Human genomics · 2026
From enrichment to interpretation: PS4-driven reclassification in Taiwanese inherited retinal degeneration.
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Huang Yu-Shu, Lin Chien-Yu, Chen Yu-An, Lee Chieh-Yu, Yang Chang-Hao, Hsu Jacob Shujui, Chen Ta-Ching, Chen Pei-Lung
Аннотация
BACKGROUND: Inherited retinal degeneration (IRD) comprises a diverse group of monogenic disorders characterized by marked genetic and phenotypic heterogeneity. Although next-generation sequencing (NGS) enables the identification of candidate variants, many remain classified as variants of uncertain significance (VUS). Ancestry-matched population data can strengthen comparative evidence, and the emergence of national biobanks provides new opportunities to operationalize ACMG/AMP criterion PS4 through case-control analyses.
METHODS: We integrated an IRD cohort of 802 probands with whole-genome allele frequency data from 1,492 individuals in the Taiwan Biobank. An allele-based case-control framework was applied, assigning PS4 when the Haldane-Anscombe-corrected odds ratio was ≥ 5 and the 95% confidence interval excluded 1. Post-PS4 triage required variants to: (i) reside in IRD-associated genes, (ii) be rare in East Asian populations in gnomAD v4.1, and (iii) be annotated in RefSeq as exonic, untranslated regions, or splicing (± 20 bp). Baseline ACMG/AMP classifications were generated using GeneBe and finalized through expert curation.
RESULTS: Incorporation of PS4 substantially refined variant interpretation, upgrading two variants from Likely Pathogenic to Pathogenic and six from VUS to Likely Pathogenic. Homozygous exemplar variants, including CNGB1 (NM_001297.5): c.2921T > G and CFAP410 (NM_004928.3): c.340_351dup, demonstrated strong genotype-phenotype concordance with confirmatory sequencing, illustrating an end-to-end workflow from statistical enrichment to clinical reporting.
CONCLUSION: An ancestry-aware case-control framework enables effective implementation of PS4 and improves the accuracy of IRD variant classification. This reproducible strategy supports the integration of population-specific genomic data into clinical workflows and is applicable to other monogenic disorders.
METHODS: We integrated an IRD cohort of 802 probands with whole-genome allele frequency data from 1,492 individuals in the Taiwan Biobank. An allele-based case-control framework was applied, assigning PS4 when the Haldane-Anscombe-corrected odds ratio was ≥ 5 and the 95% confidence interval excluded 1. Post-PS4 triage required variants to: (i) reside in IRD-associated genes, (ii) be rare in East Asian populations in gnomAD v4.1, and (iii) be annotated in RefSeq as exonic, untranslated regions, or splicing (± 20 bp). Baseline ACMG/AMP classifications were generated using GeneBe and finalized through expert curation.
RESULTS: Incorporation of PS4 substantially refined variant interpretation, upgrading two variants from Likely Pathogenic to Pathogenic and six from VUS to Likely Pathogenic. Homozygous exemplar variants, including CNGB1 (NM_001297.5): c.2921T > G and CFAP410 (NM_004928.3): c.340_351dup, demonstrated strong genotype-phenotype concordance with confirmatory sequencing, illustrating an end-to-end workflow from statistical enrichment to clinical reporting.
CONCLUSION: An ancestry-aware case-control framework enables effective implementation of PS4 and improves the accuracy of IRD variant classification. This reproducible strategy supports the integration of population-specific genomic data into clinical workflows and is applicable to other monogenic disorders.