":"pntd.0014020.ref023","doi-asserted-by":"crossref","first-page":"100724","DOI":"10.1016\/j.xgen.2024.100724","article-title":"Bridging genomics\u2019 greatest challenge: the diversity gap","volume":"5","author":"M Corpas","year":"2025","journal-title":"Cell Genom"},{"issue":"1","key":"pntd.0014020.ref024","doi-asserted-by":"crossref","first-page":"6733","DOI":"10.1038\/s41598-017-06905-6","article-title":"Inclusion of population-specific reference panel from india to the 1000 genomes Phase 3 panel improves imputation accuracy","volume":"7","author":"M Ahmad","year":"2017","journal-title":"Sci Rep"},{"key":"pntd.0014020.ref025","article-title":"IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes","volume":"49","author":"A Jain","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"pntd.0014020.ref026","first-page":"459","article-title":"miR-4432 targets FGFBP1 in human endothelial cells","volume":"12","author":"R Avvisato","year":"2023","journal-title":"Biology (Basel)"},{"issue":"7","key":"pntd.0014020.ref027","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1164\/rccm.202308-1438OC","article-title":"SARS-CoV-2 viral replication persists in the human lung for several weeks after symptom onset","volume":"209","author":"M Tomasicchio","year":"2024","journal-title":"Am J Respir Crit Care Med"},{"issue":"1","key":"pntd.0014020.ref028","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1083\/jcb.200606058","article-title":"BMP1 controls TGFbeta1 activation via cleavage of latent TGFbeta-binding protein","volume":"175","author":"G Ge","year":"2006","journal-title":"J Cell Biol"},{"issue":"6","key":"pntd.0014020.ref029","doi-asserted-by":"crossref","first-page":"2201799","DOI":"10.1183\/13993003.01799-2022","article-title":"Regulating the cell shift of endothelial cell-like myofibroblasts in pulmonary fibrosis","volume":"61","author":"X Wu","year":"2023","journal-title":"Eur Respir J"},{"issue":"6","key":"pntd.0014020.ref030","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.stem.2020.11.012","article-title":"Modeling multi-organ infection by SARS-CoV-2 using stem cell technology","volume":"27","author":"CR Simoneau","year":"2020","journal-title":"Cell Stem Cell"},{"issue":"2","key":"pntd.0014020.ref031","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1016\/j.bbrc.2006.03.158","article-title":"The TTF-1\/TAP26 complex differentially modulates surfactant protein-B (SP-B) and -C (SP-C) promoters in lung cells","volume":"344","author":"M-C Yang","year":"2006","journal-title":"Biochem Biophys Res Commun"},{"issue":"13","key":"pntd.0014020.ref032","article-title":"Is altered surfactant protein gene expression in peripheral blood associated with COVID-19 disease severity?","volume":"15","author":"S Koc","year":"2025","journal-title":"Diagnostics"},{"issue":"4","key":"pntd.0014020.ref033","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1093\/bjd\/ljae492","article-title":"Ribosomal protein L36-mediated selective loading of microRNA-4432 into extracellular vesicles contributes to perivascular cell dysfunction in venous malformations","volume":"192","author":"G-H Chen","year":"2025","journal-title":"Br J Dermatol"},{"issue":"3","key":"pntd.0014020.ref034","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.cell.2009.07.021","article-title":"DNA makes RNA makes innate immunity","volume":"138","author":"LAJ O\u2019Neill","year":"2009","journal-title":"Cell"},{"issue":"13","key":"pntd.0014020.ref035","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1001\/jama.2020.2648","article-title":"Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: summary of a report of 72\u00a0314 cases from the chinese center for disease control and prevention","volume":"323","author":"Z Wu","year":"2020","journal-title":"JAMA"},{"key":"pntd.0014020.ref036","doi-asserted-by":"crossref","first-page":"105379","DOI":"10.1016\/j.meegid.2022.105379","article-title":"Genome-wide association studies of COVID-19: connecting the dots","volume":"106","author":"LC Ferreira","year":"2022","journal-title":"Infect Genet Evol"},{"issue":"7571","key":"pntd.0014020.ref037","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":"1","key":"pntd.0014020.ref038","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1161\/HYPERTENSIONAHA.117.10268","article-title":"Blood pressure control by a secreted FGFBP1 (fibroblast growth factor-binding protein)","volume":"71","author":"E Tassi","year":"2018","journal-title":"Hypertens"},{"issue":"6","key":"pntd.0014020.ref039","doi-asserted-by":"crossref","first-page":"1924","DOI":"10.1161\/HYPERTENSIONAHA.120.15582","article-title":"Acute kidney injury sensitizes the brain vasculature to Ang II (Angiotensin II) constriction via FGFBP1 (Fibroblast growth factor binding protein 1)","volume":"76","author":"L Zhao","year":"2020","journal-title":"Hypertens"},{"issue":"1","key":"pntd.0014020.ref040","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.ccep.2021.10.003","article-title":"COVID-19-associated endothelial dysfunction and microvascular injury: from pathophysiology to clinical manifestations","volume":"14","author":"MP Canale","year":"2022","journal-title":"Card Electrophysiol Clin"},{"issue":"10","key":"pntd.0014020.ref041","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a041157","article-title":"Endothelialitis, microischemia, and intussusceptive angiogenesis in COVID-19","volume":"12","author":"SJ Mentzer","year":"2022","journal-title":"Cold Spring Harb Perspect Med"},{"issue":"6","key":"pntd.0014020.ref042","doi-asserted-by":"crossref","DOI":"10.3390\/cells11061011","article-title":"Multi-design differential expression profiling of COVID-19 lung autopsy specimens reveals significantly deregulated inflammatory pathways and SFTPC impaired transcription","volume":"11","author":"M Fassan","year":"2022","journal-title":"Cells"},{"issue":"3","key":"pntd.0014020.ref043","doi-asserted-by":"crossref","DOI":"10.1152\/ajplung.00318.2024","article-title":"Surfactant protein levels and genetic variants as biomarkers for COVID-19 severity in children","volume":"328","author":"N