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   Articles with "causal variants" as a keyword



Evaluation of a whole‐exome sequencing pipeline and benchmarking of causal germline variant prioritizers

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recommendations! Published in 2022 at "Human Mutation"

DOI: 10.1002/humu.24459

Abstract: Most causal variants of Mendelian diseases are exonic. Whole‐exome sequencing (WES) has become the diagnostic gold standard, but causative variant prioritization constitutes a bottleneck. Here we assessed an in‐house sample‐to‐sequence pipeline and benchmarked free prioritization… read more here.

Keywords: causal variants; exome sequencing; pipeline; whole exome ... See more keywords

Allele-Specific QTL Fine Mapping with PLASMA.

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recommendations! Published in 2020 at "American journal of human genetics"

DOI: 10.1016/j.ajhg.2019.12.011

Abstract: Although quantitative trait locus (QTL) associations have been identified for many molecular traits such as gene expression, it remains challenging to distinguish the causal nucleotide from nearby variants. In addition to traditional QTLs by association,… read more here.

Keywords: causal variants; qtl based; mapping; allele specific ... See more keywords

Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues

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recommendations! Published in 2017 at "Nature Genetics"

DOI: 10.1038/ng.3979

Abstract: Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive… read more here.

Keywords: causal variants; whole genome; causal; expression ... See more keywords

Functional mapping and annotation of genetic associations with FUMA

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recommendations! Published in 2017 at "Nature Communications"

DOI: 10.1038/s41467-017-01261-5

Abstract: A main challenge in genome-wide association studies (GWAS) is to pinpoint possible causal variants. Results from GWAS typically do not directly translate into causal variants because the majority of hits are in non-coding or intergenic… read more here.

Keywords: causal variants; functional mapping; mapping annotation; causal ... See more keywords

Multi-resolution localization of causal variants across the genome

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recommendations! Published in 2020 at "Nature Communications"

DOI: 10.1038/s41467-020-14791-2

Abstract: In the statistical analysis of genome-wide association data, it is challenging to precisely localize the variants that affect complex traits, due to linkage disequilibrium, and to maximize power while limiting spurious findings. Here we report… read more here.

Keywords: causal variants; method; multi resolution; genome ... See more keywords
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The flashfm approach for fine-mapping multiple quantitative traits.

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recommendations! Published in 2021 at "Nature communications"

DOI: 10.1038/s41467-021-26364-y

Abstract: Joint fine-mapping that leverages information between quantitative traits could improve accuracy and resolution over single-trait fine-mapping. Using summary statistics, flashfm (flexible and shared information fine-mapping) fine-maps signals for multiple traits, allowing for missing trait measurements… read more here.

Keywords: causal variants; mapping; single trait; fine mapping ... See more keywords

Massively parallel variant-to-function mapping determines functional regulatory variants of non-small cell lung cancer

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recommendations! Published in 2025 at "Nature Communications"

DOI: 10.1038/s41467-025-56725-w

Abstract: Genome-wide association studies have identified thousands of genetic variants associated with non-small cell lung cancer (NSCLC), however, it is still challenging to determine the causal variants and to improve disease risk prediction. Here, we applied… read more here.

Keywords: non small; causal variants; lung cancer; cell lung ... See more keywords

Potential causal variants for RA identified

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recommendations! Published in 2018 at "Nature Reviews Rheumatology"

DOI: 10.1038/s41584-018-0103-8

Abstract: Raychaudhuri and colleagues narrowed down the possible genetic associations to six potentially causal variants for RA Genome-wide association studies (GWASs) have previously revealed 101 non-MHC loci associated with rheumatoid arthritis (RA), but the causal genetic… read more here.

Keywords: causal variants; analysis; study; causal ... See more keywords
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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits.

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recommendations! Published in 2022 at "Nature genetics"

DOI: 10.1038/s41588-021-00987-9

Abstract: While large-scale, genome-wide association studies (GWAS) have identified hundreds of loci associated with brain-related traits, identification of the variants, genes and molecular mechanisms underlying these traits remains challenging. Integration of GWAS with expression quantitative trait… read more here.

Keywords: analysis; causal variants; brain related; related traits ... See more keywords

Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases.

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recommendations! Published in 2022 at "Nature genetics"

DOI: 10.1038/s41588-022-01025-y

Abstract: The resolution of causal genetic variants informs understanding of disease biology. We used regulatory quantitative trait loci (QTLs) from the BLUEPRINT, GTEx and eQTLGen projects to fine-map putative causal variants for 12 immune-mediated diseases. We… read more here.

Keywords: causal variants; fine mapping; variants immune; disease ... See more keywords

CAUSALdb2: an updated database for causal variants of complex traits

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recommendations! Published in 2024 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkae1096

Abstract: Abstract Unraveling the causal variants from genome wide association studies (GWASs) is pivotal for understanding genetic underpinnings of complex traits and diseases. Despite continuous efforts, tools to refine and prioritize GWAS signals need enhancement to… read more here.

Keywords: database; causal variants; complex traits; causaldb2 ... See more keywords