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High-Throughput Polymorphism Detection Core

The High-Throughput Polymorphism Detection Core (HTPC) provides services to DF/HCC investigators conducting molecular analyses of germline 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 polymorphisms (SNPs) in the many situations where previously defined specific nucleotide alterations are of interest.  The core provides flexible, high quality, high throughput SNP Genotyping to the DF/HCC research community.

The principal activity of the HTPC is high-throughput genotyping.  The genotyping platforms we provide are Applied Biosystems TaqMan, OpenArray, Sequenom and Illumina. In addition to the singleplex TaqMan genotyping platforms, the Core also has a TaqMan Open Array SNP genotyping platform, the OpenArray system. This platform allows users to run 16, 32 or 64 SNPs on one OpenArray.  The Illumina GoldenGate Assay is a platform that allows custom panels of SNPs that are available in 96 or 384-1536 assays per OPA (Oligo Pool All) tubes.  Sequenom allows users to run up to 40 multiplexed panels of SNPs in to a single well of a 384-well plate using Sequenom iPLEX chemistry.  The advantage of having such a diverse range of technologies is that as a Core facility HTPC is able to tailor its services to a large number of customer needs.

In addition to SNP typing, this Core provides high volume DNA extraction and sample handing services.  It is also the only Core to offer whole genome amplification as a core service.  HTPC has built substantial capacity in DNA extraction, quantitation, and mother plate preparation.  In 2002, a Qiagen 3000 liquid handling system was purchased to increase capacity, and the Core can process four 96-well plates per day in all aspects of DNA extraction (initial extraction, mother plate preparation, sub-aliquoting, sample tracking, database preparation, and DNA quantitation).  In 2009, a QiAgility was purchased to aid in sample standardization as the trend for genotyping projects has moved towards genome-wide association studies.  These services are the only sample handling services available on a large-scale to DF/HCC members.

Listed below are a few examples illustrating how the Core has contributed to various projects:

PIs:  Daniel Cramer, MD, ScD (BWH) and Susan Hankinson, MPH ScD (BWH)
Polymorphisms in the vitamin D receptor and risk of ovarian cancer in four studies.  In this study three SNPs in the vitamin D receptor (VDR) gene (Fok1, Bsm1, Cdx2) were associated with risk of epithelial ovarian cancer in a retrospective case-control study (New England Case-Control study, NECC) and a nested case-control study of three prospective cohort studies: the Nurses' Health Study (NHS), NHSII, and the Women's Health Study. Data from the cohort studies were combined and analyzed using conditional logistic regression and pooled with the results from the NECC, which were analyzed using unconditional logistic regression, using a random effects model.  A significant positive association between the number of Fok1 f alleles and ovarian cancer risk in the pooled analysis (P(trend) = 0.03) was observed. The Core genotyped the three Vitamin D receptor SNPs using TaqMan.  This study resulted in the following publication: Polymorphisms in the vitamin D receptor and risk of ovarian cancer in four studies.  Tworoger SS, Gates MA, Lee IM, Buring JE, Titus-Ernstoff L, Cramer D, Hankinson SE.  Cancer Res. 2009 Mar ;69(5):1885-91  

PI: David Hunter, MBBS, MPH, ScD (HSPH)
A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer.  A genome-wide association study (GWAS) of breast cancer was conducted by genotyping 528,173 SNPs on 1,145 post-menopausal women of European Ancestry with invasive breast cancer and 1,142 controls.  Four SNPs in intron 2 of FGFR2 were highly associated with breast cancer.  This association was confirmed in three additional studies, all four SNPs were highly statistically significant with Ptrend for rs1219648 (the most strongly associated SNP) = 1.1x10-10.  The Core used the TaqMan platform to genotype samples from the NHS 2 and WHS for the four SNPs in FGFR2.  This study resulted in the following publication: A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer.  Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE et al. Nat Genet. 2007 Jul;39(7):870-4.