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

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.

Mots clés

Allelic Imbalance Breast Neoplasms Gene Expression Profiling Gene Expression Regulation Neoplastic Genome Genotype Homozygote Humans Karyotyping Loss of Heterozygosity Genetic Polymorphism Single Nucleotide

Automation Genomics Models Ploidies

Domaines

Génomique, Transcriptomique et Protéomique [q-bio.GN] Génétique

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https://inserm.hal.science/inserm-00663915

Soumis le : vendredi 27 janvier 2012-17:19:49

Dernière modification le : mardi 12 mars 2024-10:45:45

Archivage à long terme le : mercredi 14 décembre 2016-01:46:10

Dates et versions

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

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Paternité

Identifiants

HAL Id : inserm-00663915 , version 1
DOI : 10.1186/gb-2009-10-11-r128
PRODINRA : 245453
PUBMED : 19903341
WOS : 000273344600015

Citer

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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