Essential Factors Affecting the Assessment of Homologous Recombination Deficiency by NGS

Essential Factors Affecting the Assessment of Homologous Recombination Deficiency by NGS

Abstract
Homologous recombination deficiency (HRD) arises due to a defect in DNA repair and serves as an important therapeutic biomarker to stratify ovarian and breast cancer patients and determine eligibility for clinical trials, and targeted therapies. Genomic instability leads to the accumulation of genomic rearrangements, deletions, and allelic amplifications, whose assessment benefits from accurate determination of genome-wide allelic CNV. NGS assays measuring HRD status is usually performed on FFPE biopsied tissue. To address the challenges of this sample type and complexity of analysis, a set of HRD reference materials have been developed and characterized using different assays and algorithms measuring genomic instability (GIS) scores. Comparison of commercial GIS determination approaches and whole genome sequencing under different extraction conditions highlighted the importance of accurate SNP and CNV determination for reliable HRD assessment, as well as the impact of preanalytical factors specific to FFPE tissue format. The HRD reference materials should aid the development, validation, and quality control of assays using genomic instability scores, as well as inform laboratory best practices when performing GIS analysis.