ArticlePLoS genetics2018
Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize.Genome research · 2026Article
- Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass.Plant physiology · 2025Article
- Jointly benchmarking small and structural variant calls with vcfdist.Genome biology · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Article
- Evolutionary insights into 3D genome organization and epigenetic landscape ofLife science alliance · 2024Article
- Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns.PLoS biology · 2023Article
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- Predicting Gene Regulatory Interactions Using Natural Genetic Variation.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing.Frontiers in plant science · 2022Article
- The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock.Genes · 2020Review
- uORFlight: a vehicle toward uORF-mediated translational regulation mechanisms in eukaryotes.Database : the journal of biological databases and curation · 2020Article
- Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy.Frontiers in genetics · 2019Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Short insertions, deletions (INDELs) and larger structural variants have been increasingly employed in genetic association studies, but few improvements over SNP-based association have been reported. In order to understand why this might be the case, we analysed two publicly available datasets and observed that 63% of INDELs called in A. thaliana and 64% in D. melanogaster populations are misrepresented as multiple alleles with different functional annotations, i.e. where the same underlying variant is represented by inconsistent alignments leading to different variant calls. To address this issue, we have developed the software Irisas to reclassify and re-annotate these variants, which we then used for single-locus tests of association. We also integrated them to predict the functional impact of SNPs, INDELs, and structural variants for burden testing. Using both approaches, we re-analysed the genetic architecture of complex traits in A. thaliana and D. melanogaster. Heritability analysis using SNPs alone explained on average 27% and 19% of phenotypic variance for A. thaliana and D. melanogaster respectively. Our method explained an additional 11% and 3%, respectively. We also identified novel trait loci that previous SNP-based association studies failed to map, and which contain established candidate genes. Our study shows the value of the association test with INDELs and integrating multiple types of variants in association studies in plants and animals.
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