ArticleNature biotechnology2013
Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers.
Article in Nature biotechnology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 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
88 citing papers in PubMed.
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- Advances in mutant characterization for detecting causal mutations in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Article
- MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.BMC bioinformatics · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Article
- A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes.G3 (Bethesda, Md.) · 2024Article
- Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences.Frontiers in plant science · 2024Article
- Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit byCurrent issues in molecular biology · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources.Frontiers in plant science · 2023Article
- The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis.International journal of molecular sciences · 2022Review
- Bulk segregant linkage mapping for rodent and human malaria parasites.Parasitology international · 2022Review
- Fine Mapping of Stripe-Rust-Resistance GenePlants (Basel, Switzerland) · 2022Article
- Critical roles of mitochondrial fatty acid synthesis in tomato development and environmental response.Plant physiology · 2022Article
- Article
- Review
- Article
- Identification and mapping of major-effect flowering time lociFrontiers in plant science · 2022Article
28 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
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.
Indexed as
Identifiers
23475072What 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.