Bioinformatics Seminar
Time:
Venue: Na
23 February 2016
NaAnalysing exomes with superFreq
Christoffer FlensburgWEHI Cancer & Haematology
A cancer evolves over time. The changes can grant competitive advantages over other cells ; such as transformation to a more aggressive disease ; metastasis or resistance to drugs. To understand these phenomena ; it is central to track the mutations in the cancer cells as they evolve. Exome sequencing of cancer samples is a powerful tool that can identify key mutations as well as accurately track changes over samples ; and comes at a relatively low price.
Our group has analysed a large number of cancer exomes in various settings ; with different research questions ; and have found the existing tools unable to find all the answers. Driven by these questions ; we have developed superFreq: an R package that analyses cancer exomes. It identifies somatic mutations ; both SNVs and copy number alterations (CNAs) ; and tracks them over samples from the same individual. superFreq puts all available samples to full use. Even unrelated normal samples are used in superFreq to estimate variance and blacklist common miscalls ; which allows a detailed analysis of disease progression even without a matched normal sample.