TaiwanGenomes

TaiwanGenomes provides comprehensive genomic analysis and medically relevant variant interpretation from Taiwan Biobank (TWB) whole-genome sequencing (WGS) of 1,496 Taiwanese individuals for population and clinical genomics research.

Key Features:

• Extensive Genomic Data: Contains Illumina-based WGS data for 1,496 individuals with ≥30X coverage and reports over 6,870 globally novel variants per individual.
• Precision Variant Analysis: Reanalyzes WGS using Sentieon DNAscope (precisionFDA challenge-winning method) for calling and recalibration of single nucleotide variants (SNVs) and small insertions/deletions (Indels).
• Variant Quality Scoring: Applies a recalibrated sequence quality scoring system to distinguish true variants from technical false positives and improve minor allele frequency (MAF) estimates.
• Clinical Annotation: Integrates clinician reviews and highlights PharmGKB-reported Cytochrome P450 (CYP) haplotype–drug pairs and human leukocyte antigen (HLA) risk alleles.
• Actionable Findings: Identifies ACMG secondary findings with an observed ~1.67% of individuals carrying at least one medically actionable variant and estimates carrier rates for pathogenic variants including alpha thalassemia and spinal muscular atrophy (SMA).
• Population Carrier Risk Assessment: Estimates that approximately 4.52% of couples are at risk of having offspring with at least one pathogenic variant, consistent with rates reported in Japanese and Singaporean populations.

Scientific Applications:

• Population Genomics: Enables characterization of the Taiwanese and broader East Asian genetic landscape using WGS-derived variant catalogs and MAF data.
• Clinical Genomics and Genetic Counseling: Supports interpretation of ACMG secondary findings and carrier status to inform genetic counseling and risk assessment.
• Pharmacogenomics and Immunogenetics: Facilitates analysis of PharmGKB CYP haplotype–drug associations and HLA risk alleles for pharmacogenomic and disease-susceptibility studies.

Methodology:

Reanalysis of Illumina-based WGS from TWB (1,496 samples, ≥30X) using Sentieon DNAscope for joint calling and variant recalibration, with sequence quality score recalibration applied to SNV and Indel calls.