Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole- exome sequencing data

do Valle, Italo Faria ; Giampieri, Enrico ; Simonetti, Giorgia ; Padella, Antonella ; Manfrini, Marco ; Ferrari, Anna ; Papayannidis, Cristina ; Zironi, Isabella ; Garonzi, Marianna ; Bernardi, Simona ; Delledonne, Massimo ; Martinelli, Giovanni ; Remondini, Daniel ; Castellani, Gastone (2016) Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole- exome sequencing data. BMC Bioinformatics, 17 . pp. 109-212. ISSN 1471-2105
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Abstract

Background: Detecting somatic mutations in whole exome sequencing data of cancer samples has become a popular approach for profiling cancer development, progression and chemotherapy resistance. Several studies have proposed software packages, filters and parametrizations. However, many research groups reported low concordance among different methods. We aimed to develop a pipeline which detects a wide range of single nucleotide mutations with high validation rates. We combined two standard tools – Genome Analysis Toolkit (GATK) and MuTect – to create the GATK-LODN method. As proof of principle, we applied our pipeline to exome sequencing data of hematological (Acute Myeloid and Acute Lymphoblastic Leukemias) and solid (Gastrointestinal Stromal Tumor and Lung Adenocarcinoma) tumors. We performed experiments on simulated data to test the sensitivity and specificity of our pipeline. Results: The software MuTect presented the highest validation rate (90 %) for mutation detection, but limited number of somatic mutations detected. The GATK detected a high number of mutations but with low specificity. The GATK-LODN increased the performance of the GATK variant detection (from 5 of 14 to 3 of 4 confirmed variants), while preserving mutations not detected by MuTect. However, GATK-LODN filtered more variants in the hematological samples than in the solid tumors. Experiments in simulated data demonstrated that GATK-LODN increased both specificity and sensitivity of GATK results. Conclusion: We presented a pipeline that detects a wide range of somatic single nucleotide variants, with good validation rates, from exome sequencing data of cancer samples. We also showed the advantage of combining standard algorithms to create the GATK-LODN method, that increased specificity and sensitivity of GATK results. This pipeline can be helpful in discovery studies aimed to profile the somatic mutational landscape of cancer genomes.

Abstract
Document type
Article
Creators
CreatorsAffiliationORCID
do Valle, Italo Faria
Giampieri, Enrico
Simonetti, Giorgia
Padella, Antonella
Manfrini, Marco
Ferrari, Anna
Papayannidis, Cristina
Zironi, Isabella
Garonzi, Marianna
Bernardi, Simona
Delledonne, Massimo
Martinelli, Giovanni
Remondini, Daniel
Castellani, Gastone
Subjects
ISSN
1471-2105
DOI
Deposit date
11 Nov 2016 10:49
Last modified
11 Nov 2016 10:49
Project name
NGS-PTL - Next Generation Sequencing platform for targeted Personalized Therapy of Leukemia
Funding program
EC - FP7
URI

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