Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy
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 Java...
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2024.1492602/full |
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| author | Edwin Ardiansyah Anca-Lelia Riza Sofiati Dian Sofiati Dian Ahmad Rizal Ganiem Ahmad Rizal Ganiem Bachti Alisjahbana Bachti Alisjahbana Todia P. Setiabudiawan Arjan van Laarhoven Reinout van Crevel Vinod Kumar Vinod Kumar |
| author_facet | Edwin Ardiansyah Anca-Lelia Riza Sofiati Dian Sofiati Dian Ahmad Rizal Ganiem Ahmad Rizal Ganiem Bachti Alisjahbana Bachti Alisjahbana Todia P. Setiabudiawan Arjan van Laarhoven Reinout van Crevel Vinod Kumar Vinod Kumar |
| author_sort | Edwin Ardiansyah |
| collection | DOAJ |
| description | 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 1,000 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 West-Javanese genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies. |
| format | Article |
| id | doaj-art-6a6de0d56512450cb28d66ae9deaf230 |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj-art-6a6de0d56512450cb28d66ae9deaf2302025-02-07T13:54:54ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-02-011510.3389/fgene.2024.14926021492602Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracyEdwin Ardiansyah0Anca-Lelia Riza1Sofiati Dian2Sofiati Dian3Ahmad Rizal Ganiem4Ahmad Rizal Ganiem5Bachti Alisjahbana6Bachti Alisjahbana7Todia P. Setiabudiawan8Arjan van Laarhoven9Reinout van Crevel10Vinod Kumar11Vinod Kumar12Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, IndonesiaLaboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, Craiova, RomaniaResearch Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, IndonesiaDepartment of Neurology, Hasan Sadikin Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, IndonesiaResearch Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, IndonesiaDepartment of Neurology, Hasan Sadikin Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, IndonesiaResearch Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, IndonesiaDepartment of Internal Medicine, Hasan Sadikin Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, IndonesiaDepartment of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, NetherlandsDepartment of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, NetherlandsDepartment of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, NetherlandsDepartment of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, NetherlandsExisting 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 1,000 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 West-Javanese genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies.https://www.frontiersin.org/articles/10.3389/fgene.2024.1492602/fullwhole genome sequencingimputation reference panelIndonesian genetic architectureGWASWest Javanese geneticsimputation accuracy |
| spellingShingle | Edwin Ardiansyah Anca-Lelia Riza Sofiati Dian Sofiati Dian Ahmad Rizal Ganiem Ahmad Rizal Ganiem Bachti Alisjahbana Bachti Alisjahbana Todia P. Setiabudiawan Arjan van Laarhoven Reinout van Crevel Vinod Kumar Vinod Kumar Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy Frontiers in Genetics whole genome sequencing imputation reference panel Indonesian genetic architecture GWAS West Javanese genetics imputation accuracy |
| title | Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy |
| title_full | Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy |
| title_fullStr | Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy |
| title_full_unstemmed | Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy |
| title_short | Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy |
| title_sort | sequencing whole genomes of the west javanese population in indonesia reveals novel variants and improves imputation accuracy |
| topic | whole genome sequencing imputation reference panel Indonesian genetic architecture GWAS West Javanese genetics imputation accuracy |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2024.1492602/full |
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