Robust Assessment of Homologous Recombination Deficiency Genomic Instability by OncoScan Microarrays

Area of Science:

• Genomics
• Oncology
• Biotechnology

Background:

• Genomic instability scars are key biomarkers for homologous recombination deficiency (HRD) in ovarian cancer.
• Accurate HRD status is crucial for predicting response to poly (ADP-ribose) polymerase (PARP) inhibitor therapy.
• Existing commercial assays for genomic instability scars are limited, necessitating development of accessible alternatives.

Purpose of the Study:

• To assess the feasibility of using the OncoScan copy number variant assay for quantifying genomic instability scores.
• To develop an open-access online platform for calculating genomic instability scores.
• To establish a reliable and accessible method for HRD determination in ovarian cancer.

Main Methods:

• Utilized the OncoScan copy number variant assay for genomic data acquisition.
• Developed open-source software for analyzing copy number variations and calculating genomic instability scores.
• Validated the laboratory-developed test against established methods for HRD classification.

Main Results:

• The OncoScan assay combined with open-source software accurately classified samples as homologous recombination-proficient or deficient.
• Internally evaluated genomic instability scores showed 92% overall agreement with external scores, with a higher success rate.
• The developed assay and platform demonstrated high accuracy and accessibility for HRD determination.

Conclusions:

• The OncoScan assay and open-source software provide a feasible, reliable, and accessible method for quantifying genomic instability scores.
• The open-access online platform simplifies HRD determination, potentially increasing patient eligibility for PARP inhibitor therapy.
• This approach enhances the clinical utility of HRD testing in ovarian cancer management.