Seminar featuring Dr. Ben Raphael

  • Date: Tuesday, May 24, 2011
  • Location:
    3400 Boelter

Tuesday, May 24, 2011
3400 Boelter

Ben Raphael, Ph.D.
Assistant Professor
Computer Science Department
Brown University

Title: Algorithms for Cancer Genomics

Recent advances in DNA sequencing technologies are enabling biologists to sequence ever increasing numbers of genomes. One major application of genome sequencing is to measure the somatic mutations that accumulate in the genome during an individual’s lifetime and that lead to cancer. I will describe algorithms to address two challenges in interpreting data from these large-scale sequencing studies: (1) Deriving reliable measurements of structural rearrangements in cancer genomes from the short DNA sequences produced by sequencing machines; (2) Distinguishing the functional driver mutations responsible for cancer from random passenger mutations. For detection of structural rearrangements, I will describe algorithms to analyze paired-end, mate pair, and strobe sequencing data from different sequencing technologies. For driver mutation prediction, I will describe two approaches for identification of driver pathways, groups of genes containing driver mutations, in a large cohort of cancer samples. In the first approach, we use prior information about interactions between genes to identify pathways (or networks) of genes that are frequently mutated across samples. In the second approach, we optimize a measure derived from the statistical properties of mutations on driver pathways. I will illustrate the applications of these algorithms to mutation data from The Cancer Genome Atlas.