Overview of Services

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

Sample preparation

IGO performs 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. We also have a number of single cell and spatial transcriptomics platforms.

After an internal quality assessment, we provide feedback and recommendations as to which downstream platform is most practical. These recommendations are based off the performance of thousands of past samples and are meant to allow researchers to make the most informed decision possible.

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:

Sequencing

IGO houses a full range of Illumina sequencing instruments including MiSeq, NextSeq 1000 and 2000, NovaSeq 6000, and NovaSeq X, 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 bicrequest@mskcc.org.

IGO also offers full-lane sequencing for users who prepare their own libraries. Lane sizes range from 1 million reads (MiSeq Nano kit) to multiples of 400M reads (Next/NovaSeq) all the way to 10B reads (NovaSeq). We can assist with planning and pooling of libraries and make suggestions to ensure quality data output. Please contact the core at any time with your 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 custom fragment analysis and Cell Line Authentication by STR analysis. Fragment analysis on the ABI SeqStudio is ideal for allelic detection and identification and microsatellite analysis, while STR is commonly used for human cell line authentication and T/N matching confirmation.

Digital PCR

As an alternative to real-time quantitative PCR, IGO provides digital PCR (dPCR) services for mutation detection, fusion detection, viral detection or CNV. IGO has already verified many genes, and the full list can be requested by e-mailing genomics@mskcc.org or checking https://genomics.mskcc.org/ddpcr.

Digital PCR New Assay Design

If your gene of interest has not been verified, IGO can perform new assay design and optimization

Leadership:

Director: Neeman Mohibullah, Ph.D., Schwartz S-730

Many of our services are now available with off-the-shelf price:

Pricing List