Clinical variant interpretation comparing two saturation genome editing-based functional studies for BRCA2

Two saturation genome editing (SGE) studies for BRCA2 using haploid human HAP1 cells and mouse embryonic stem cells, respectively, demonstrated contradictory functional results in 16.9% (1,052/6,208) of the variants. We performed clinical variant interpretation and tried to address the discordance by comparing two studies combined with 24 years of clinicopathological data collected at a single institution.

Retrospectively, we collected data from patients with BRCA2 variants evaluated in the SGE studies. The variants were reassessed according to the ClinGen BRCA1/2 guidelines and/or multifactorial likelihood analysis. For variants with concordant SGE functional results, either PS3 or BS3 was assigned. Major error rates were compared for variants with discordant results.

Among the 88 variants from 526 patients, 13, including three potentially hypomorphic variants, showed discordant results. Major error rates were lower for HAP1-SGE dataset, but without statistical significance. Among the 75 variants with concordant results, 28 and 47 were assigned PS3 and BS3, respectively. Consequently, 93.1% (27/29) of the variants of uncertain significance were reclassified as likely pathogenic (n = 3) or likely benign (n = 24).

Concordant SGE results are clinically useful for variant reclassification. When discordant results are present, functional evidence should not be assigned, but HAP1-SGE dataset is suggested to be more consistent with patient-specific data. Further segregation analysis and long-term follow-up are needed to resolve discordant cases.