BRCA1 Circos: A Visualisation Resource for Functional Analysis of Missense Variants

J Med Genet. 2015 Apr;52(4):224-30. doi: 10.1136/jmedgenet-2014-102766. Epub 2015 Feb 2.

Abstract

Background: Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes.

Methods and results: To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant.

Conclusions: This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.

Keywords: BRCA1; Cancer: breast; Clinical genetics; Molecular genetics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • BRCA1 Protein / genetics*
  • Breast Neoplasms / genetics
  • Computational Biology / methods*
  • Computer Graphics*
  • DNA Mutational Analysis
  • Database Management Systems
  • Databases, Genetic
  • Datasets as Topic
  • Female
  • Genetic Predisposition to Disease
  • Genetic Testing
  • Humans
  • Internet*
  • Mutation, Missense*
  • Ovarian Neoplasms / genetics
  • Software*

Substances

  • BRCA1 Protein
  • BRCA1 protein, human