Cancer is a disease driven by mutations that alter gene structure, function, and regulation.
These mutations may be single nucleotide substitutions or larger-scale genomic alterations including translocations, inversions, duplications and deletions. In some types of cancer these large-scale alterations are directly implicated in the pathogenesis of cancer and are targets for cancer diagnostics and therapeutics. While many such alterations have been recorded in individual tumors, little is known about the detailed architecture of tumor genomes. I will describe computational methods for reconstructing tumor genome architectures and analyzing rearrangements in tumor genomes at high resolution using a technique called End Sequence Profiling (ESP). These methods are inspired by techniques in comparative genomics and view a tumor genome as a rearranged version of the normal human genome. A parsimonious sequence of rearrangements that transform one genome into another is then computed. I will also discuss how analysis of ESP data suggests mechanisms that produce complicated patterns of overlapping rearrangement and duplication events that are observed in some tumor genomes
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Joel Bader Seminar
Andrew Smith Seminar
Gene Regulatory Networks Special Feature (PNAS)
Abstract
These mutations may be single nucleotide substitutions or larger-scale genomic alterations including translocations, inversions, duplications and deletions. In some types of cancer these large-scale alterations are directly implicated in the pathogenesis of cancer and are targets for cancer diagnostics and therapeutics. While many such alterations have been recorded in individual tumors, little is known about the detailed architecture of tumor genomes. I will describe computational methods for reconstructing tumor genome architectures and analyzing rearrangements in tumor genomes at high resolution using a technique called End Sequence Profiling (ESP). These methods are inspired by techniques in comparative genomics and view a tumor genome as a rearranged version of the normal human genome. A parsimonious sequence of rearrangements that transform one genome into another is then computed. I will also discuss how analysis of ESP data suggests mechanisms that produce complicated patterns of overlapping rearrangement and duplication events that are observed in some tumor genomes