A searchable database of core laboratory facilities. Core Facilities

Genotyping and Genetics for Population Sciences Core (DF/HCC)

Director: de Vivo, Immaculata, M.P.H., Ph.D.

Location: Harvard T.H. Chan School of Public Health, 665 Huntington Ave., Bldg 2. Room 255, Boston MA 02115

Core Summary:

The mission of the Genotyping and Genetics for Population Sciences 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.

  • Dana-Farber/Harvard Cancer Center
Personnel/Contact Information:

Director: de Vivo, Immaculata, M.P.H., Ph.D.
Phone: (617) 432-1642

Member: General Inquiries

Facilities and Equipment:

Location of Core: Harvard T.H. Chan School of Public Health, 665 Huntington Ave., Bldg 2. Room 255, Boston MA 02115

Major Equipment:

  • ABI PRISM 7900HT sequence detection system
  • Beckman Coulter Biomek FX laboratory automation workstation
  • Deerac Fluidics Equator nanopipetter
  • Illumina iSCAN reader and Autoloader 2.0
  • Ion Torrent PGM
  • OpenArray
  • Perkin Elmer Janus liquid Handler
  • Tecan Freedom EVO 150 liquid handler
  • 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.

  • Ion Torrent Targeted Sequencing

    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.

  • SNP Analysis using OpenArray Genotyping

    The Taqman OpenArray platform allows users to run 16, 32 or 64 SNPs in parallel using Taqman reagents.

    The per genotype cost varies with the number of samples and the number of SNPs. Please contact Hardeep Ranu for exact pricing information.

  • SNP Analysis using Taqman

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

  • Telomere Length Analysis

  • Whole genome amplification service

    DNA extraction, plating, and whole genome amplification.

Departmental Web Link(s):

Last updated: 2016-01-26T12:56:20.494-06:00