ArticlePLoS computational biology2020
RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic constraint and hypervariability correlate with fitness effects in elite tetraploid potato breeding material.PLoS genetics · 2026Article
- Candidate genes for stem rust resistance in Italian ryegrass revealed by nested association mapping.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Interpretable multi-omics machine learning reveals drought-driven shifts in plant-microbe interactions.Environmental microbiome · 2026Article
- Integration of proxy intermediate omics traits into a nonlinear two-step model for accurate phenotypic prediction.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Facilitating genomic breeding in citrus via reference panel-based whole-genome imputation of low-coverage sequencing-derived genotype data.Breeding science · 2026Article
- Exploring standing genetic variation for barley leaf rust resistance in Australian breeding panel.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction.Plants (Basel, Switzerland) · 2025Article
- A genome-wide association study reveals additive and recessive alleles affecting male fertility in pigs.Journal of animal science and biotechnology · 2025Article
- Haplotype analysis and molecular marker development for the cold tolerance gene OsCTS11 at the seedling stage of rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Inheritance characteristics and potential of genomic prediction for pungency levels in FBreeding science · 2025Article
- Multimodal analysis stratifies genetic susceptibility and reveals the pathogenic mechanism of kidney injury in diabetic nephropathy.Cell reports. Medicine · 2025Article
- Dissecting the genetic basis of response to salmonid alphavirus in Atlantic salmon.BMC genomics · 2025Article
- Integrating multi-omics and machine learning for disease resistance prediction in legumes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Optimization of crossing strategy based on the usefulness criterion in interpopulation crosses considering different marker effects among populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- QTN detection and candidate gene identification for improved eating and cooking quality in rice using GWAS and PLS regression analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Review
- Phenotypic simulation for fruit-related traits in FMolecular genetics and genomics : MGG · 2025Article
- Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines.G3 (Bethesda, Md.) · 2024Article
- Genome-wide association studies from spoken phenotypic descriptions: a proof of concept from maize field studies.G3 (Bethesda, Md.) · 2024Article
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Abstract
Difficulty in detecting rare variants is one of the problems in conventional genome-wide association studies (GWAS). The problem is closely related to the complex gene compositions comprising multiple alleles, such as haplotypes. Several single nucleotide polymorphism (SNP) set approaches have been proposed to solve this problem. These methods, however, have been rarely discussed in connection with haplotypes. In this study, we developed a novel SNP-set method named "RAINBOW" and applied the method to haplotype-based GWAS by regarding a haplotype block as a SNP-set. Combining haplotype block estimation and SNP-set GWAS, haplotype-based GWAS can be conducted without prior information of haplotypes. We prepared 100 datasets of simulated phenotypic data and real marker genotype data of Oryza sativa subsp. indica, and performed GWAS of the datasets. We compared the power of our method, the conventional single-SNP GWAS, the conventional haplotype-based GWAS, and the conventional SNP-set GWAS. Our proposed method was shown to be superior to these in three aspects: (1) controlling false positives; (2) in detecting causal variants without relying on the linkage disequilibrium if causal variants were genotyped in the dataset; and (3) it showed greater power than the other methods, i.e., it was able to detect causal variants that were not detected by the others, primarily when the causal variants were located very close to each other, and the directions of their effects were opposite. By using the SNP-set approach as in this study, we expect that detecting not only rare variants but also genes with complex mechanisms, such as genes with multiple causal variants, can be realized. RAINBOW was implemented as an R package named "RAINBOWR" and is available from CRAN (https://cran.r-project.org/web/packages/RAINBOWR/index.html) and GitHub (https://github.com/KosukeHamazaki/RAINBOWR).
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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 Socratic graph.