Molecular Epidemiology Core

The DF/HCC Molecular Epidemiology Core provides flexible, high-quality, high-throughput single nucleotide polymorphisms (SNP) genotyping to the DF/HCC research community. Its mission is to provide services to DF/HCC members conducting molecular analyses of germline and somatic DNA collected as part of a wide range of investigations into the molecular epidemiology of cancer, including Genome Wide Association Studies (GWAS). This core provides high-throughput assays of specific gene mutations and SNPs in the many situations where previously defined specific nucleotide alterations are of interest.

Key Services

  • SNP analysis using Taqman
  • SNP analysis using the Taqman OpenArray Genotyping System
  • Targeted sequencing using Ion Torrent PGM
  • DNA extraction, plating, and whole genome amplification
  • SNP analysis and sequencing using Illumina technologies
  • Telomere length analysis

Highlighted Projects

Project Title: Aspirin use, 8q24 single nucleotide polymorphism rs6983267, and colorectal cancer according to CTNNB1 alterations
Principal Investigator: Andrew Chan, MD, MPH (MGH)
Description of the Project: The results support an influence of aspirin on WNT/CTNNB1 signaling andsuggest that aspirin chemoprevention may be tailored according to rs6983267 genotype.
Contribution of the Core: The Core performed DNA Extraction of 5,233 individuals and TaqMan and OpenArray genotyping on 5,233 individuals.

Project Title: Common genetic variation of the calcium-sensing receptor and lethal prostate cancer risk
Principal Investigator: Edward Giovannucci, MD, ScD (HSPH)
Description of the Project: The joint association of SNPs in the calcium-sensing receptor (CaSR) was significant for lethal Prostate Cancer (P = 0.04). The findings indicate that the CaSR may be involved in Prostate Cancer progression.
Contribution of the Core: The Core performed OpenArray genotyping and DNA extraction and whole genome amplification of 2,924 individuals.

Project Title: Plasma vitamin D biomarkers and leukocyte telomere length
Principal Investigator: Immaculata DeVivo, MPH, PhD (BWH)
Description of the Project: Higher plasma 25(OH)D levels may be associated with longer telomeres, and this association may be modified by calcium intake.
Contribution of the Core: The Core performed DNA Extraction of 1,424 individuals, Telomere Length Analysis on 1,424 individuals and OpenArray genotyping on 480 individuals.


PUBLICATION ACKNOWLEDGEMENT:

If research supported by this core facility results in publication, please acknowledge this support by including the following in your publication(s):
"We thank Dana-Farber/Harvard Cancer Center in Boston, MA, for the use of the Molecular Epidemiology Core, which provided __________ service. Dana-Farber/Harvard Cancer Center is supported in part by an NCI Cancer Center Support Grant # NIH 5 P30 CA06516."