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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.

Ion Torrent PGM

The Core is offering a targeted sequencing service using the Ion Torrent PGM. The capabilities of this service include:

Custom Amplicon Sequencing of DNA and RNA Panels

Ready-to-use Ion AmpliSeq Panels: 

Cancer Hotspot Panel – 50 genes, > 2,800 Cosmic Mutations, 207 Amplicons
Comprehensive Cancer Panel – 409 genes, 16,000 Amplicons
Inherited Disease Panel – 700 disease, 328 genes, 10,000 Amplicons

The system requires only 10ng of input DNA and DNA from FFPE samples can also be used. Additionally, only one or two samples can be run at a time.

There are three different Chip formats:

  • Ion 314 Chip: 1 million wells,  400-550 thousand reads for 200bp sequencing
  • Ion 316 Chip: 6 million wells, 2-3 million reads for 200bp sequencing
  • Ion 318 Chip: 11 million wells, 4-5.5 million reads for 200bp sequencing


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.

Please contact Hardeep Ranu (Tel: 617 432 4469) for more information on Ion Torrent PGM, TaqMan or OpenArray.

Please click here for Taqman Submission Guidelines

DNA Extraction

We provide a DNA extraction service.  We are able to extract DNA from buffy coat, whole blood and buccal samples.  

A Whole Genome Amplification service is also avaiable , using the GenomiPhi DNA Amplification Kit from GE Inc.  The typical yield is 3–7 micrograms of amplified DNA from as little as 10–20 ng of genomic DNA template.

For more information about DNA Extraction and Whole Genome Amplification services please contact Pati Soule

Telomere Length Analysis

We use a quantitative PCR-based method adapted to assess relative telomere length (RTL) in peripheral blood lymphocytes (PBL).  

Please contact Pati Soule for more information.

Custom Illumina GoldenGate genotyping

This platform is 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 out in large multiplexes of between 384-1536 SNPs, in multiples of 96 SNPs, using Illumina custom SNP panels or standard validated pre-manufactured panels. The Golden Gate assay is an allele-specific oligo hybridization, ligation and extension assay followed by universal PCR amplification, allowing that no amplification bias can occur. These amplification products then bind to the 3 uM microbeads in 32-sample BeadChips and alleles are read by fluorescent readout using the iSCAN reader.

Custom SNP assay design is carried out using Illumina's SNP Knowledge Resource, which consists of a large SNP database and expert support service. The PCPGM Genotyping Facility is happy to help navigate this process for customers. This resource provides access to more than 1,000,000 high confidence, mapped, and annotated SNP markers and to validated SNP assays across the human genome. Customers should be aware that this process can take several weeks to complete.

Illumina Infinium genotyping

The Infinium assay from Illumina allows whole genome genotyping at different levels of coverage using a variety of fixed content chips. The most recently released chips use 700,000 to 5 million markers for genotyping. The Genotyping Facility is happy to offer any chips currently available from Illumina, including the newest chips detailed at Illumina’s website. This facility is also willing to offer custom Infinium iSelect genotyping to interrogate up to 60K custom SNPs.

The latest Infinium HD assay is a PCR independent assay. It uses hybridization of the loci of interest to 50-mer probes, stopping one base before the interrogated marker. Single base extension is then carried out to incorporate a labeled nucleotide. Dual color (red/green) staining allows the nucleotide to be detected by the iSCAN reader and is converted to genotype during analysis with the GenomeStudio analysis software.

Raw data is delivered via GIGPAD and is in the form of a .csv file which connects sample ID with marker ID and genotype.

Illumina methylation analysis

This facility offers Methylation Analysis from genomic DNA or bisulfite treated DNA using the Illumina 450K Infinium Methylation BeadChip covering 99% of RefSeq genes, including the promoter region, 5’UTR, first exon, gene body and 3’UTR regions.  After bisulfite conversion the process follows the Infinium HD assay detailed above.  Raw data is delivered via GIGPAD and is in the form of a .csv file which connects sample ID with CpG site and methylation status.

Please contact Ashley Blau (ablau@partners.org, Tel: 617-768-8557) for quotes and information on the Illumina platform.

Click here for more information.

Leadership and Staff

Core Co-Director: David Kwiatkowski, MD
Content Contributor: Hardeep Ranu

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.