M Callari, S-J Sammut, L De Mattos-Arruda, A Bruna, OM Rueda, S-F Chin, C Caldas
Journal name: 
Genome Med
Citation info: 
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate. The ITC approach increased the sensitivity up to 17.1%, without increasing the false positive rate per megabase (FPR/Mb) and its validity was confirmed in a set of clinical samples.
Research group: 
Caldas Group
E-pub date: 
18 Apr 2017
Users with this publication listed: 
Alejandra Bruna
Carlos Caldas
Maurizio Callari
Stephen-John Sammut
Suet-Feung Chin