Exon splicing analysis of intronic variants in multigene cancer panel testing for hereditary breast/ovarian cancer

Cancer Sci. 2020 Oct;111(10):3912-3925. doi: 10.1111/cas.14600. Epub 2020 Sep 2.

Abstract

The use of multigene panel testing for patients with a predisposition to breast/ovarian cancer is increasing as the identification of variants is useful for diagnosis and disease management. We identified pathogenic and likely pathogenic (P/LP) variants of high-and moderate-risk genes using a 23-gene germline cancer panel in 518 patients with hereditary breast and ovarian cancers (HBOC). The frequency of P/LP variants was 12.4% (64/518) for high- and moderate-penetrant genes, namely, BRCA2 (5.6%), BRCA1 (3.3%), CHEK2 (1.2%), MUTYH (0.8%), PALB2 (0.8%), MLH1 (0.4%), ATM (0.4%), BRIP1 (0.4%), TP53 (0.2%), and PMS2 (0.2%). Five patients possessed two P/LP variants in BRCA1/2 and other genes. We also compared the results from in silico splicing predictive tools and exon splicing patterns from patient samples by analyzing RT-PCR product sequences in six P/LP intronic variants and two intronic variants of unknown significance (VUS). Altered transcriptional fragments were detected for P/LP intronic variants in BRCA1, BRIP1, CHEK2, PARB2, and PMS2. Notably, we identified an in-frame deletion of the BRCA1 C-terminal (BRCT) domain by exon skipping in BRCA1 c.5152+6T>C-as known VUS-indicating a risk for HBOC. Thus, exon splicing analysis can improve the identification of veiled intronic variants that would aid decision making and determination of hereditary cancer risk.

Keywords: RNA splicing; germline mutation; hereditary breast and ovarian cancer syndrome; next-generation sequencing; pathogenic/likely Pathogenic.

MeSH terms

  • Adult
  • BRCA1 Protein / genetics*
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Checkpoint Kinase 2 / genetics
  • Exons / genetics
  • Fanconi Anemia Complementation Group Proteins / genetics
  • Female
  • Germ-Line Mutation / genetics
  • Humans
  • Middle Aged
  • Mismatch Repair Endonuclease PMS2 / genetics
  • Neoplasm Proteins / genetics*
  • Ovarian Neoplasms / genetics*
  • Ovarian Neoplasms / pathology
  • RNA Helicases / genetics

Substances

  • BRCA1 Protein
  • BRCA1 protein, human
  • Fanconi Anemia Complementation Group Proteins
  • Neoplasm Proteins
  • Checkpoint Kinase 2
  • CHEK2 protein, human
  • PMS2 protein, human
  • Mismatch Repair Endonuclease PMS2
  • BRIP1 protein, human
  • RNA Helicases

Supplementary concepts

  • Breast Cancer, Familial