A research-based gene panel to investigate breast, ovarian and prostate cancer genetic risk

PLoS One. 2019 Aug 15;14(8):e0220929. doi: 10.1371/journal.pone.0220929. eCollection 2019.

Abstract

There is a need to investigate and better understand the inherited risk of cancer to ensure that clinical applications provide more accurate assessments and management strategies. Developing research-based next-generation sequencing gene panels that not only target (present-day) clinically actionable susceptibility genes but also genes that currently lack sufficient evidence for risk as well as candidate genes, such as those in DNA repair pathways, can help aid this effort. Therefore, gene panel B.O.P. (Breast, Ovarian, and Prostate) was developed to evaluate the genetic risk of breast, ovarian and/or prostate cancer, and this manuscript serves as an introduction to B.O.P. and highlights its initial analytical validity assessment. B.O.P targets 87 genes that have been suggested, predicted, or clinically proven to be associated with breast, ovarian, and/or prostate cancer risk using Agilent Technologies Haloplex probes. The probes were designed for 100 base pair reads on an Illumina platform and target both coding and non-coding exons as well as 10 intronic base pairs flanking the intron-exon boundaries. The initial B.O.P screening involved 43 individuals from the Alabama Hereditary Cancer Cohort, and an average sequencing depth of 809X was obtained. Upon variant filtering and validation, true positives had an average sequencing depth of 659X and allele balance of 0.51. The average false positive sequencing depth was 34X and allele balance was 0.33. Although low sequencing depth was not always indicative of a false positive, high sequencing depths (>100X) signified a true positive. Furthermore, sensitivity and specificity of BRCA1/2 were calculated to be 100% and 92.3%, respectively. Overall, this screening enabled the establishment of criteria to alleviate future validation efforts and strongly supports the use of B.O.P. to further elucidate hereditary cancer susceptibility. Ultimately, continued B.O.P. screening will provide insights toward the genetic risk of and overlap between breast, ovarian, and/or prostate cancer.

Publication types

  • Clinical Trial
  • Multicenter Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adult
  • BRCA1 Protein / genetics*
  • BRCA2 Protein / genetics*
  • Breast Neoplasms / genetics*
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Middle Aged
  • Ovarian Neoplasms / genetics*
  • Prostatic Neoplasms / genetics*
  • Risk Factors

Substances

  • BRCA1 Protein
  • BRCA1 protein, human
  • BRCA2 Protein
  • BRCA2 protein, human

Grants and funding

This research was supported by the American Association of Colleges of Pharmacy (AACP) New Investigator Award (https://www.aacp.org/resource/new-investigator-award), AU Research Initiative in Cancer (AURIC) Seed Grant (https://www.vetmed.auburn.edu/auric/), the Joy to Life Foundation Grant (https://joytolifefoundation.org/), the AU Innovative Research grant through the Internal Grant Program (https://joytolifefoundation.org/) with matching funds provided by AURIC and the Joy to Life Foundation, and the National Science Foundation (NSF) Research Excellence for Undergraduates (REU; Award number: 1560115) (N.D.M.). This research was also supported by the AURIC Graduate Fellowship Program (https://www.vetmed.auburn.edu/auric/; to M.R.B. and A.L.W.H.), the AU Cellular and Molecular Biosciences (CMB) Peaks of Excellence Research Fellowship (to M.R.B. and A.L.W.H.; NSF-EPS-1158862, grant G00006750), the NSF REU Fellowship (to J.H.), the Department of Drug Discovery and Development in the AU Harrison School of Pharmacy, the Department of Pathobiology in the AU College of Veterinary Medicine, and the AU College of Sciences and Mathematics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.