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ORIGINAL RESEARCH article

Front. Genet.
Sec. Evolutionary and Population Genetics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1492602

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

Provisionally accepted
Edwin Ardiansyah Edwin Ardiansyah 1Anca-Lelia Riza Anca-Lelia Riza 2Sofiati Dian Sofiati Dian 3Ahmad Rizal Ganiem Ahmad Rizal Ganiem 3Bachti Alisjahbana Bachti Alisjahbana 4Todia P Setiabudiawan Todia P Setiabudiawan 5Arjan Van Laarhoven Arjan Van Laarhoven 5Reinout Van Crevel Reinout Van Crevel 5Vinod Kumar Vinod Kumar 5*
  • 1 Research Center for Care and Control of Infectious Diseases, Padjadjaran University, Bandung, West Java, Indonesia
  • 2 Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, Craiova, Dolj, Romania
  • 3 Department of Neurology, Hasan Sadikin Hospital, Faculty of Medicine, Padjadjaran University, Bandung, West Java, Indonesia
  • 4 Department of Internal Medicine, Hasan Sadikin Hospital, Faculty of Medicine, Padjadjaran University, Bandung, West Java, Indonesia
  • 5 Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, Gelderland, Netherlands

The final, formatted version of the article will be published soon.

    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 West-Javanese genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies.

    Keywords: whole genome sequencing, imputation reference panel, Indonesian genetic architecture, GWAS, West Javanese genetics, Imputation accuracy

    Received: 04 Oct 2024; Accepted: 12 Dec 2024.

    Copyright: © 2024 Ardiansyah, Riza, Dian, Ganiem, Alisjahbana, Setiabudiawan, Van Laarhoven, Van Crevel and Kumar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Vinod Kumar, Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, 6525 GA, Gelderland, Netherlands

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