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Genome-wide association
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Genome–phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genomewide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases.
15p
vibransone
28-03-2024
3
2
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After years of concentrated research efforts, the exact cause of Crohn’s disease (CD) remains unknown. Its accurate diagnosis, however, helps in management and preventing the onset of disease. Genomewide association studies have identified 241 CD loci, but these carry small log odds ratios and are thus diagnostically uninformative.
15p
vibransone
28-03-2024
3
1
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Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or environmental factors that affect specific disease risks and outcomes.
22p
vibransone
28-03-2024
4
2
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Very low-coverage (0.1 to 1×) whole genome sequencing (WGS) has become a promising and aford‑ able approach to discover genomic variants of human populations for genome-wide association study (GWAS).
18p
vicwell
29-02-2024
2
1
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Polygenic scores (PGS) can be used for risk stratification by quantifying individuals’ genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation.
14p
vicwell
29-02-2024
2
2
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Hyperuricemia is associated with multiple diseases, including gout, cardiovascular disease, and renal disease. Serum urate is highly heritable, yet association studies of single nucleotide polymorphisms (SNPs) and serum uric acid explain a small fraction of the heritability.
13p
vinarcissa
21-03-2023
2
1
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Multiple layers of genetic and epigenetic variability are being simultaneously explored in an increasing number of health studies. We summarize here different approaches applied in the Data Mining and Machine Learning group at the GAW20 to integrate genome-wide genotype and methylation array data.
8p
vihagrid
30-01-2023
3
3
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This paper summarizes the contributions from the Genome-wide Association Study group (GWAS group) of the GAW20. The GWAS group contributions focused on topics such as association tests, phenotype imputation, and application of empirical kinships. The goals of the GWAS group contributions were varied.
9p
vihagrid
30-01-2023
7
3
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Levels of sex hormone-binding globulin (SHBG) and the androgen testosterone have been associated with risk of diseases throughout the lifecourse. Although both SHBG and testosterone have been shown to be highly heritable, only a fraction of that heritability has been explained by genetic studies.
11p
vihagrid
30-01-2023
11
3
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The driver tissues or cell types in which susceptibility genes initiate diseases remain elusive. We develop a unified framework to detect the causal tissues of complex diseases or traits according to selective expression of diseaseassociated genes in genome-wide association studies (GWASs).
19p
vielonmusk
30-01-2022
12
0
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Genome-wide association studies (GWAS) search for marker variants indirectly associated with certain diseases and/or traits. They assume that markers are in linkage disequilibrium (LD) with underlying causal variants.
3p
vialfrednobel
29-01-2022
15
0
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The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription.
25p
viarchimedes
26-01-2022
6
0
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Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.
25p
viarchimedes
26-01-2022
10
0
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Osteoporosis is a complex disease with a strong genetic contribution. A recently published genomewide association study (GWAS) for estimated bone mineral density (eBMD) identified 1103 independent genomewide significant association signals. Most of these variants are non-coding, suggesting that regulatory effects may drive many of the associations.
13p
viarchimedes
26-01-2022
11
0
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Face morphology is strongly determined by genetic factors. However, only a small number of genes related to face morphology have been identified to date. Here, we performed a two-stage genome-wide association study (GWAS) of 85 face morphological traits in 7569 Koreans (5643 in the discovery set and 1926 in the replication set).
17p
vibeauty
23-10-2021
8
1
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Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds’ growth and welfare. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood.
10p
vibeauty
23-10-2021
16
1
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The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the present study, we took advantage of a unique model of two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle (PM-pHu) in order to decipher the genetic control of this trait.
14p
vibeauty
23-10-2021
11
1
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There exist few, if any, practical guidelines for predictive and falsifiable multi-omic data integration that systematically integrate existing knowledge. Disease modules are popular concepts for interpreting genomewide studies in medicine but have so far not been systematically evaluated and may lead to corroborating multiomic modules.
13p
vitzuyu2711
29-09-2021
11
1
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Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm.
16p
visilicon2711
20-08-2021
9
1
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Proximity ligation based techniques, like Hi-C, involve restriction digestion followed by ligation of formaldehyde cross-linked chromatin. Distinct chromatin states can impact the restriction digestion, and hence the visibility in the contact maps, of engaged loci.
15p
vijeeni2711
24-07-2021
4
0
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