Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

被引：42

作者：

Callari, Maurizio ^{[1
]}

Sammut, Stephen-John ^{[1
]}

De Mattos-Arruda, Leticia ^{[1
]}

Bruna, Alejandra ^{[1
]}

Rueda, Oscar M. ^{[1
]}

Chin, Suet-Feung ^{[1
]}

Caldas, Carlos ^{[1
]}

机构：

[1] Univ Cambridge, CRUK Cambridge Inst, Cambridge, England

来源：

GENOME MEDICINE | 2017年 / 9卷

关键词：

Somatic mutation; Variant calling; Whole exome sequencing; NA12878; Platinum genome; Mutect2; Strelka; BWA; Novoalign; Filtering; CANCER; DISCOVERY; GENOMICS; DNA;

D O I：

10.1186/s13073-017-0425-1

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页数：11

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