ReviewGenome medicine2020
Best practices for variant calling in clinical sequencing.
Review in Genome medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 220 papers, 2 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
220 citing papers in PubMed, 2 syntheses or guidelines pooled it, 402 citations in OpenAlex.
- Diagnosis, management and treatment of the Alport syndrome - 2024 guideline on behalf of ERKNet, ERA and ESPN.Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association · 2025Guideline
- ClinicalFrontiers in microbiology · 2025Pooled it
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Identification of Novel Transcriptional Alleles in Primary Prostate Cancer Cells and Cancer Stem Cells by Bulk RNA-Seq and Single-Cell RNA-Seq Analyses.Biomolecules · 2026Article
- Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.Nature biotechnology · 2026Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.Genome research · 2026Article
- T-rex: standardized analysis of germline variants in whole-exome sequencing trios.Scientific reports · 2026Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- ITHindex: An integrated web-based platform for intratumor heterogeneity evaluation.PLOS digital health · 2026Article
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- Pansoma, a machine learning tool for identifying somatic variants using pangenome graphs.bioRxiv : the preprint server for biology · 2026Article
- Integrating Mutation-Derived and Expression Features from Single-Cell RNA Sequencing: Pitfalls of Standard Cross-Validation in Small-Cohort Settings.International journal of molecular sciences · 2026Article
- Pipettes and Pipelines: The Weapons of Omics Sciences for a New Age of Clinical Studies.Current issues in molecular biology · 2026Review
- Distinct genomic landscape of colorectal signet ring cell carcinoma reveals frequent KMT2 family alterations and SMAD4 inactivation.BMC cancer · 2026Article
- Perspectives From an Expert-Guided Discussion on Maximizing the Research Potential of Small Biopsy Tissue.JCO precision oncology · 2026Article
- Discovery metabolomics and genetic analysis reveal lipid pathway alterations associated with malignant phenotype acquisition in pleomorphic adenoma and a novel NTF3::ITPR2 fusion in carcinoma ex pleomorphic adenoma.Virchows Archiv : an international journal of pathology · 2026Article
- A near telomere-to-telomere genome assembly of the Amur stickleback (Zoological research · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- igv-reports: embedding interactive genomic visualizations in HTML reports to aid variant review.Bioinformatics (Oxford, England) · 2026Article
160 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely. Just as NGS technologies have evolved considerably over the past 10 years, so too have the software tools and approaches for detecting sequence variants in clinical samples. In this review, I discuss the current best practices for variant calling in clinical sequencing studies, with a particular emphasis on trio sequencing for inherited disorders and somatic mutation detection in cancer patients. I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection. Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance. Although NGS technologies are continually evolving, and new capabilities (such as long-read single-molecule sequencing) are emerging, the "best practice" principles in this review should be relevant to clinical variant calling in the long term.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.