Integrated Genomics Operation (IGO)

IGO Services


The Integrated Genomics Operation offers a full range of services from sample preparation through sequencing.

Sample preparation

We help with the extraction of RNA and DNA from both standard and challenging sources, followed by sample quality assessment. Sample preparation may also include pathological review, phenotypic characterization, and microdissection from FFPE or OCT preserved tissues. IGO also provides feedback and recommendations as to which platform is most practical given the quality of the samples.

Based on the performance of thousands of past samples, IGO has worked to define pass/fail criteria for samples entering our downstream applications. After our internal quality assessment, we provide processing recommendations so that the researchers can make the most informed decision possible. View our pass/fail criteria.

Library preparation

IGO prepares Illumina libraries for diverse Next-generation sequencing (NGS) applications. While we have optimized our standard preparation to be run on an automated platform, manual preparation is employed for technically challenging samples.

Library preparation services currently offered by IGO:

  • Whole genome sequencing
    • Human (deep and shallow)
    • all other genomes
  • Whole transcriptome sequencing
    • Poly A enrichment
    • Ribo depletion
    • SMART-Seq for ultra-low input
    • Fusion discovery
  • ChIP-Seq
  • ATAC-Seq
  • Amplicon sequencing
  • Custom PCR panel
  • Targeted sequencing (for full gene list, please contact us at
      • Mouse
      • Human
    • HemePACT
    • Whole exome sequencing
      • Mouse
      • Human 
    • Custom target sequencing*
  • TCR-Seq
  • $70 CRISPR cut site sequencing
  • CRISPR and shRNA screening 
  • Archer FusionPlex assay


IGO houses a full range of Illumina sequencing instruments including MiSeq, NextSeq, HiSeq 2500, HiSeq 4000 and NovaSeq, allowing researchers to choose from a variety of read lengths and depths.

Before sequencing, users must consider how many reads are required (read depth) and how long the reads should be (read length). We encourage users to discuss their experimental design with their bioinformatician prior to starting an experiment and collecting samples. MSK’s Bioinformatics Core Facility (BIC) can help you define these values, if you’re unsure of what sequencing parameters are required to answer your biological questions. You can contact them at

IGO also offers full-lane sequencing for users who prepare their own libraries. Lane sizes range from 15 million reads (MiSeq) to multiples of 350M reads (HiSeq) We can assist with planning and pooling of libraries, and make suggestions to ensure quality data output. Please contact the core at any time to review any user-made libraries for sequencing so that we can ensure the library is compatible with Illumina sequencers.

Other Platforms

Fragment and STR Analysis

In addition to NGS, IGO also offers Sanger and STR analysis services. Sanger’s fragment analysis is ideal for allelic detection and identification, while STR is commonly used for cell-line for authentication.

Digital PCR

As an alternative to real-time quantitative PCR, IGO provides digital PCR (ddPCR) services for mutation detection, fusion detection, viral detection or CNV. IGO has already verified many genes, and the full list can be requested.

Digital PCR New Assay Design

If your gene of interest has not been verified, IGO can perform new assay designs.

*Custom Bait Design

IGO can assist with developing custom sequencing panels that target one or many genes utilizing positive capture based enrichment methods. Please contact us at to set up an appointment to discuss a new panel design.