The Geoffrey Beene Translational Oncology Core Facility was established in 2007 to take full advantage of the wealth of clinical samples and emerging information issuing from Memorial Sloan Kettering clinical trials by applying state-of-the-art genome-scale molecular profiling technologies. It is located on the sixth floor of the Zuckerman Research Building.
The Core offers the following services:
- 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, and cytospins. 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 resequencing (Sanger or next-generation sequencing with the Genomics Core Lab). We currently have primers for approximately 800 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 Sanger sequencing through outside contractors, with greatly discounted operational costs due to large scale. Automated mutation detection and data analysis of Sanger sequences using software applications designed by the Bioinformatics Core.
- Mass-spectrometry-based SNP genotyping or mutation detection (MassArray iPlex), and DNA methylation studies (Epityper), using the Sequenom platform. 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 an SNP genotyping assay for DNA fingerprinting – for sample identification, unequivocal paring of multiple samples from the same individual, cell lines, etc.
- mRNA, miRNA expression analysis and copy number variation analysis with 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 20 to 800 targets simultaneously.
- Reverse protein arrays using Zeptosens technology. This technology facilitates high-throughput profiling of protein levels in tumors and cell line. The system is much more sensitive, considerably faster, and less expensive than Western blots, requiring much smaller sample quantities. More than 300 validated antibodies in various signaling pathways, including Akt, MAPK, lipid, cAMP, insulin, and many others, are available for use on Zeptosens reverse arrays. The system uses direct fluorescence readout with high sensitivity provided by planar waveguide technology. The lowest level of detection is approximately 2,100 protein molecules per spot.
In addition to these services, the Core also is working to develop the capability to evaluate, and eventually offer, emerging technologies such as mutation or expression profiling from a few cells or a very limited amount of starting material.