دورية أكاديمية
أعرض في EDS

Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.

التفاصيل البيبلوغرافية
العنوان: Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.
المؤلفون: Ardiansyah E; Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia., Riza AL; Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania., Dian S; Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia.; Department of Neurology, Hasan Sadikin Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia., Ganiem AR; Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia.; Department of Neurology, Hasan Sadikin Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia., Alisjahbana B; Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, Indonesia.; Department of Internal Medicine, Hasan Sadikin Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia., Setiabudiawan TP; Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands., van Laarhoven A; Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands., van Crevel R; Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands., Kumar V; Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands.; University of Groningen, University Medical Center Groningen, department of Genetics, Groningen, the Netherlands.
المصدر: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 14. Date of Electronic Publication: 2024 Jun 14.
نوع المنشور: Journal Article; Preprint
اللغة: English
بيانات الدورية: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
مستخلص: Existing genotype imputation reference panels are mainly derived from European populations, limiting their accuracy in non-European populations. To improve imputation accuracy for Indonesians, the world's fourth most populous country, we combined Whole Genome Sequencing (WGS) data from 227 West Javanese individuals with East Asian data from the 1000 Genomes Project. This created three reference panels: EAS 1KGP3 (EASp), Indonesian (INDp), and a combined panel (EASp+INDp). We also used ten West-Javanese samples with WGS and SNP-typing data for benchmarking. We identified 1.8 million novel single nucleotide variants (SNVs) in the West Javanese population, which, while similar to the East Asians, are distinct from the Central Indonesian Flores population. Adding INDp to the EASp reference panel improved imputation accuracy (R2) from 0.85 to 0.90, and concordance from 87.88% to 91.13%. These findings underscore the importance of including Indonesian genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies.
Competing Interests: Declaration of interests The authors declare no competing interests.
References: Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
Sci Rep. 2016 Dec 22;6:39313. (PMID: 28004816)
Hum Mol Genet. 2016 Aug 1;25(15):3245-3254. (PMID: 27346520)
Nature. 2019 Dec;576(7785):106-111. (PMID: 31802016)
Eur J Hum Genet. 2011 Jun;19(6):662-6. (PMID: 21364697)
Front Genet. 2019 Feb 05;10:34. (PMID: 30804980)
Nature. 2022 Jul;607(7920):732-740. (PMID: 35859178)
PLoS Genet. 2009 Jun;5(6):e1000529. (PMID: 19543373)
Nature. 2015 Oct 1;526(7571):68-74. (PMID: 26432245)
Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33. (PMID: 25431634)
Lancet Neurol. 2020 Apr;19(4):326-335. (PMID: 31986256)
Eur J Hum Genet. 2017 Jun;25(7):869-876. (PMID: 28401899)
Am J Hum Genet. 2009 Feb;84(2):235-50. (PMID: 19215730)
Hum Genet. 2018 Jul;137(6-7):431-436. (PMID: 29855708)
Genome Res. 2010 Sep;20(9):1297-303. (PMID: 20644199)
Nucleic Acids Res. 2010 Sep;38(16):e164. (PMID: 20601685)
Tuberculosis (Edinb). 2021 May;128:102085. (PMID: 34022506)
Eur J Hum Genet. 2015 Jul;23(7):975-83. (PMID: 25293720)
Nat Genet. 2011 May;43(5):491-8. (PMID: 21478889)
Commun Biol. 2021 Nov 5;4(1):1269. (PMID: 34741098)
BMC Res Notes. 2014 Dec 11;7:901. (PMID: 25495213)
Nucleic Acids Res. 2023 Jan 6;51(D1):D977-D985. (PMID: 36350656)
Hum Genet. 2018 Apr;137(4):281-292. (PMID: 29637265)
Nat Rev Genet. 2010 Jul;11(7):499-511. (PMID: 20517342)
Nat Methods. 2011 Dec 04;9(2):179-81. (PMID: 22138821)
NAR Genom Bioinform. 2020 May 06;2(2):lqaa030. (PMID: 33575586)
معلومات مُعتمدة: R01 AI145781 United States AI NIAID NIH HHS
فهرسة مساهمة: Keywords: GWAS; Indonesian genetic architecture; West Javanese genetics; imputation accuracy; imputation reference panel; whole genome sequencing
تواريخ الأحداث: Date Created: 20240625 Latest Revision: 20240703
رمز التحديث: 20240703
مُعرف محوري في PubMed: PMC11195206
DOI: 10.1101/2024.06.14.598981
PMID: 38915501
قاعدة البيانات: MEDLINE
الوصف
تدمد:2692-8205
DOI:10.1101/2024.06.14.598981