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Open Access Research article

Bivariate segmentation of SNP-array data for allele-specific copy number analysis in tumour samples

David Mosén-Ansorena* and Ana María Aransay

Author Affiliations

Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technologic Park of Bizkaia, Building 502, 48160 Derio, Spain

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BMC Bioinformatics 2013, 14:84  doi:10.1186/1471-2105-14-84

Published: 5 March 2013

Additional files

Additional file 1:

Recall rates by normal cell contamination and alteration pattern, and alteration length for different parameterisations. Recall rates (y-axis) by normal cell contamination level, sample pattern and alteration length (x-axis) for two different parameterisations of ASCAT (violet: default; brown: segmentation penalisation scaled by a factor of 0.35). Recall rates converge as region length increases, suggesting that both parameterisations achieve similar recall rates at long lengths, but the one that focuses on sensitivity is able to recall more short regions.

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Additional file 2:

Description of the procedures to couple CnaStruct with GAP, ASCAT and TAPS.

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Additional file 3:

Recall rates by normal cell contamination and alteration pattern, and alteration length for assessed methods. Recall rates (y-axis) of each of the assessed methods, calculated by normal cell contamination and alteration length (x-axis) over each of the five sample patterns. Colour code: purple (ASCAT), orange (GAP), black (GPHMM), blue (OncoSNP). Thicker lines correspond to the workflows in which CnaStruct was integrated.

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Additional file 4:

Results of the analyses of real data with a combination of CnaStruct and other methods. The analyzed samples are: (i) Two samples from the Affymetrix platform, which are bundled with the TAPS software package (example02 and example16). These samples were analyzed with CnaStruct-TAPS. Provided TAPS results format: columns “Start” and “End” specify probe genomic positions within chromosome (ii) Two samples from the Illumina plaform, which come from a cell-line dilution series [8]. The two picked samples present normal cell contaminations of 0% and 53%. Chromosomes 6 and 16 were excluded beforehand (see [8,17]). These samples were analyzed with CnaStruct-GAP and CnaStruct-ASCAT. The compressed file contains one tab-delimited table per analysis. ASCAT results format: columns “start” and “end” specify probe indexes; “nA” and “nB” specify the number of A and B alleles, so the called copy numbers can be calculated from their sum. GAP results format: columns “Ind” and “Ind_K” specify probe indexes; “CN1” specifies the copy number. “Chromosome”; “Cn” specifies the copy number.

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Additional file 5:

Plots for the analysis of real data with a combination of CnaStruct and other methods. The LRR profiles of several samples as analyzed with different combinations of CnaStruct and other methods are displayed. Colour code: blue, segment is called as being CN4 or higher; green, CN3; grey, CN2; red, CN1 or CN0. Only segments with more than 10 SNPs are superimposed. Even though ASCAT fails at the calling step on the 53% contamination sample, both ASCAT and GAP detect a loss on chromosome 13 not present in the pure tumour sample.

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