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Derivation and Consequences of Rearranged Cancer Genomes

Mathematical Systems Biology of Cancer II October 24, 2007 - October 26, 2007

October 26, 2007 (03:30 PM PDT - 04:15 PM PDT)

Speaker(s): Ben Raphael

Primary Mathematics Subject Classification No Primary AMS MSC

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Abstract

As part of the LBNL Integrated Cancer Biology Program, copy number changes in 51 breast cancer cell lines were measured using array Comparative Genomic Hybridization (aCGH). However, other genomic alterations in these cell lines are invisible to aCGH including copy neutral rearrangements such as inversions and translocations. These rearrangements are also common in cancer and can produce novel fusion genes or alter gene regulation. A technique called End Sequence Profiling (ESP) can identify these rearrangements by mapping paired-end sequences of cancer genome fragments to the reference human genome sequence. We have performed ESP for three of the cell lines in the LBNL ICBP. I will describe the ESP data and its integration with other genomic data. In particular, I will show how to determine candidate fusion genes using ESP data, and I will describe how to combine data from both ESP and CGH to derive the organization of the cancer genome. Finally, I will demonstrate potential consequences of cancer genome organization by examining Chromatin Immunopreciptation (ChIP) data in the context of the rearranged cancer genome.

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