ReviewGenome biology2023
Genomic variant benchmark: if you cannot measure it, you cannot improve it.
Review in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
28 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Recent advances in understanding the spectrum of genetic determinants of lipoprotein(a) levels.Current opinion in lipidology · 2026Review
- A systematic assessment of machine learning for structural variant filtering.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive survey of genome language models in bioinformatics.Briefings in bioinformatics · 2026Review
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- Benchmark for simple and complex genome inversions.bioRxiv : the preprint server for biology · 2025Article
- Constellation illuminates rare disease genetics.medRxiv : the preprint server for health sciences · 2025Article
- Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions.bioRxiv : the preprint server for biology · 2025Article
- Performance comparison of germline variant calling tools in sporadic disease cohorts.Molecular genetics and genomics : MGG · 2025Article
- The Platinum Pedigree: a long-read benchmark for genetic variants.Nature methods · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis.BMC genomics · 2025Article
- Comprehensive genome analysis and variant detection at scale using DRAGEN.Nature biotechnology · 2025Article
- Analytical validation of germline small variant detection using long-read HiFi genome sequencing.Genome research · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.Genome research · 2025Article
- Analysis and benchmarking of small and large genomic variants across tandem repeats.Nature biotechnology · 2025Article
- GREGoR: Accelerating Genomics for Rare Diseases.ArXiv · 2024Article
- The GIAB genomic stratifications resource for human reference genomes.Nature communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.
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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.