Cancer Genomics at CSHL focuses on approaches to understanding tumor development, progression and therapeutic response. Members of this program attack the cancer problem from three distinct perspectives.
First, several research groups focus on genomic changes in breast cancer, ovarian cancer, prostate cancer, liver cancer, pancreatic cancer, leukemia, lymphoma and other cancers. These researchers have focused on the development and application of sophisticated tools for genome analysis that permit high resolution mapping of deletions, amplifications and changes in the sequence or epigenetic status of chromosomal loci.
More recently, CSHL scientists have developed methods for selective resequencing of the genome for probing cancer-related genomic alterations and methods for querying copy number alterations and sequence variations from individual cancer cells. Sequencing methods have also been applied for the determination of epigenetic states.
The second perspective of this program is the development and application of genetic tools in cell culture and animal models. These include sophisticated chromosome engineering techniques as well as applications of large-scale RNAi screens to identify both driver genes and tumor-cell-specific dependencies. Researchers have initiated construction of a third generation RNAi library and developed powerful and rapid methods for engineering mice with inducible gene knockdown in many tissues. These genetic tools allow biological validation of loci discovered by analysis of cancer genomes.
The third perspective of this program centers around a group of investigators who focus on harnessing the large scale data sets from genomic analyses and the development of tools that can be used community wide. Examples include the study of allelic variation in the human genome and the development of computational methods for the discovery of cancer-associated genes and diagnostic cancer markers using genomic profiles derived from multiple tumors.