IGO Services

Integrated Genomics Operation (IGO)
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IGO Services
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IGO Services

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IGO Lab

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.

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:

  • Whole genome sequencing
    • Human/mouse (deep and shallow)
    • Bacteria/yeast
    • Shotgun metagenomics
  • Whole transcriptome sequencing
    • Poly A enrichment
    • Ribodepletion
    • SMART-Seq for ultra-low input
  • ChIP-Seq/CUT&RUN
  • ATAC-Seq
  • Amplicon sequencing
    • CRISPR Screens
    • 16S sequencing
  • Targeted sequencing (for full gene lists, please contact us at [email protected])
    • MSK-IMPACT (mouse and human)
    • IMPACT-Heme
    • MSK ACCESS
    • Whole exome sequencing (mouse and human)
    • Custom targeted panels (contact [email protected] for more information)
  • TCR-Seq
    • IGO in-house platform
    • 10x genomics VDJ
  • CRISPR cut site sequencing

Single Cell & Spatial Transcriptomics

IGO maintains a full complement of technologies to interrogate gene expression, immune repertoire, protein expression, chromatin accessibility, and DNA-based SNVs/CNVs of single cells. We also offer frozen- and FFPE-based high resolution spatial transcriptomics platforms to examine expression in context of a tissue or tumor.

  • 10X Genomics scRNA-Seq
    • 3’ or 5’ GEX
    • Optional VDJ enrichment
    • Optional feature barcoding or cell hashing
  • 10X Genomics Multiome
    • Single nuclei ATAC-Seq + RNA-Seq
  • 10X Genomics Visium
  • 10X Genomics Xenium
  • Nanostring GeoMx
  • SmartSeq
    • SMART-Seq 3 method for low cell numbers
  • Direct Library Prep
  • Nanostring CosMx

Sequencing

Illumina

IGO houses a full range of Illumina sequencing instruments including MiSeq, NextSeq 1000 and 2000, and NovaSeq 6000 and X Plus, 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 [email protected].

IGO also offers Sequencing Only Services for investigators who prepare their own libraries. Read blocks come in a range of sizes from 1, 4, 20 million reads all the way up to 25 billion reads. 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 libraries are compatible with Illumina sequencers.

 

Oxford Nanopore

Long read sequencing on the Oxford Nanopore PromethIon is also offered at IGO. We provide long-read PCR-free WGS or cDNAseq. Targeted sequencing with the adaptive sampling technology, epigenetic modification detection with methylation basecalling and direct RNAseq are also available.

 

Element Biosciences

MSK investigators can now sequence at their own convenience with IGO’s walk-up sequencing service on the Element Aviti. For more information about the instrument, visit Element’s website. For more information about the service, please email us at [email protected].

Other Platforms

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 [email protected].

Digital PCR New Assay Design

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