Sicher","year":"2025","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"pntd.0014020.ref044","first-page":"1","article-title":"Integration of GWAS and multi-omic QTLs identifies uncharacterized COVID-19 gene- biotype and phenotype associations","author":"M Oliva","year":"2024","journal-title":"bioRxiv"},{"issue":"5","key":"pntd.0014020.ref045","article-title":"Surfactant protein C dampens inflammation by decreasing JAK\/STAT activation during lung repair","volume":"314","author":"H Jin","year":"2018","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"issue":"10","key":"pntd.0014020.ref046","doi-asserted-by":"crossref","DOI":"10.1093\/rheumatology\/kead385","article-title":"Comment on: Nailfold capillaroscopy: a survey of current UK practice and \u201cnext steps\u201d to increase uptake among rheumatologists: reply","volume":"62","author":"M Eden","year":"2023","journal-title":"Rheumatology (Oxford)"},{"issue":"2","key":"pntd.0014020.ref047","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18332\/pne\/204755","article-title":"Heterotopic ossification in COVID-19: a case report","volume":"38","author":"C Karakatsanis","year":"2025","journal-title":"Pneumon"},{"key":"pntd.0014020.ref048","doi-asserted-by":"crossref","first-page":"112419","DOI":"10.1016\/j.biopha.2021.112419","article-title":"Interleukin-6 in SARS-CoV-2 induced disease: interactions and therapeutic applications","volume":"145","author":"J Majidpoor","year":"2022","journal-title":"Biomed Pharmacother"},{"key":"pntd.0014020.ref049","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.65445","article-title":"Molecular characterization of projection neuron subtypes in the mouse olfactory bulb","volume":"10","author":"S Zeppilli","year":"2021","journal-title":"Elife"},{"issue":"13","key":"pntd.0014020.ref050","doi-asserted-by":"crossref","first-page":"2321","DOI":"10.1096\/fj.06-6324com","article-title":"The spleen as a target in severe acute respiratory syndrome","volume":"20","author":"J Zhan","year":"2006","journal-title":"FASEB J"},{"issue":"3","key":"pntd.0014020.ref051","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.ajhg.2013.07.006","article-title":"Genetic evidence for recent population mixture in India","volume":"93","author":"P Moorjani","year":"2013","journal-title":"Am J Hum Genet"},{"issue":"6","key":"pntd.0014020.ref052","doi-asserted-by":"crossref","first-page":"1594","DOI":"10.1073\/pnas.1513197113","article-title":"Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure","volume":"113","author":"A Basu","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"10332","key":"pntd.0014020.ref053","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1016\/S0140-6736(22)00462-7","article-title":"Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study","volume":"399","author":"T Nyberg","year":"2022","journal-title":"Lancet"},{"key":"pntd.0014020.ref054","doi-asserted-by":"crossref","first-page":"100348","DOI":"10.1016\/j.ijregi.2024.03.003","article-title":"Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam","volume":"11","author":"L Van Nam","year":"2024","journal-title":"IJID Reg"},{"issue":"9","key":"pntd.0014020.ref055","article-title":"Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections","volume":"20","author":"K Li","year":"2024","journal-title":"PLoS Comput Biol"},{"issue":"6484","key":"pntd.0014020.ref056","doi-asserted-by":"crossref","DOI":"10.1126\/science.aay5012","article-title":"Insights into human genetic variation and population history from 929 diverse genomes","volume":"367","author":"A Bergstr\u00f6m","year":"2020","journal-title":"Science"},{"issue":"11","key":"pntd.0014020.ref057","doi-asserted-by":"crossref","first-page":"2693","DOI":"10.1111\/trf.14953","article-title":"Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 genomes project","volume":"58","author":"C Montemayor-Garcia","year":"2018","journal-title":"Transfusion"},{"key":"pntd.0014020.ref058","doi-asserted-by":"crossref","first-page":"3934","DOI":"10.1038\/ncomms4934","article-title":"Integrating sequence and array data to create an improved 1000 genomes project haplotype reference panel","volume":"5","author":"1000 Genomes Project Consortium","year":"2014","journal-title":"Nat Commun"},{"issue":"14","key":"pntd.0014020.ref059","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: an R package for interfacing with genome browsers","volume":"25","author":"M Lawrence","year":"2009","journal-title":"Bioinformatics"},{"issue":"3","key":"pntd.0014020.ref060","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A one-penny imputed genome from next-generation reference panels","volume":"103","author":"BL Browning","year":"2018","journal-title":"Am J Hum Genet"},{"issue":"1","key":"pntd.0014020.ref061","article-title":"Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels","volume":"25","author":"M Shi","year":"2023","journal-title":"Brief Bioinform"},{"key":"pntd.0014020.ref062","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa420","article-title":"SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)","volume":"48","author":"J Oscanoa","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pntd.0014020.ref063","article-title":"SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine","volume":"46","author":"AZ Dayem Ullah","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pntd.0014020.ref064","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1093\/bib\/bbt004","article-title":"A practical guide for the functional annotation of genetic variations using SNPnexus","volume":"14","author":"AZ Dayem Ullah","year":"2013","journal-title":"Brief Bioinform"}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0014020","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T18:31:03Z","timestamp":1772562663000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0014020"}},"subtitle":[],"editor":[{"given":"Max Carlos","family":"Ram\u00edrez-Soto","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,3,3]]},"references-count":64,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0014020","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,3]]}}}