Detection of Quantitative Trait Loci From Genome-Wide Association Studies

2019 ◽  
pp. 287-353
Author(s):  
David A. Spade
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Trait Loci

scholarly journals Identification, deployment, and transferability of quantitative trait loci from genome-wide association studies in plants

2020 ◽  
Vol 24 ◽  
pp. 100145 ◽  
Author(s):  
Mohsen Mohammadi ◽  
Alencar Xavier ◽  
Travis Beckett ◽  
Savannah Beyer ◽  
Liyang Chen ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Trait Loci

scholarly journals Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

2020 ◽  
Vol 127 (6) ◽  
pp. 761-777 ◽  
Author(s):  
Wilson Lek Wen Tan ◽  
Chukwuemeka George Anene-Nzelu ◽  
Eleanor Wong ◽  
Chang Jie Mick Lee ◽  
Hui San Tan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Quantitative Trait Loci ◽  
Genetic Variants ◽  
Quantitative Trait ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Trait Loci

Rationale: Identifying genetic markers for heterogeneous complex diseases such as heart failure is challenging and requires prohibitively large cohort sizes in genome-wide association studies to meet the stringent threshold of genome-wide statistical significance. On the other hand, chromatin quantitative trait loci, elucidated by direct epigenetic profiling of specific human tissues, may contribute toward prioritizing subthreshold variants for disease association. Objective: Here, we captured noncoding genetic variants by performing epigenetic profiling for enhancer H3K27ac chromatin immunoprecipitation followed by sequencing in 70 human control and end-stage failing hearts. Methods and Results: We have mapped a comprehensive catalog of 47 321 putative human heart enhancers and promoters. Three thousand eight hundred ninety-seven differential acetylation peaks (FDR [false discovery rate], 5%) pointed to pathways altered in heart failure. To identify cardiac histone acetylation quantitative trait loci (haQTLs), we regressed out confounding factors including heart failure disease status and used the G-SCI (Genotype-independent Signal Correlation and Imbalance) test 1 to call out 1680 haQTLs (FDR, 10%). RNA sequencing performed on the same heart samples proved a subset of haQTLs to have significant association also to gene expression (expression quantitative trait loci), either in cis (180) or through long-range interactions (81), identified by Hi-C (high-throughput chromatin conformation assay) and HiChIP (high-throughput protein centric chromatin) performed on a subset of hearts. Furthermore, a concordant relationship between the gain or disruption of TF (transcription factor)-binding motifs, inferred from alternative alleles at the haQTLs, implied a surprising direct association between these specific TF and local histone acetylation in human hearts. Finally, 62 unique loci were identified by colocalization of haQTLs with the subthreshold loci of heart-related genome-wide association studies datasets. Conclusions: Disease and phenotype association for 62 unique loci are now implicated. These loci may indeed mediate their effect through modification of enhancer H3K27 acetylation enrichment and their corresponding gene expression differences (bioRxiv: https://doi.org/10.1101/536763 ). Graphical Abstract: A graphical abstract is available for this article.

scholarly journals Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

2020 ◽  
Author(s):  
Grazyella Yoshida ◽  
José Manuel Yáñez
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Nile Tilapia ◽  
Statistical Power ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Trait Loci

Abstract Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

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