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Improved methods for multi-trait fine mapping of pleiotropic risk loci
[article]
2016
bioRxiv
pre-print
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Next, we show that jointly modeling pleiotropic risk regions improves fine-mapping resolution compared to standard single trait and pleiotropic fine mapping strategies. ...
In this work we introduce a new approach, fastPAINTOR, that leverages evidence across correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at pleiotropic risk loci ...
The power of our multi-trait fine-mapping framework hinges on the assumption that causal variants are shared at pleiotropic risk regions. ...
doi:10.1101/054684
fatcat:pp7idrzfazg5ra532xw22kccoy
Improved methods for multi-trait fine mapping of pleiotropic risk loci
2016
Bioinformatics
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fastPAINTOR, that leverages evidence across correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at pleiotropic risk loci. ...
Next, we show that jointly modeling pleiotropic risk regions improves fine-mapping resolution relative to standard single trait and pleiotropic fine mapping strategies. ...
The power of our multi-trait fine-mapping framework hinges on the assumption that causal variants are shared at pleiotropic risk regions. ...
doi:10.1093/bioinformatics/btw615
pmid:27663501
pmcid:PMC5254076
fatcat:w5sbazxqmvgjfmfpa35ji66oqu
Analysis across Taiwan Biobank, Biobank Japan and UK Biobank identifies hundreds of novel loci for 36 quantitative traits
[article]
2021
medRxiv
pre-print
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Genome-wide association studies (GWAS) have identified tens of thousands of genetic loci associated with human complex traits and diseases. ...
We release all GWAS summary statistics, fine-mapping results, and single nucleotide polymorphism (SNP) weights and TWB-based PRS reference distributions for polygenic prediction (link to appear upon publication ...
We thank the National Center for Genome Medicine of Taiwan for the technical support in genotyping. ...
doi:10.1101/2021.04.12.21255236
fatcat:c6nbdkzmsfeohfxgwn7usc6f4u
Identification of novel variants associated with osteoporosis, type 2 diabetes and potentially pleiotropic loci using pleiotropic cFDR method
2018
Bone
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The aim of this study was to identify novel genetic variants for osteoporosis and/or T2D. ...
However, the total genetic variance for each of these two diseases and the shared genetic determination between them are largely unknown. ...
Ecology (0713) and the Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486). ...
doi:10.1016/j.bone.2018.08.020
pmid:30172742
pmcid:PMC6364698
fatcat:svom4u2sy5devh2jz3xyhb7gqu
Multitrait genetic association analysis identifies 50 new risk loci for gastro-oesophageal reflux, seven new loci for Barrett's oesophagus and provides insights into clinical heterogeneity in reflux diagnosis
2021
Gut
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multitrait model identified many novel risk loci for GERD and BE. ...
We present strong evidence for a genetic underpinning of disease heterogeneity in GERD and show that GERD loci associated with depressive symptoms are not strong predictors of BE/EA relative to obesity-driven ...
We finally also thank the 23andMe staff members and 23andMe research participants for generating the replication data in this publication. ...
doi:10.1136/gutjnl-2020-323906
pmid:34187846
fatcat:24dyguatpjevroazd3fjbmyhne
A global view of pleiotropy and genetic architecture in complex traits
[article]
2018
bioRxiv
pre-print
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We show that trait associated loci cover more than half of the genome, and 90% of those loci are associated with multiple trait domains. ...
For a subset of well-powered GWAS on 558 unique traits, we provide an extensive overview of pleiotropy and genetic architecture. ...
region to fine-map by taking 50kb around the top SNPs of the trait-associated 780 loci. ...
doi:10.1101/500090
fatcat:77gtykmhvzen3lh5rviqfycl4a
Genome wide association study of body weight, body mass index, adiposity, and fasting glucose in 3,173 outbred rats
[article]
2018
bioRxiv
pre-print
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Highly recombinant populations allow for genetic fine-mapping of complex traits, greatly reducing the number of plausible candidate genes. ...
Our results demonstrate the potential for rodent studies to add to our understanding of the molecular genetic factors that contribute to obesity-relevant traits and emphasize the importance of sample size ...
This work demonstrates the power of HS rats for fine-mapping and gene identification of adiposity traits, including the power to identify genetic loci across multiple institutions and environmental influence ...
doi:10.1101/422428
fatcat:yfungx7p3ffpphg56uceuj3cyy
Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for twelve immune-mediated diseases
[article]
2020
bioRxiv
pre-print
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Here we use data from the BLUEPRINT project to identify regulatory quantitative trait loci (QTL) for three primary human immune cell types and use these to fine-map putative causal variants for twelve ...
The identification of causal genetic variants for common diseases improves understanding of disease biology. ...
We thank Lu Chen and Valentina Iotchkova for the initial technical discussion on analysis strategy, and Katrina M de Lange for helping with IBD GWAS data. ...
doi:10.1101/2020.01.15.907436
fatcat:tzt5tr4ulvhnfdxouwv2mysjxm
Dissecting the genetics of complex traits using summary association statistics
[article]
2016
bioRxiv
pre-print
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These studies have produced vast repositories of genetic variation and trait measurements across millions of individuals, providing tremendous opportunities for further analyses. ...
Here we review recent progress on statistical methods that leverage summary association data to gain insights into the genetic basis of complex traits and diseases. ...
Shi for helpful discussions. We are grateful to G. Kichaev and R. Johnson for help with Figure 3 . This work was funded by NIH grants R01 HG006399, R01 MH101244, R01 GM105857 and R01 MH107649. ...
doi:10.1101/072934
fatcat:c7onk6qsrjd5zj2aa3izbzly4q
The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers
2016
Cancer Epidemiology, Biomarkers and Prevention
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the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for diseasespecific risk, and jointly model genetic, environmental, and lifestyle-related exposures. ...
Conclusions: Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess ...
Moss for his help in organizing this manuscript submission.
Grant Support ...
doi:10.1158/1055-9965.epi-16-0106
pmid:27697780
pmcid:PMC5224974
fatcat:ero45y2p7bawjml7wryqkvaqqm
Investigating asthma heterogeneity through shared and distinct genetics: insights from genome-wide cross-trait analysis
2020
Journal of Allergy and Clinical Immunology
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We also make recommendations for future directions: 1) ethnicity-specific asthma GWASs, and 2) application of cross-trait methods to multi-omics data to dissect the heritability found in GWAS. ...
The genome-wide cross-trait analysis features in several analytical aspects: genetic correlation, cross-trait meta-analysis, Mendelian randomization, polygenic risk score and functional analysis. ...
region are difficult to map in fine resolution. ...
doi:10.1016/j.jaci.2020.07.004
pmid:32693092
pmcid:PMC7368660
fatcat:jmiujfjxubhbdhcnfz5zanqz6u
Integrative analysis of genome-wide association studies identifies novel loci associated with neuropsychiatric disorders
2021
Translational Psychiatry
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In the multi-trait joint analyses, we found five novel genome-wide significant loci for ADHD, one novel locus for BIP, and ten novel loci for MDD. ...
We conducted fine-mapping and functional annotation through an integrative multi-omics approach and identified causal variants and potential target genes at each novel locus. ...
for Applied Genomics at CHOP. ...
doi:10.1038/s41398-020-01195-5
pmid:33479212
pmcid:PMC7820351
fatcat:ts2ylwpmgrh3fc4nlvbmtntwzy
48th European Mathematical Genetics Meeting (EMGM) 2020
2020
Human Heredity
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While many methods have been proposed in literature for the detection of pleiotropic locus, their applicability is to a large extent defined by the type of data available and their relative performance ...
Local gene expression quantitative trait loci (cis-eQTLs) regularly implicate multiple putative target genes whose disease relevance and function is often poorly understood. ...
Using summary statistics, flashfm (FLexible And SHared information Fine-Mapping) fine-maps association signals for multiple quantitative traits, allowing for missing trait measurements and related individuals ...
doi:10.1159/000507248
pmid:32268327
fatcat:3aneluafpnes3a2ayzn53uffca
Integrated Analysis of Summary Statistics to Identify Pleiotropic Genes and Pathways for the Comorbidity of Schizophrenia and Cardiometabolic Disease
2020
Frontiers in Psychiatry
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Here we integrated comprehensive multi-dimensional data from GWAS, expression quantitative trait loci (eQTL), and gene set database to systematically identify potential pleiotropic genes and biological ...
Our study provides insights into the pleiotropic genes and biological pathways underlying mechanisms for the comorbidity of SCZ and CMD. ...
Dao Wen Wang for their cultivation and learning support. ...
doi:10.3389/fpsyt.2020.00256
pmid:32425817
pmcid:PMC7212438
fatcat:c7shqaidyve6vfftdhemta6m2y
Integrative Analyses Reveal Novel Disease-associated Loci and Genes for Idiopathic Pulmonary Fibrosis
[article]
2021
medRxiv
pre-print
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Methods: By leveraging shared genetic information and transcriptome data, we conducted an integrative analysis to identify novel genes for IPF. ...
We first considered observed phenotypes, polygenic risk scores, and genetic correlations to investigate associations between IPF and other traits in the UK Biobank. ...
These findings motivated us to further fine-map local pleiotropic effects and find candidate pleiotropic genes. ...
doi:10.1101/2021.05.11.21257064
fatcat:oyjtngvitnc4dhsxhpi6x5qg74
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