Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment.

Calling gene deletions For the detection of gene deletion, application of the same method that was used before for the detection of gene amplifications was not feasible because the thresholds would be CN < 0.52 for significant (multiple testing correction for tumors) gene losses and CN < 0.014 for highly significant (multiple testing correction only tumors and amplicons) gene losses.

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We are aware that the p-values for CDH1 and PTEN were only borderline significant.

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