ArticleGenome biology2019
Is it time to change the reference genome?
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 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
113 citing papers in PubMed.
- Taming the reference genome jungle: the refget sequence collection standard.Bioinformatics (Oxford, England) · 2026Article
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Beyond the linear genome: how reference bias threatens preventive medicine and geroscience.GeroScience · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Lossless pangenome indexing using tag arrays.Algorithms for molecular biology : AMB · 2026Article
- The pangenome ofiScience · 2026Article
- Review
- Diverse reference genomes detect variants in the US winter wheat.The plant genome · 2026Article
- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- Lossless Pangenome Indexing Using Tag Arrays.Research square · 2026Article
- Pangenome analysis of nine soybean cyst nematode genomes reveals hidden variation contributing to diversity and adaptation.BMC genomics · 2026Article
- The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Pangenome-guided sequence assembly via binary optimization.Briefings in bioinformatics · 2026Article
- Telomeric assemblies ofbioRxiv : the preprint server for biology · 2025Article
- Taming the reference genome jungle: the refget sequence collection standard.bioRxiv : the preprint server for biology · 2025Article
- Methodological opportunities in genomic data analysis to advance health equity.Nature reviews. Genetics · 2025Review
- Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.Horticulture research · 2025Article
- Pangenome-aware DeepVariant.bioRxiv : the preprint server for biology · 2025Article
53 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
3 authors.
Funding
Abstract
The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following opinion, we outline the history, properties, and pitfalls of the current human reference genome. In a few illustrative analyses, we focus on its use for variant-calling, highlighting its nearness to a 'type specimen'. We suggest that switching to a consensus reference would offer important advantages over the continued use of the current reference with few disadvantages.
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What OpenQuestion holds
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.