A Differential Depth Sequencing Method, SPRE-Seq, for Enhancing Targeted Region Coverage in Hybridization Capture-Based NGS.

ABSTRACT: Sequencing depth is a crucial parameter for variant calling accuracy and sensitivity. The trade-off between sequencing breadth and depth is a well-known limitation in capture-based targeted next-generation sequencing (NGS). Herein, we propose a differential depth sequencing method, SPRE-Seq, to acquire different sequencing depths for different targeted regions in an NGS panel. The SPRE-Seq performance was evaluated using a panel of reference standards and clinical samples based on our custom-designed homologous recombination deficiency (HRD) assay. By applying SPRE-Seq, the effective sequencing depths of the homologous recombination repair (HRR) and HRD regions of all seven HRD reference standards met the required thresholds with only half the sequencing data volume (reduced from 12 to 6 G

SUBMITTER: Chen HJ 

PROVIDER: S-EPMC12552348 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature