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Implicit Causal Models for Genome-wide Association Studies
[article]
2017
arXiv
pre-print
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For the first, we describe implicit causal models, a class of causal models that leverages neural architectures with an implicit density. ...
For the second, we describe an implicit causal model that adjusts for confounders by sharing strength across examples. ...
Causality with population-confounders has primarily been studied for genome-wide association studies (GWAS). ...
arXiv:1710.10742v1
fatcat:cu3hbwu2vjbqhdcd6nk3slbwlm
Genomweite Assoziationsstudien
2011
Deutsche Medizinische Wochenschrift
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For the first, we describe implicit causal models, a class of causal models that leverages neural architectures with an implicit density. ...
For the second, we describe an implicit causal model that adjusts for confounders by sharing strength across examples. ...
Causality with population-confounders has primarily been studied for genome-wide association studies (GWAS). ...
doi:10.1055/s-0030-1269446
pmid:21225557
fatcat:fodl7ef35fafxbav7kde47v3mu
Familial Risk and a Genome-Wide Supported DRD2 Variant for Schizophrenia Predict Lateral Prefrontal-Amygdala Effective Connectivity During Emotion Processing
2017
Schizophrenia Bulletin
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Finally, we investigated in HC association of LPFC-amygdala effective connectivity with a genome-wide supported variant increasing genetic risk for SCZ and possibly relevant to emotion processing (DRD2 ...
Key words: endophenotype/DRD2 rs2514218/dynamic causal model/implicit emotion processing/explicit emotion processing ...
We also would like to express our thanks to all the volunteers for having participated to the study. ...
doi:10.1093/schbul/sbx128
pmid:28981847
fatcat:5qvxhw2mdfhjbl7zbarx5vx6aa
What are genome-wide association studies telling us about B-cell tumor development?
2010
OncoTarget
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The advent of genome-wide association studies (GWAS) has allowed the search for this class of susceptibility allele to be conducted on a genome-wide basis. ...
It has long been speculated that common genetic variation influences the development of B-cell malignancy, however until recently evidence for this assertion was lacking. ...
genome-wIde AssocIAtIon studIes of cll And All To identify common disease causing alleles for CLL and ALL we have recently conducted GWA studies of these diseases using a two-stage strategy [8] [9] [10 ...
doi:10.18632/oncotarget.100904
pmid:21307401
pmcid:PMC3157732
fatcat:ey6vrlpp7bfvrp35vzx3l7r53m
What are genome-wide association studies telling us about B-cell tumor development?
2010
OncoTarget
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The advent of genome-wide association studies (GWAS) has allowed the search for this class of susceptibility allele to be conducted on a genome-wide basis. ...
It has long been speculated that common genetic variation influences the development of B-cell malignancy, however until recently evidence for this assertion was lacking. ...
genome-wIde AssocIAtIon studIes of cll And All To identify common disease causing alleles for CLL and ALL we have recently conducted GWA studies of these diseases using a two-stage strategy [8] [9] [10 ...
doi:10.18632/oncotarget.169
fatcat:ek7c5r4bwzabxljx4inev26pz4
Admixed Populations Improve Power for Variant Discovery and Portability in Genome-wide Association Studies
[article]
2021
bioRxiv
pre-print
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Genome-wide association studies (GWAS) are primarily conducted in single-ancestry settings. ...
1,000 causal SNPs, training on 10,000 individuals, testing on 1,000 in each population, p=3.78e-6, 6.19e-101, ~0 for FST = 0.2, 0.5, 0.8, respectively). ...
Introduction Genome-wide association studies (GWAS) have allowed for significant progress in the field of human complex traits. ...
doi:10.1101/2021.03.09.434643
fatcat:bix56ycbxjcrdl47puqqvaf4ca
Admixed Populations Improve Power for Variant Discovery and Portability in Genome-Wide Association Studies
2021
Frontiers in Genetics
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Genome-wide association studies (GWAS) are primarily conducted in single-ancestry settings. ...
1,000 causal SNPs, training on 10,000 individuals, testing on 1,000 in each population, p = 3.78e-6, 6.19e-101, ∼0 for FST = 0.2, 0.5, 0.8, respectively). ...
INTRODUCTION Genome-wide association studies (GWAS) have allowed for significant progress in the field of human complex traits. ...
doi:10.3389/fgene.2021.673167
pmid:34108994
pmcid:PMC8181458
fatcat:en5qxr237rezjjklacz6sljngu
Genome-wide approaches in pharmacogenomics: heritability estimation and pharmacoethnicity as primary challenges
2012
Pharmacogenomics (London)
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Acknowledgments ER Gamazon gratefully acknowledges NJ Cox for her continued support. ...
