Sequenza

Exome sequencing of tumor specimens is an important component of the PREDICT Consortium’s quest to identify determinants of drug response in renal cancer.

In PREDICT research and cancer research in general, exome sequencing is typically used to identify small scale somatic mutations, whereas large scale mutations such as copy number aberrations are typicall detected with SNP microarrays. However, exome sequencing has potential to deliver copy number profiles as well, rendering SNP array analysis unnecessary.

Sequenza is a state-of-the-art software to determine tumor copy number profiles directly from matched tumor/normal exome sequencing data. To the best of our knowledge, it is the only software to produce allele-specific copy number profiles from exome sequencing in a manner that accounts for and models tumor ploidy and cellularity.

Importantly, these accurate copy number profiles enable model-based interpretation of point mutations (variant allele frequency), which in turn enables more accurate detection of mutations, as well as detection of selection among subclonal populations.

Sequenza was developed by members of the PREDICT Consortium and has been freely available to the cancer research community since December 2013.

A manuscript describing Sequenza has been submitted for publication.

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