Genomics Core Laboratory (GCL) -- Core Facility

Agnès Viale (Core Facility Head)
E-mail(s)
vialea@mskcc.org

The Genomics Core Lab (GCL) at Memorial Sloan Kettering is a full-service microarray and sequencing facility.

The GCL supports basic and clinical research by providing DNA and RNA analysis services, from experimental design and sample preparation to basic data analysis and training. Since its inception in January 2001, the GCL has processed more than 15,000 samples and served more than 150 New York state laboratories and numerous out–of-state research institutions.

Sample preparation services include RNA and DNA extraction from standard and challenging sources as well as sample quality control assessment. The functional genomics applications available are gene expression, array comparative genomic hybridization (aCGH), microRNA, SNP, chromatin immunoprecipitation and methylation analysis measured with Affymetrix, Illumina or Agilent microarrays. Microarray validation by real-time PCR is also provided.

Recently, the GCL has expanded its portfolio of measurement technologies to include several Next Generation Sequencing instruments, the PGM from Ion Torrent, two HiSeq2000 and a MiSeq from Illumina, a 454FLX and a 454Junior from Roche and a SOLiD5500 from Life Technologies. The availability of these different sequencing technologies enables high-throughput analysis of a range of genomics applications, such as variant detection, epigenomics, transcriptome sequencing and more.

GCL staff also provides basic bioinformatics analysis, training and support for the tri-institutional community on in-house bioinformatics tools such as Partek Genomics Suite Software, Ingenuity, 454 analysis tools, DNASTAR Lasergene and others.

Services

RNA Analysis

  • RNA extraction
    • from tissue
    • from cell
    • from blood
  • RNA quality control and quantification
    • on Agilent Bioanalyzer
    • with Nanodrop
  • cDNA synthesis
    • for Quantitative-PCR
    • for other purposes
  • Microarray
    • experimental design
    • Affymetrix GeneChip® array
    • Illumina expression chip
    • data analysis (see below)
  • Next generation sequencing
    • RNA-Seq on Applied Biosystem SOLiD
  • Real-time PCR
    • on Applied Biosystem 7500

DNA Analysis

  • DNA extraction
    • from tissue
    • from cell
    • from blood
  • SNP analysis
    • Affymetrix Human Mapping SNP6 system
  • Chromosomal abnormality — CGH BAC array
    • for mouse (1MB resolution clone set)
    • for human (1MB resolution clone set)
  • Next generation sequencing
    • sequencing on 454 or SOLiD systems
  • Sanger sequencing

Microarray Data Analysis

  • Weekly workshop for Memorial Sloan Kettering users
    • for Partek Software
    • for in-house analytical tools
  • Monthly training
    • for Partek
  • Tutorial
    • introduction to microarray tools and analysis
    • next generation sequencing analysis

Visit the Tri-Institutional Web site, www.triiprograms.org, for more information.

Publications