Retrospective Re-evaluation of Variants of Uncertain Significance Identified by Clinical Exome Sequencing in Breast Cancer Patients

VUS in Breast Cancer Patients

Abstract

Objective: Variants of uncertain significance (VUSs) remain a major challenge in clinical molecular genetics because their interpretation may change as population, computational, and disease-specific evidence accumulates. This retrospective descriptive study aimed to re-evaluate VUSs identified by clinical exome sequencing in breast cancer patients and to characterize recurrent observations and genes of potential biological interest.
Methods: Clinical exome sequencing data from 25 individuals referred for breast cancer mutation analysis were retrospectively re-evaluated. The study population comprised individuals with breast cancer or a first-degree family history of breast cancer. Sequencing was performed on the Illumina NextSeq 550 platform. Thirteen individuals were analyzed using Sophia Clinical Exome Solution v2 with Sophia DDM, and 12 were analyzed using the Berry Genomics Clinical Exome workflow with Verita Trekker Variants Detection System and/or the Enliven Variants Annotation Interpretation System. An exploratory filtering strategy was used to focus on VUS observations outside genes already prioritized in the literature for breast cancer or cancer. Candidate variants were subsequently reviewed using public variant resources and in silico evidence.
Results: After sequential filtering and manual re-evaluation, four candidate observations in the once-observed group and seven candidate observations in the twice-observed group were examined in detail. Variants were identified in ZDHHC15, COL17A1, MFN1, ZNF141, MUC6, VEZT, MYBPC1, ZSWIM1, TDRD3, PRDM6, and PIGG. MUC6 and ZNF141 were considered of exploratory interest. Two different MUC6 variants were observed among four individuals; however, two carriers of one MUC6 variant were related and were not considered independent observations. Two ZNF141 missense VUSs were identified in a single breast cancer patient. No control cohort, statistical enrichment analysis, segregation analysis, or functional validation was available.
Conclusion: The findings represent descriptive and hypothesis-generating observations rather than evidence of a causal or statistical association with breast cancer. MUC6 and ZNF141 may warrant further investigation in larger, population-matched cohorts with segregation, gene-level enrichment, and functional studies. The study also emphasizes the importance of transparent and periodic reinterpretation of VUSs.