Abstract
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.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
