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Complete genomic profiles of 1496 Taiwanese reveal curated medical insights

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Title: Complete genomic profiles of 1496 Taiwanese reveal curated medical insights
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
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  Data: Complete genomic profiles of 1496 Taiwanese reveal curated medical insights
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  Data: <searchLink fieldCode="AR" term="%22Jacob+Shujui+Hsu%22">Jacob Shujui Hsu</searchLink><br /><searchLink fieldCode="AR" term="%22Dung-Chi+Wu%22">Dung-Chi Wu</searchLink><br /><searchLink fieldCode="AR" term="%22Shang-Hung+Shih%22">Shang-Hung Shih</searchLink><br /><searchLink fieldCode="AR" term="%22Jen-Feng+Liu%22">Jen-Feng Liu</searchLink><br /><searchLink fieldCode="AR" term="%22Ya-Chen+Tsai%22">Ya-Chen Tsai</searchLink><br /><searchLink fieldCode="AR" term="%22Tung-Lin+Lee%22">Tung-Lin Lee</searchLink><br /><searchLink fieldCode="AR" term="%22Wei-An+Chen%22">Wei-An Chen</searchLink><br /><searchLink fieldCode="AR" term="%22Yi-Hsuan+Tseng%22">Yi-Hsuan Tseng</searchLink><br /><searchLink fieldCode="AR" term="%22Yi-Chung+Lo%22">Yi-Chung Lo</searchLink><br /><searchLink fieldCode="AR" term="%22Hong-Ye+Lin%22">Hong-Ye Lin</searchLink><br /><searchLink fieldCode="AR" term="%22Yi-Chieh+Chen%22">Yi-Chieh Chen</searchLink><br /><searchLink fieldCode="AR" term="%22Jing-Yi+Chen%22">Jing-Yi Chen</searchLink><br /><searchLink fieldCode="AR" term="%22Ting-Hsuan+Chou%22">Ting-Hsuan Chou</searchLink><br /><searchLink fieldCode="AR" term="%22Darby+Tien-Hao+Chang%22">Darby Tien-Hao Chang</searchLink><br /><searchLink fieldCode="AR" term="%22Ming+Wei+Su%22">Ming Wei Su</searchLink><br /><searchLink fieldCode="AR" term="%22Wei-Hong+Guo%22">Wei-Hong Guo</searchLink><br /><searchLink fieldCode="AR" term="%22Hsin-Hsiang+Mao%22">Hsin-Hsiang Mao</searchLink><br /><searchLink fieldCode="AR" term="%22Chien-Yu+Chen%22">Chien-Yu Chen</searchLink><br /><searchLink fieldCode="AR" term="%22Pei-Lung+Chen%22">Pei-Lung Chen</searchLink>
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  Data: 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.
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