Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.
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ABSTRACT:
SUBMITTER: Popova T
PROVIDER: S-EPMC2810663 | biostudies-literature | 2009
REPOSITORIES: biostudies-literature
Publications
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.
Popova Tatiana T Manié Elodie E Stoppa-Lyonnet Dominique D Rigaill Guillem G Barillot Emmanuel E Stern Marc Henri MH
Genome biology 20091111 11
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genom ...[more]
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