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Genome Biology

, 10:R128

First Online: 11 November 2009Received: 02 February 2009Revised: 24 September 2009Accepted: 11 November 2009

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.

AbbreviationsBAFB allele frequency

BLCbasal-like breast carcinoma

CBScircular binary segmentation

CNcopy number

CNVcopy-number variation

FCMflow cytometry

LOHloss of heterozygosity

LRRLog R ratios

mBAFmirrored BAF

MDA 175MDA-MB-175-VII breast cancer cell line

MDA 468MDA-MB-468 breast cancer cell line

SNPsingle-nucleotide polymorphism.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2009-10-11-r128 contains supplementary material, which is available to authorized users.

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Autor: Tatiana Popova - Elodie Manié - Dominique Stoppa-Lyonnet - Guillem Rigaill - Emmanuel Barillot - Marc Henri Stern

Fuente: https://link.springer.com/







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