The Harvard Partners Genotyping Facility, part of the Harvard Partners Center for Genetics and Genomics, provides flexible, high quality, high throughput SNP genotyping to the Harvard Partners research community, including investigators in the Dana Farber / Harvard Cancer Center, and the Harvard School of Public Health. The portfolio of Genotyping methods at the HPCGG now includes Illumina, Sequenom, and TaqMan.

The Illumina Bead Station GoldenGate assay system for SNP genotyping is a platform most suitable for researchers engaged in large scale association studies: whole genome linkage mapping panels and large scale fine mapping panels. The genotyping is carried our in 384, 768, and 1536 plex formats using Illumina custom SNP panels. Standing panels are also available from Illumina for linkage mapping. The technology operates using microbead technology assembled into 96 sample arrays with redundant bead types for increased confidence calls. The bead arrays are manufactured based on the custome SNP sets selected and configured onto the array surface. Incubation of the processed gDNA on the bead array allows hybridization to the appropriate probe on the bead and allows identification of a particular SNP.

Sequenome genotyping is performed using MALDI-TOF (Matrix-assisted laser desorption ionization - time of flight) mass spectrometry, or with Taqman allelic discrimination, and other methods as tertiary techniques. The facility can also perform custom micro-satellite genotyping for users. SNP genotyping by MALDI-TOF mass spectrometry is performed using the Sequenom mass spectrometry system. Our service includes primer and assay design through to production of genotypes. All steps involved are highly automated and are tracked using a laboratory management system with bar coding. In this method, multiplexed PCR and then a mini-sequencing reaction are performed in a single well. The size of reaction products is determined directly by MALDI-TOF mass spectrometry, yielding genotype information. Multiplexing permits determination of up to 12 SNPs in a single well of a 384 well plate. Specialized equipment for this work includes a Biomek multi-pipettor robot, a Multimek multi-pipettor robot, a nanoliter plotting robot for spotting the extension products onto chips, and the mass spectrometer.

Taqman SNP allelic discrimination is performed on the ABI 7700/7900. In this method, specialized probe oligonucleotides are used to distinguish the SNPs during or at the end of a PCR reaction. Depending upon a number of factors, including previous implementation of the method for a particular SNP, this method will be the first approach for genotyping in some cases. Please click here for more details.

Director: David Kwiatkowski, M.D., Ph.D.
Phone: (617) 355-9005
Fax: (617) 355-9016
Email: dk@rics.bwh.harvard.edu

Other Staff:

Associate Director for DF/HCC: David Hunter, Sc.D., M.D.
Phone: (617) 525-2755
nhdjh@channing.harvard.edu

Sequenom and Illumina Genotyping Lab Manager: Alison Brown
Phone: (617) 768-8470
Email: abrown13@partners.org

Taqman Genotyping Manager: Hardeep Ranu, Ph.D.
Phone: (617) 432-4469
Email: hranu@hsph.harvard.edu

Location of Core:

The facility is located at 65 Landsdowne St, Cambridge

Major Equipment:

Biomek and Multimek robotic pipetting device
384 well ABI 7900 Taqman machine
Chip spotting device
Mass spectrometry system for determining the absolute mass of short DNA sequences

►SNP analysis using Sequenom Mass Spectrometry
►Fragment Analysis using Capillary Electrophoresis
►ABI Prism Taqman Allelic Discrimination Assay

To access the core, please contact David Kwiatkowski at (617) 355-9005 or by email at
dk@rics.bwh.harvard.edu. Please also see website at http://www.hpcgg.org.

http://www.hpcgg.org