MSK CMO Group

     Semi-automated high throughput nucleic acid (DNA and RNA) extraction from both archived and newly acquired clinical specimens, including frozen tissue, formalin fixed paraffin embedded samples, cytospins, etc. We also archive the DNA and maintain a DNA database of all material that is processed by our lab.

     Whole genome amplification (WGA) of DNA extracted from these samples.

     Fully automated high throughput PCR in 384 well plates, to provide templates for exon re-sequencing (Sanger or next-generation sequencing-with Genomics Core Lab), and for genotyping or DNA methylation studies using Sequenom technology. (We now have our own Sequenom Machine.) The Core maintains an extensive fully annotated library of primers for human exon amplification or for genotyping. We currently have primers for ~400 genes of interest to the cancer genomics community. Primers for the entire human genome are already designed and will be ordered upon request for specific projects.

High volume sequencing through outside contractors, with greatly discounted operational costs due to large scale.  

     Automated mutation detection and data analysis using software applications designed by the Bioinformatics Core. The Geoffrey Beene Translational Oncology Core will also maintain a centralized database of sequences and genotypes.

Genotyping [d1] of known mutations and DNA methylation analysis using Sequenom technology (mass spectrometry-based)

Multiplexed gene expression analysis using Nanostring[d2]  technology

In addition to these services, the Core will also develop the capability to evaluate and eventually implement emerging technologies --