Geoffrey Beene Translational Oncology -- Core Facility

Geoffrey Beene Translational Oncology Staff Members

The Geoffrey Beene Translational Oncology Core Facility was established in 2007 to take full advantage of the wealth of clinical samples and the emerging information issuing from Memorial Sloan-Kettering Cancer Center clinical trials by applying state of the art genome-scale molecular profiling technologies. It is located on the 6th floor of the Mortimer Zuckerman Research Building. We are now fully operational and are running several projects for various Memorial Sloan-Kettering investigators.

The Core offers the following services:

1. 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 (FFPE) samples, blood, cytospins, etc. We also archive the DNA and maintain a DNA database of all material that is processed by our lab.
2. Whole genome amplification (WGA) of DNA extracted from these samples.
3. Fully automated high throughput PCR in 384 well plates, to provide templates for exon re-sequencing (Sanger or next-generation sequencing (454 or SOLiD -with Genomics Core Lab). The Core maintains an extensive fully annotated library of primers for human exon amplification. We currently have primers for ~500 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. LI>High volume sequencing through outside contractors, with greatly discounted operational costs due to large scale.
4. Automated mutation detection and data analysis using software applications designed by the Bioinformatics Core. The Core will also maintain a centralized database of sequences and genotypes.
5. Mass-spectrometry-based SNP genotyping or mutation detection, and DNA methylation studies, using the Sequenom MassARRAY and Epityper platforms. Dr. Timothy Chan (HOPP) provides expert consultations and support on all methylation related projects. In collaboration with physician scientists at Memorial Sloan-Kettering, we have designed and validated several panels for detection of common mutations in various types of human tumors. We have also designed a SNP genotyping assay for DNA fingerprinting, for sample identification, unequivocal paring of multiple samples from the same individual, cell lines, etc.
6. mRNA, miRNA expression analysis and copy number variation analysis using Nanostring technology, which uses color-coded molecular barcodes that can hybridize directly to many different types of target molecules, and allows for a multiplexing level of detection of 800 targets simultaneously.

By centralizing the necessary resources, the Core aims to optimize the Memorial Sloan-Kettering Cancer Center infrastructure needed for state of the art genomic analyses of clinical material. As integral part of its operations, the Core maintains an archive of DNA samples, pre- and post-genome amplification, trackable within a centralized database. As a result, nucleic acid samples can be easily retrieved, and routed to other relevant analysis platforms at Memorial Sloan-Kettering (e.g. Genomics Core for array CGH, SNP or expression analysis, Molecular Pathology R&D Core for Sequenom genotyping), as needed.

In addition to these services, the Core will also develop the capability to evaluate and eventually implement emerging technologies with potential to become services in the future, such as mutation or expression profiling from a few cells or very limited amounts of starting materials.