Meanwhile, methodological advances, such as the genome-wide association study (GWAS) approach, have facilitated the discovery of genetic variation with considerable clinical relevance [3] . ...
Genetic studies in admixed populations can facilitate the fine-mapping and identification of causal variants in regions of the genome first identified in studies involving European samples [31] . ...
doi:10.2217/pgs.12.88
pmid:22909197
pmcid:PMC3710727
fatcat:obcoqxb74bb5bew6lb5szdw2qu
Transethnic differences in GWAS signals: A simulation study
2018
Annals of Human Genetics
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K E Y W O R D S Causal SNP, complex human diseases, genome-wide association studies, transethnic differences Ann Hum Genet. 2018;1-7. ...
Genome-wide association studies (GWASs) have allowed researchers to identify thousands of single nucleotide polymorphisms (SNPs) and other variants associated with particular complex traits. ...
INTRODUCTION In the past decade, through collaborative efforts and with the aid of genome-wide association studies (GWASs), the genetic basis of common complex traits has been greatly clarified (for examples ...
doi:10.1111/ahg.12251
pmid:29733446
fatcat:dhtruj5akza55k4dxcfecocjmq
Varmole: A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes
[article]
2020
bioRxiv
pre-print
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Population studies such as GWAS have identified a variety of genomic variants associated with human diseases. ...
However, how to interpret molecular mechanisms from such associations, especially across omics is still challenging. ...
For example, genome-wide association study (GWAS) analyses have identified a number of disease risk single-nucleotide polymorphisms (SNPs) from population genetic data. ...
doi:10.1101/2020.03.02.973743
fatcat:olvp76azdndalgt6kt56n6np4a
Moving towards causality in attention-deficit hyperactivity disorder: overview of neural and genetic mechanisms
2016
Lancet psychiatry
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Furthermore, we review approaches being developed to understand the neurobiological underpinnings of this complex disorder including the use of animal models, neuromodulation, and pharmaco-imaging studies ...
Whether these underlying neurobiological factors are causally related to symptom presentation remains unresolved. ...
GWAS=genome-wide association studies Lancet Psychiatry. ...
doi:10.1016/s2215-0366(16)00096-1
pmid:27183902
pmcid:PMC4893880
fatcat:3upskqxfvnamvldhrds6ybowru
The functional impact of structural variation in humans
2008
Trends in Genetics
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Structural variation includes many different types of chromosomal rearrangement and encompasses millions of bases in every human genome. ...
As disparate indications of the important biological consequences of genome dynamism are accumulating rapidly, we review the evidence that structural variation has an appreciable impact on cellular phenotypes ...
Genomewide association studies are currently only practicable using SNPs, and allow the detection of associated haplotypes containing the causal variant. ...
doi:10.1016/j.tig.2008.03.001
pmid:18378036
pmcid:PMC2869026
fatcat:lrq2wsfj5za73dtmm3zvq6aqz4
Genetic association and causal inference converge on hyperglycaemia as a modifiable factor to improve lung function
2021
eLife
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A transcriptome-wide association study (TWAS) of lung function was then performed which identified several drug-gene interactions with predicted lung function increasing modes of action. ...
In summary, we provided genetic justification for a number of novel drug repurposing opportunities that could improve lung function. ...
We further adjusted each of these models for genome-wide PGS at the same P T for which the PES was calculated. ...
doi:10.7554/elife.63115
fatcat:p2rl4nlegjd55cvqlyqzbcqi6y
Varmole: A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes
2020
Bioinformatics
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Summary Population studies such as genome-wide association study (GWAS) have identified a variety of genomic variants associated with human diseases. ...
However, how to interpret molecular mechanisms from such associations, especially across omics, is still challenging. ...
Introduction Statistical analyses have associated a variety of genomic variants with phenotypes in human diseases such as cancers and brain disorders. ...
doi:10.1093/bioinformatics/btaa866
pmid:33031552
pmcid:PMC8289382
fatcat:gz3wayjoqvdcjfm5jxzykh2r6e
Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits
2014
Briefings in Functional Genomics
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Genome-wide association studies have been successful in identifying common variants that impact complex human traits and diseases. ...
In this review, we describe a general framework for modelling the joint effects of rare genetic variants on complex traits in association studies of unrelated individuals. ...
Traditional statistical methods for the analysis of common SNPs in genome-wide association studies are underpowered for rare variants. ...
doi:10.1093/bfgp/elu012
pmid:24916163
pmcid:PMC4168660
fatcat:nftvlmgwyvg2xg5vrpyuqf57vq
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