ArticleGenome medicine2017
Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- An Annotated Biobank of Triple-Negative Breast Cancer Patient-Derived Xenografts Features Treatment-Naïve and Longitudinal Samples during Neoadjuvant Chemotherapy.Cancer research · 2025Trial
- Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA.Genome medicine · 2019Trial
- Multiomic profiling of T cell lymphoma after therapy with anti-BCMA CAR T cells and GPRC5D-directed bispecific antibody.Nature medicine · 2025Article
- A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing.Briefings in bioinformatics · 2024Article
- A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer.International journal of molecular sciences · 2024Article
- Article
- Performance analysis of conventional and AI-based variant callers using short and long reads.BMC bioinformatics · 2023Article
- The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer.Cancer research · 2023Article
- Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy.Frontiers in immunology · 2023Review
- Somatic Variants in SVIL in Cerebral Aneurysms.Neurology. Genetics · 2022Article
- The origin of bladder cancer from mucosal field effects.iScience · 2022Article
- Identification of biomarkers of response to preoperative talazoparib monotherapy in treatment naïve gBRCA+ breast cancers.NPJ breast cancer · 2022Article
- Computational analysis of cancer genome sequencing data.Nature reviews. Genetics · 2022Review
- Early Breast Cancer Evolution by Autosomal Broad Copy Number Alterations.International journal of genomics · 2022Article
- Multi-region exome sequencing reveals the intratumoral heterogeneity of surgically resected small cell lung cancer.Nature communications · 2021Article
- iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data.Briefings in bioinformatics · 2021Article
- Synergistic Anticancer Activity ofInternational journal of molecular sciences · 2021Article
- Improvement of Neoantigen Identification Through Convolution Neural Network.Frontiers in immunology · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
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.
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