Core Facilities

High-Throughput Polymorphism Detection

High-Throughput Polymorphism Detection Core

The mission of the High-Throughput Polymorphism Detection Core is to provide services to investigators conducting molecular analyses of somatic DNA collected as part of a wide range of investigations. 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.

OpenArray

The OpenArray SNP Genotyping Platform is a nanofluidic chip based platform that allows us to run assays that we know work well using traditional 384- well format TaqMan assays. The OpenArray system allows users to run 16, 32 or 64 SNPs on one OpenArray. Depending on the number of SNPs on an OpenArray up to 144 samples can be run per OpenArray (in a 16-plex assay).

Taqman

SNP Analysis using ABI Prism Taqman Allelic Discrimination Assay
Single SNP allelic discrimination is carried out using the ABI 7900HT, which allows single-plex SNP interrogation over a large volume of samples.

Taqman Submission Guidelines

Sequenom

SNP genotyping by MALDI-TOF mass spectrometry is performed using the Sequenom mass spectrometry system. Sequenom iPLEX chemistry and software allows interrogation of up to 40 custom SNPs in one well, using minimal genomic DNA. This platform is suitable for researchers with projects containing 20 to 384 SNPs or insertion deletion polymorphisms.

Sequenom Submission Guidelines

To use the Sequenom SNP Genotyping service, we require that you register at our secure site to submit DNA samples and SNP flanking sequence.

Once you have registered and have had your application approved you can then go on to submit SNP flank sequence for assay design and DNA sample sheet information.

Leadership and Staff

Core Director: Immaculata De Vivo, MPH PhD

Core Co-Director: David Kwiatkowski, MD

Content Contributor: Hardeep Ranu

Links

NCI Cohort Consortium - Taqman Genotyping Call Key
CHIP Bioinformics
BLAST Human Sequences
Applied Biosystems Assays - Applied Biosystems provides a wide selection of almost 2 million “off the shelf” Taqman SNP assays. Included are approximately 160,000 validated assays, 30,000 coding assays and 1.8 million pre-designed asssays that provide high density, genome-wide marker coverage.
A collection of Taqman Drug Metabolism Assays- This is a collection of over 2000 genotyping assays target polymorphisms in 220 genes within the drug metabolism pathways that code for phase I, phase II, and transporter enzymes. Each assay has gone through an extensive amount of bioinformatics that include mapping to correctly identify the SNP and eliminate interference from pseudo genes.

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 High-Throughput Polymorphism Detection Core, which provided __________ service. Dana-Farber/Harvard Cancer Center is supported in part by an NCI Cancer Center Support Grant # NIH 5 P30 CA06516.