ArticleScientific reports2020
Systematic comparison of somatic variant calling performance among different sequencing depth and mutation frequency.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Low-level mosaic variants causing the pancreatic disease congenital hyperinsulinism can be detected from blood DNA.EBioMedicine · 2026Article
- Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies.Scientific reports · 2026Article
- Molecular origin, discovery, validation and application of neoantigens.Asian journal of pharmaceutical sciences · 2026Review
- Removal of Transgenes and Evaluation of Yield Penalties in Genome Edited Bacterial Blight Resistant Rice Varieties.Plant biotechnology journal · 2026Article
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- Benchmarking major somatic structural variant callers on the HG008 genome.Frontiers in genetics · 2026Article
- Computational Methods for Cancer Neoantigen Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Benchmarking Ploidy Estimation Methods for Bulk and Single-Cell Whole Genome Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Systematic evaluation of de novo mutation calling tools using whole genome sequencing data.Briefings in bioinformatics · 2025Article
- Current status and future perspectives of multi-modal bacteria-based cancer therapies.Clinical and translational medicine · 2025Review
- A Differential Depth Sequencing Method, SPRE-Seq, for Enhancing Targeted Region Coverage in Hybridization Capture-Based NGS.Engineering in life sciences · 2025Article
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- Scaling for African Inclusion in High-Throughput Whole Cancer Genome Bioinformatic Workflows.Cancers · 2025Review
- GENOMICON-Seq enables realistic simulation of amplicon and exome sequencing for low-frequency mutation detection.Scientific reports · 2025Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- hDNApipe: streamlining human genome analysis and interpretation with an intuitive and user-friendly interface.NAR genomics and bioinformatics · 2025Article
- Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants.Genome medicine · 2025Article
- Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice.Plant biotechnology journal · 2025Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the past decade, treatments for tumors have made remarkable progress, such as the successful clinical application of targeted therapies. Nowadays, targeted therapies are based primarily on the detection of mutations, and next-generation sequencing (NGS) plays an important role in relevant clinical research. The mutation frequency is a major problem in tumor mutation detection and increasing sequencing depth is a widely used method to improve mutation calling performance. Therefore, it is necessary to evaluate the effect of different sequencing depth and mutation frequency as well as mutation calling tools. In this study, Strelka2 and Mutect2 tools were used in detecting the performance of 30 combinations of sequencing depth and mutation frequency. Results showed that the precision rate kept greater than 95% in most of the samples. Generally, for higher mutation frequency (≥20%), sequencing depth ≥200X is sufficient for calling 95% mutations; for lower mutation frequency (≤10%), we recommend improving experimental method rather than increasing sequencing depth. Besides, according to our results, although Strelka2 and Mutect2 performed similarly, the former performed slightly better than the latter one at higher mutation frequency (≥20%), while Mutect2 performed better when the mutation frequency was lower than 10%. Besides, Strelka2 was 17 to 22 times faster than Mutect2 on average. Our research will provide a useful and comprehensive guideline for clinical genomic researches on somatic mutation identification through systematic performance comparison among different sequencing depths and mutation frequency.
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