CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation

Maria Ortiz-Estevez (1, 2) , Ander Aramburu (1) , Henrik Bengtsson (3, 4) , Pierre Neuvial (5, 3) , Angel Rubio (1)

1 CEIT and Tecnun
2 Biology Group
3 Department of Statistics [Berkeley]
4 Department of Epidemiology and Biostatistics, University of California, San Francisco
5 SG - Laboratoire Statistique et Génome

CalMaTe calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina. Availability: The method is available on CRAN (http://cran.r-project. org/) in the open-source R package calmate, which also includes an add-on to the Aroma Project framework (http://www.aroma-project. org/).

Keywords: LOSS-OF-HETEROZYGOSITY

Keywords: ABERRATIONS; TUMORS

Domains: Bioinformatics [q-bio.QM]; Statistics [math.ST]

Maria Ortiz-Estevez, Ander Aramburu, Henrik Bengtsson, Pierre Neuvial, Angel Rubio. CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation. Bioinformatics, 2012, 28 (13), pp.1793-1794. ⟨10.1093/bioinformatics/bts248⟩. ⟨hal-01200761⟩