A simple consensus approach improves somatic mutation prediction accuracy.
Differentiating true somatic mutations from artifacts in massively parallel sequencing data is an immense challenge. To develop methods for optimal somatic mutation detection and to identify factors influencing somatic mutation prediction accuracy, we validated predictions from three somatic mutation detection algorithms, MuTect, JointSNVMix2 and SomaticSniper, by Sanger sequencing. Full consensus predictions had a validation rate of >98%, but some partial consensus predictions validated too. In cases of partial consensus, read depth and mapping quality data, along with additional prediction methods, aided in removing inaccurate predictions. Our consensus approach is fast, flexible and provides a high-confidence list of putative somatic mutations.
Peter MacCallum Cancer Centre, Sarcoma Genetics and Genomics Laboratory, St. Andrew's Place, East Melbourne, Victoria, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
David L
DL
Goode
Peter MacCallum Cancer Centre, Cancer Genetics Laboratory, St. Andrew's Place, East Melbourne, Victoria, Australia.
Sally M
SM
Hunter
Peter MacCallum Cancer Centre, Bioinformatics Core Facility, St. Andrew's Place, East Melbourne, Victoria, Australia.
Maria A
MA
Doyle
Peter MacCallum Cancer Centre, Bioinformatics Core Facility, St. Andrew's Place, East Melbourne, Victoria, Australia ; Bioinformatics Graduate Program, University of Melbourne, Parkville, Victoria, Australia.
Tao
T
Ma
Peter MacCallum Cancer Centre, Cancer Genetics Laboratory, St. Andrew's Place, East Melbourne, Victoria, Australia.
Simone M
SM
Rowley
Peter MacCallum Cancer Centre, Cancer Genetics Laboratory, St. Andrew's Place, East Melbourne, Victoria, Australia.
David
D
Choong
Peter MacCallum Cancer Centre, Cancer Genetics Laboratory, St. Andrew's Place, East Melbourne, Victoria, Australia ; Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
Georgina L
GL
Ryland
Peter MacCallum Cancer Centre, Cancer Genetics Laboratory, St. Andrew's Place, East Melbourne, Victoria, Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia ; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia.
Ian G
IG
Campbell