Reconstructing cancer genomes from paired-end sequencing data
Open Access
- 19 April 2012
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 13 (S6), S10
- https://doi.org/10.1186/1471-2105-13-s6-s10
Abstract
A cancer genome is derived from the germline genome through a series of somatic mutations. Somatic structural variants - including duplications, deletions, inversions, translocations, and other rearrangements - result in a cancer genome that is a scrambling of intervals, or "blocks" of the germline genome sequence. We present an efficient algorithm for reconstructing the block organization of a cancer genome from paired-end DNA sequencing data.Keywords
This publication has 43 references indexed in Scilit:
- Mapping copy number variation by population-scale genome sequencingNature, 2011
- Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer DevelopmentCell, 2011
- BreakDancer: an algorithm for high-resolution mapping of genomic structural variationNature Methods, 2009
- Maximum Likelihood Genome AssemblyJournal of Computational Biology, 2009
- High-resolution mapping of copy-number alterations with massively parallel sequencingNature Methods, 2008
- Expression of Yes-associated protein in common solid tumorsHuman Pathology, 2008
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencingNature Genetics, 2008
- Patterns of somatic mutation in human cancer genomesNature, 2007
- Fine-scale structural variation of the human genomeNature Genetics, 2005