Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer
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Natalie C. Fonville1, Zalman Vaksman1, Lauren J. McIver1, Harold R. Garner1
1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
Harold R. Garner, e-mail: [email protected]
Keywords: Ovarian Cancer, Biomarkers, The Cancer Genome Atlas, Breast Cancer, 1,000 Genomes Project
Received: October 22, 2014 Accepted: December 16, 2014 Published: March 04, 2015
Ovarian cancer (OV) ranks fifth in cancer deaths among women, yet there remain few informative biomarkers for this disease. Microsatellites are repetitive genomic regions which we hypothesize could be a source of novel biomarkers for OV and have traditionally been under-appreciated relative to Single Nucleotide Polymorphisms (SNPs). In this study, we explore microsatellite variation as a potential novel source of genomic variation associated with OV. Exomes from 305 OV patient germline samples and 54 tumors, sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation and compared to healthy females sequenced as part of the 1,000 Genomes Project. We identified a subset of 60 microsatellite loci with genotypes that varied significantly between the OV and healthy female populations. Using these loci as a signature set, we classified germline genomes as ‘at risk’ for OV with a sensitivity of 90.1% and a specificity of 87.6%. Cross-analysis with a similar set of breast cancer associated loci identified individuals ‘at risk’ for both diseases. This study revealed a genotype-based microsatellite signature present in the germlines of individuals diagnosed with OV, and provides the basis for a potential novel risk assessment diagnostic for OV and new personal genomics targets in tumors.
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