Abstract 4956: Droplet digital PCR in validating copy number variations in hereditary prostate cancer families from Louisiana
Authors: Kirsten Wood, Ratish Gambhira, Elisa Ledet, Oliver Sartor, Diptasri Mandal
Journal: Cancer Research (2016)

Abstract Prostate cancer (PCa) is the second leading cause of death in American men, and approximately 27,540 men will die from the disease in the US this year. Louisiana has one of the highest rates of PCa in the country, with approximately 4,000 new cases each year. Family history is one of the most prominent predictors of PCa risk, and approximately 10% of PCa cases are attributable to inheritable genetic factors. However, identifying PCa genetic susceptibility has been extremely difficult due to genetic heterogeneity. Genomic copy number variations (CNVs) have been detected in prostate tumors and several other cancers, but changes in copy number have not been studied extensively in germ-line DNAs from hereditary PCa (HPC) cases. The goal of the present study is to validate the presence of CNVs using a cutting edge technology Droplet Digital Polymerase Chain Reaction (ddPCR). ddPCR provides absolute quantification of target DNA copies and can measure small fold differences in target DNA copy numbers. We hypothesize that ddPCR will precisely validate the CNVs identified using array comparative genomic hybridization (aCGH) technology. In our preliminary study, we have identified CNVs in germline DNAs from 7 HPC cases from 7 Louisiana HPC families of European ancestry by using aCGH technology. The regions identified were 2q22, 11q22, and 16q23, and these regions were found to be duplicated in all HPC cases analyzed. In addition, a 68 kb duplication was observed at 2q14 in all 7 HPC cases of European ancestry, and this region was further identified by using linkage analysis in 4 of the 7 HPC families (heterogeneity LOD-score = 1.94). In order to validate the duplication observed at 2q14 (BIN1), we performed ddPCR. Each ddPCR reaction uses duplex TaqMan assay reagents for the target region and the reference gene. Analysis of ddPCR data is conducted using QuantaSoft Analysis software. From this study we found that several of our HPC cases had germline copy number values of 2.2 or higher in the BIN1 region, suggesting that these samples may have partial gene amplification at the 2q14 region rather than duplication of the entire gene. These findings suggest that ddPCR is capable of providing absolute quantification of copy number differences. Using the recently launched custom design ddPCR Copy Number assays for our specific regions of interest, we will perform analysis on additional CNV regions in affected as well as in other unaffected family members from these HPC families. The absolute quantification of copy number differences using ddPCR will contribute to the impending need of cancer biomarker identification in the era of precision medicine, and will allow us to facilitate prostate cancer screening in HPC families. Citation Format: Kirsten Wood, Ratish Gambhira, Elisa Ledet, Oliver Sartor, Diptasri Mandal. Droplet digital PCR in validating copy number variations in hereditary prostate cancer families from Louisiana. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4956.