Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.
2009
Popova, Tatiana | Manié, Elodie | Stoppa-Lyonnet, Dominique | Rigaill, Guillem | Barillot, Emmanuel | Stern, Marc, Henri | Unité de génétique et biologie des cancers (U830) ; Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM) | Département de Biologie des Tumeurs ; Institut Curie [Paris] | Mathématiques et Informatique Appliquées (MIA-Paris) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Département de Recherche Translationnelle ; Institut Curie [Paris] | Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe ; Mines Paris - PSL (École nationale supérieure des mines de Paris) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM) | This work is part of the "Cancéropôle Ile-de-France-Région Ile-de-France-Hereditary Breast Cancer" program coordinated by DSL and MHS. This work also was supported by the INSERM, the Institut Curie, and its Translational Research Department. TP is supported by a grant from the Cancéropôle Ile-de-France-Région Ile-de-France. GR is supported by a grant from the Institut National du Cancer (INCa).
International audience
Mostrar más [+] Menos [-]Inglés. 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.
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