ArticleeLife2018
Association mapping from sequencing reads using
Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 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.
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Who cites it
70 citing papers in PubMed.
- BiTUGA: scalable prevalence-based unitig association testing for binary traits.G3 (Bethesda, Md.) · 2026Article
- NodeGWAS: Leveraging graph pangenomes for sensitive and accurate association analyses across diverse diploid and polyploid species.Plant communications · 2026Article
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- KCFtools: rapid alignment-free method for introgression screening and GWAS using k-mer profiles.Bioinformatics (Oxford, England) · 2026Article
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Different sex determination systems in two closely related Eurasian minnow (Phoxinus) species.Heredity · 2026Article
- Genome-wide association analysis provides insights into the genomics and extracellular expression ofVirulence · 2025Article
- k-mer-based GWAS reveals a candidate avirulence gene and structural variation in Puccinia triticina linked to gain of Lr20 virulence.BMC genomics · 2025Article
- Article
- Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.G3 (Bethesda, Md.) · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Article
- Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes.Applied and environmental microbiology · 2025Review
- Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad.Genome research · 2025Article
- Pseudoassembly of k-mers.bioRxiv : the preprint server for biology · 2025Article
- Hiding in plain sight: the Y chromosome and its reinvigorated role in evolutionary processes.Evolution letters · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- An alignment- and reference-free strategy usingMycology · 2025Article
- Article
10 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
4 authors.
Funding
Abstract
Genome wide association studies (GWAS) rely on microarrays, or more recently mapping of sequencing reads, to genotype individuals. The reliance on prior sequencing of a reference genome limits the scope of association studies, and also precludes mapping associations outside of the reference. We present an alignment free method for association studies of categorical phenotypes based on counting [Formula: see text]-mers in whole-genome sequencing reads, testing for associations directly between [Formula: see text]-mers and the trait of interest, and local assembly of the statistically significant [Formula: see text]-mers to identify sequence differences. An analysis of the 1000 genomes data show that sequences identified by our method largely agree with results obtained using the standard approach. However, unlike standard GWAS, our method identifies associations with structural variations and sites not present in the reference genome. We also demonstrate that population stratification can be inferred from [Formula: see text]-mers. Finally, application to an
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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.