Academic Journal
Complete genomic profiles of 1496 Taiwanese reveal curated medical insights
| Title: | Complete genomic profiles of 1496 Taiwanese reveal curated medical insights |
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| Authors: | Jacob Shujui Hsu, Dung-Chi Wu, Shang-Hung Shih, Jen-Feng Liu, Ya-Chen Tsai, Tung-Lin Lee, Wei-An Chen, Yi-Hsuan Tseng, Yi-Chung Lo, Hong-Ye Lin, Yi-Chieh Chen, Jing-Yi Chen, Ting-Hsuan Chou, Darby Tien-Hao Chang, Ming Wei Su, Wei-Hong Guo, Hsin-Hsiang Mao, Chien-Yu Chen, Pei-Lung Chen |
| Source: | Journal of Advanced Research, Vol 66, Iss , Pp 197-207 (2024) |
| Publisher Information: | Elsevier, 2024. |
| Publication Year: | 2024 |
| Collection: | LCC:Medicine (General) LCC:Science (General) |
| Subject Terms: | Taiwan Biobank, Whole genome sequence, Population allele frequency, ACMG secondary finding, V3 gene list, Carrier rates, Medicine (General), R5-920, Science (General), Q1-390 |
| More Details: | Introduction: The population of Taiwan has a long history of ethno-cultural evolution. The Taiwanese population was isolated from other large populations such as the European, Han Chinese, and Japanese population. The Taiwan Biobank (TWB) project has built a nationwide database, particularly for personal whole-genome sequence (WGS) to facilitate basic and clinical collaboration nationally and internationally, making it one of the most valuable public datasets of the East Asian population. Objectives: This study provides comprehensive medical genomic findings from TWB WGS data, for better characterization of disease susceptibility and the choice of ideal treatment regimens in Taiwanese population. Methods: We reanalyzed 1496 WGS using a PrecisionFDA Truth challenge winner method Sentieon DNAscope. Single nucleotide variants (SNV) and small insertions/deletions (INDEL) were benchmarked. We also analyzed pharmacogenomic (PGx) drug-associated alleles, and copy number variants (CNV). Multiple practicing clinicians reviewed and curated the clinically significant variants. Variant annotations can be browsed at TaiwanGenomes (https://genomes.tw). Results: We found that each participant had an average of 6,870.7 globally novel variants and 75.3% (831/1103) of the participants harbored at least one PharmGKB-selected high evidence level human leukocyte antigen (HLA) risk allele. 54 PharmGKB-reported high-level instances of evidence of Cytochrome P450 variant-drug pairs, with a population frequency of over 13.2%. We also identified 23 variants in the ACMG secondary finding V3 gene list from 25 participants, suggesting that 1.67% (25/1496) of the population is harboring at least one medical actionable variant. Our carrier status analyses suggest that one in 25 couples (3.94%) would risk having offspring with at least one pathogenic variant, which is in line with rates found in Japan and Singapore. For pathogenic CNV, we detected 6.88% and 2.02% carrier rates for alpha thalassemia and spinal muscular atrophy, respectively. Conclusion: Our study highlights the overall medical insights of a complete Taiwanese genomic profile. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 2090-1232 |
| Relation: | http://www.sciencedirect.com/science/article/pii/S2090123223004058; https://doaj.org/toc/2090-1232 |
| DOI: | 10.1016/j.jare.2023.12.018 |
| Access URL: | https://doaj.org/article/49ac97eecdc7451c9babc92fcaee68af |
| Accession Number: | edsdoj.49ac97eecdc7451c9babc92fcaee68af |
| Database: | Directory of Open Access Journals |
| ISSN: | 20901232 |
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| DOI: | 10.1016/j.jare.2023.12.018 |
| Published in: | Journal of Advanced Research |
| Language: | English |