Integrated Genomic Biomarkers to Identify Aggressive Disease in African Americans with Prostate Cancer
Technical Report,01 Sep 2016,31 Aug 2017
Henry Ford Health System Detroit United States
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The purpose of our research is to identify somatic copy number alterations and methylation markers in the primary tumors of African American AA men that can serve as a component of their recurrence risk assessment and be applied in treatment planning in attempt to reduce the racially disparate rates of mortality from prostate cancer. Through whole genome copy number alteration and methylation scans, the study will identify individual and integrated DNA-based biomarkers of biochemical recurrence in 200 AA men 100 with and 100 without biochemical recurrence. These biomarkers will then be validated in an independent set of 200 AA men. In the first year of funding, we have enumerated both discovery and validation samples have obtained formalin fixed paraffin embedded blocks from 300 of these men have completed pathology review of the complete discovery sample tumors macrodissected and performed DNA extraction from 141 tumors completed the running and quality control of 60 tumors on the copy number assay completed the running and quality control of 48 tumors on the Illumina EPIC methylation microarrays. From the resulting copy number and methylation data, we have preliminary results for Aim 1 suggesting the utility of using the GEMCaP for prediction of biochemical recurrence in AA men, and further encouraging findings that suggest many, but not all, previously identified CpG methylation sites associated with biochemical recurrence in European American men are also associated with risk of recurrence in AA men. In addition, we also present finding from The Cancer Genome Atlas on copy number alterations that differ by race-ethnicity in AA vs. EA men with prostate cancer and are consistent with race-ethnicity differences observed in breast cancer. We intend to test these cross tumor site race-differentiated copy number alterations with biochemical recurrence in our study following completion of the discovery cohort.
- Medicine and Medical Research