2011
DOI: 10.1186/gb-2011-12-10-r108
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Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

Abstract: We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analys… Show more

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Cited by 86 publications
(121 citation statements)
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“…Aberration calling from Illumina chips was as previously described 33 . The Chromosome Analysis Suite (ChAS, Affymetrix) Software was used to analyse Affymetrix Cytoscan HD data, followed by bioinformatic analysis with TAPS 34 . Copy number aberrations were considered if 10 or more consecutive markers/SNPs qualified as loss or gain.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…Aberration calling from Illumina chips was as previously described 33 . The Chromosome Analysis Suite (ChAS, Affymetrix) Software was used to analyse Affymetrix Cytoscan HD data, followed by bioinformatic analysis with TAPS 34 . Copy number aberrations were considered if 10 or more consecutive markers/SNPs qualified as loss or gain.…”
Section: Discussionmentioning
confidence: 99%
“…When nondiploid, calculations were normalized for tumour cell ploidy as obtained by SNP array assessment, or cytogenetic analyses in cases where SNP array interpretation was ambiguous with respect to ploidy. The bioinformatic tool TAPS 34 was used for Affymetrix arrays to estimate absolute allele-specific copy numbers and identify genomic regions with copy number heterogeneity and the most likely composition of copy numbers behind each such observation, as described 34 . The median intensity ratio (2 log ratio ; or BAF in case of copy-neutral heterogeneity) of an identified region was used to calculate relative prevalence of each copy number in the composition, using genomic segments with the involved copy numbers in all tumour cells as reference points.…”
Section: Discussionmentioning
confidence: 99%
“…Absolute ploidy and clonal fractions of selected samples were validated with Tumor Aberration Prediction Suite (TAPS) as previously described (31).…”
Section: Snp Array Analysismentioning
confidence: 99%
“…The Tumor Aberration Prediction Suite algorithm (22) (25,26). PAM50 classification was as described for the Guy's (27), METABRIC (23), and TCGA cohorts (6).…”
Section: Dna Copy-number and Gene-expression Analysismentioning
confidence: 99%