Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. - Archive ouverte HAL Access content directly
Journal Articles Genome Biology Year : 2009

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

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Abstract

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 genomes.

Domains

Life Sciences [q-bio] Biochemistry, Molecular Biology Genomics [q-bio.GN] Life Sciences [q-bio] Genetics
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https://www.hal.inserm.fr/inserm-00663915

Submitted on : Friday, January 27, 2012-5:19:49 PM

Last modification on : Monday, November 7, 2022-2:44:08 PM

Long-term archiving on: Wednesday, December 14, 2016-1:46:10 AM

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inserm-00663915 , version 1 (27-01-2012)

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Attribution - CC BY 4.0

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Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, et al.. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.. Genome Biology, 2009, 10 (11), pp.R128. ⟨10.1186/gb-2009-10-11-r128⟩. ⟨inserm-00663915⟩

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