Microsatellite genotyping reveals a signature in breast cancer exomes

L. J. McIver, N. C. Fonville, E. Karunasena, H. R. Garner

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Genomic instability at microsatellite loci is a hallmark of many cancers, including breast cancer. However, much of the genomic variation and many of the hereditary components responsible for breast cancer remain undetected. We hypothesized that variation at microsatellites could provide additional genomic markers for breast cancer risk assessment. A total of 1,345 germline and tumor DNA samples from individuals diagnosed with breast cancer, exome sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation. The comparison group for our analysis, representing healthy individuals, consisted of 249 females which were exome sequenced as part of the 1,000 Genomes Project. We applied our microsatellite-based genotyping pipeline to identify 55 microsatellite loci that can distinguish between the germline of individuals diagnosed with breast cancer and healthy individuals with a sensitivity of 88.4 % and a specificity of 77.1 %. Further, we identified additional microsatellite loci that are potentially useful for distinguishing between breast cancer subtypes, revealing a possible fifth subtype. These findings are of clinical interest as possible risk diagnostics and reveal genes that may be of potential therapeutic value, including genes previously not associated with breast cancer.

Original languageEnglish (US)
Pages (from-to)791-798
Number of pages8
JournalBreast Cancer Research and Treatment
Issue number3
StatePublished - Jun 2014
Externally publishedYes


  • Breast cancer risk assessment
  • Cancer genomics
  • Microsatellite variation
  • The Cancer Genome Atlas

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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