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 prof...

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Detalles Bibliográficos
Autores principales: Popova, Tatiana, Manié, Elodie, Stoppa-Lyonnet, Dominique, Rigaill, Guillem, Barillot, Emmanuel, Stern, Marc Henri
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810663/
https://www.ncbi.nlm.nih.gov/pubmed/19903341
http://dx.doi.org/10.1186/gb-2009-10-11-r128
Descripción
Sumario: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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