Evaluation of somatic copy number variation detection by NGS techonologies and bioinformatics tools

We have benchmarked the performance of cancer CNV calling by six most recent software tools on their detection accuracy, sensitivity, and reproducibility. We also explored the consistency of CNV calling across different orthogonal technologies, including optical mapping and microarrays. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we established a high-confidence CNV call set for the reference sample. Three replicate preparations of the tumor cell line HCC1395 were compared to three replicate preparations of its matched normal control cell line HCC1395BL using the Illumina Infinium CytoSNP-850K BeadChip.