Accelerating genetic diagnostics in retinitis pigmentosa: implementation of a semi-automated bespoke cohort analysis workflow for Hong Kong Genome Project

Abstract

<p>The study aims to enhance the efficiency of the genetic variant curation process at the Hong Kong Genome Institute by developing a Semi-Automated Bespoke Cohort Analysis Workflow (S-BCAW) for patients with, or suspected to have, retinitis pigmentosa (RP) in the Hong Kong Genome Project (HKGP), leveraging advances in next-generation sequencing (NGS). A comparative analysis involving 79 RP patients was conducted using both the conventional manual workflow and the novel S-BCAW, which integrates initial filtering and variant classification based on ACMG guidelines, followed by detailed manual review. The diagnostic yields from both methods were identical, but the bespoke workflow reduced analysis time by approximately 60% (1.5 h/sample). This efficiency increase resulted from automated application of ACMG rules and systematic aggregation of supportive data, including disease-specific information. The study reports 25 positive cases with a diagnostic yield of 32%, including three novel variants. The S-BCAW significantly improves efficiency, helping to end the diagnostic odyssey for patients in the HKGP. This approach facilitates rapid assessment of variant pathogenicity, enhancing the feasibility and timeliness of NGS technology for clinical applications, especially in urgent scenarios.</p>