To maintain and build on the Sidney Kimmel Comprehensive Cancer Center’s (SKCCC) record of excellence in the fields of cancer genetics and epigenetics, the SKCCC has established a new Next Generation Sequencing Center (NGSC) as a shared resource since January 2009. A product of a convergence of advances in molecular biology, engineering, computer science, and bioinformatics, Next Generation Sequencing features the ability to sequence billions of base pairs of DNA in a single run, at a cost that is several orders of magnitude less than previous gold standard sequencing technologies. Next Generation Sequencing is an extremely versatile technology and can be used to investigate a multitude of genomic processes in a previously unimaginable genome-wide and unbiased fashion. In order to facilitate widespread adoption of this relatively new technology, rather than administering the Center as a “black-box” core facility, the Core operates as a “collaborative core” center in which users can consult and collaborate with NGSC faculty and staff to:
- identify the optimal molecular biology approaches (prior to sequencing library construction) to synapse their research questions with the capabilities of the Center,
- prepare the appropriate libraries and carry out massively parallel sequencing, and
- carry out the appropriate primary, secondary, and tertiary bioinformatics analyses to analyze and interpret the results. The NGSC features two Applied Biosystems SOLiD V3 Next Generation Sequencing instruments capable of generating >20 Gigabases of sequencing data in a single run, state-of-the-art equipment for sequencing library preparation and quality control, and powerful computational resources including a server with 6 compute nodes (each containing Quad Core Intel Xeon processors and 16 Gigabytes of memory) and 100 terabytes of storage for dedicated bioinformatics analyses.
The center is currently administered by an overall faculty director overseeing all activities, an associate faculty director overseeing bioinformatics support, a laboratory manager, and a bioinformatics manager. The Center’s goal is to be as flexible as possible in assisting researchers in exploring all aspects of cancer genetics and epigenetics, including, but not limited to, germline and somatic variation/mutation, genomic structural variations/alterations, transcriptome analysis, transcription factor binding sites, chromatin modifications, and DNA methylation.
Srinivasan Yegnasubramanian, M.D., Ph.D., Resource Director
Sarah Wheelan,M.D., Ph.D., Co-Resource Director