PT  - JOURNAL ARTICLE
AU  - Donatien Chedom-Fotso
AU  - Ahmed Ashour Ahmed
AU  - Christopher Yau
TI  - OncoPhase: Quantification of somatic mutation cellular prevalence using phase information
AID  - 10.1101/046631
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 046631
4099  - http://biorxiv.org/content/early/2016/03/31/046631.short
4100  - http://biorxiv.org/content/early/2016/03/31/046631.full
AB  - The impact of evolutionary processes in cancer and its implications for drug response, biomarker validation and clinical outcome requires careful consideration of the evolving mutational landscape of the cancer. Genome sequencing allows us to identify mutations but the prevalence of those mutations in heterogeneous tumours must be inferred. We describe a method that we call OncoPhase to compute the prevalence of somatic point mutations from genome sequencing analysis of heterogeneous tumours that combines information from nearby phased germline variants. We show using simulations that the use of phased germline information can give improved prevalence estimates over the use of somatic variants only.