COPS

Copy Number Alterations (CNAs) such as deletions and duplications;
compose a larger percentage of genetic variations than single nucleotide
polymorphisms or other structural variations in cancer genomes that
undergo major chromosomal re-arrangements. It is, therefore, imperative
to identify cancer-specific somatic copy number alterations (SCNAs),
with respect to matched normal tissue, in order to understand their
association with the disease. We have devised an accurate, sensitive,
and easy-to-use tool, COPS, COpy number using Paired Samples, for
detecting SCNAs. We rigorously tested the performance of COPS using
short sequence simulated reads at various sizes and coverage of SCNAs,
read depths, read lengths and also with real tumor:normal paired
samples. We found COPS to perform better in comparison to other known
SCNA detection tools for all evaluated parameters, namely, sensitivity
(detection of true positives), specificity (detection of false
positives) and size accuracy. COPS performed well for sequencing reads
of all lengths when used with most upstream read alignment tools.
Additionally, by incorporating a downstream boundary segmentation
detection tool, the accuracy of SCNA boundaries was further improved.
Here, we report an accurate, sensitive and easy to use tool in detecting
cancer-specific SCNAs using short-read sequence data. In addition to
cancer, COPS can be used for any disease as long as sequence reads from
both disease and normal samples from the same individual are available.
An added boundary segmentation detection module makes COPS detected SCNA
boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”.