ReviewBiology2017
SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?
Review in Biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
What it found
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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
47 citing papers in PubMed.
- Chromosome-level genome assembly of Xuefeng Black-bone chicken and comparative genomics analysis.BMC genomics · 2026Article
- Harnessing genomic resources for passion fruit improvement: Progress and prospects.The plant genome · 2026Review
- Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Mechanistic Perspectives From Genomics and Pangenomics of Medicinal and Aromatic Plants: Linking Genome Architecture to Phytochemical Diversity.International journal of genomics · 2026Review
- Plasmid transmission dynamics and evolution of partner quality in a natural population ofmBio · 2025Article
- Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot.Molecular ecology resources · 2025Article
- The developments and prospects of plant super-pangenomes: Demands, approaches, and applications.Plant communications · 2025Review
- Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes inInternational journal of molecular sciences · 2025Article
- The role of pangenomics in orphan crop improvement.Nature communications · 2025Review
- Genomic and cell-specific regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy.Journal of experimental botany · 2025Review
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus).BMC genomic data · 2024Article
- Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.Cell reports methods · 2023Article
- Chaining for accurate alignment of erroneous long reads to acyclic variation graphs.Bioinformatics (Oxford, England) · 2023Article
- Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences.Systematic biology · 2023Article
- Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.Life (Basel, Switzerland) · 2023Review
- Investigating Pangenome Graphs Using Wheat Panache.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources.Frontiers in plant science · 2023Article
- Legume Pangenome: Status and Scope for Crop Improvement.Plants (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation. The advent of next-generation sequencing (NGS) coupled with the heritability of SNPs make them ideal markers for genetic analysis of human, animal, and microbial data. SNPs have also been extensively used in crop genetics for association mapping, quantitative trait loci (QTL) analysis, analysis of genetic diversity, and phylogenetic analysis. This review focuses on the use of pangenomes for SNP discovery. It highlights the advantages of using a pangenome rather than a single reference for this purpose. This review also demonstrates how extra information not captured in a single reference alone can be used to provide additional support for linking genotypic data to phenotypic data.
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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.