In the past Columbia University researchers have accessed genomic technology and expertise at the CGC either through academic collaborations or via ad hoc service contracts. As key genomic technologies become more widely used, we envision that standardized fee-for-service components will be developed at the CGC. In each of the four areas described below CGC investigators are conducting state-of-the-art research or technology development, and are planning to implement University-wide service facilities.
- Microaray Gene Expression Analysis and Informatics
Original Research: Drs. Noble (Grundy), Bussemaker, and Pavlidis.
Service Component: Dr. Paul Pavlidis is Head of Gene Expression Analysis at the CGC and will oversee the service component. Dr. Pavlidis, together with Dr. Noble, has published several novel studies of gene expression and has developed, with Dr. Jie Qin, a web-based platform for data analysis, MiNK (microarray.cpmc.columbia.edu/toolkit/html/). The service component will feature some combination of on-site training, workshops, and contracted data analysis.
- DNA Sequencing and Mutation Scanning
Original Research: Drs. Ju, Russo.
Service Component: We envision offering high throughput capillary-based DNA sequencing (for example; cDNA libraries, SAGE libraries, genome libraries) and re-sequencing of gene targets in large sample populations. Dr. Ju pioneered the sequencing chemistry for the high throughput sequencing operation at Incyte Pharmaceuticals and continues, with Dr. Russo, to develop similar operations at the CGC. The group uses Amersham MegaBACE 96 capillary sequencers. Dr. Bill Iannuccilli, formerly Senior Technology Specialist at Amersham Pharmacia Biotech, will assist Drs. Russo and Ju with the service component.
Dr.Ju’s group is developing several novel technology platforms for high throughput DNA sequencing and mutation detection. As these technologies mature, we envision that they will be added to the service component.
- Microsatellite Genotyping and Analysis
Original Research: Drs. Gilliam, Terwilliger, Juo and Greenberg.
Service Component: The CGC currently runs a high throughput microsatellite genotyping facility with capacity for about 1.25 million genotypes per year. In the past, we have worked collaboratively, or on occasion, contracted with Columbia researchers to perform whole genome microsatellite scans. The group currently uses gel-based ABI model 377 technologies, but plans to shift to capillary based genotyping in the near future. Statistical geneticists at the CGC have worked collaboratively with and on a contract basis with Columbia researchers.
- New York State Bioinformatics Core Facility
Original Research: Drs. Rzhetsky, Annastassiou, Noble (Grundy), Bussemaker, Smith
Service Component: Kenneth Smith, PhD, Director. In affiliation with the Academic Medical Development Company (AMDeC) scientists at the CGC are funded to provide bioinformatics support and service to academic institutes throughout the state of New York. A detailed description of this resource is being developed for the AMDeC website and will be posted once it become available.