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Genome-wide
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The Ras pathway genes KRAS, BRAF, or ERBBs have somatic mutations in ~ 60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway or whether they have acquired mutations in genes hitherto unknown to belong to the pathway.
13p
vibransone
28-03-2024
6
2
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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 Wright’s fixation index (Fst) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful.
15p
vihagrid
30-01-2023
6
3
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(BQ) Ebook Chemical and functional genomic approaches to stem cell biology and regenerative medicine: Part 1 presents the following content: Embryonic stem cells; adult stem cells; genomewide expression analysis technologies; genomic cdna and rnai functional profiling and its potential application to the study of mammalian stem cells; chemical technologies: probing biology with small molecules.
162p
runordie7
30-08-2022
3
2
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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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DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalization, and identification of differentially methylated CpGs and regions.
26p
viarchimedes
26-01-2022
8
0
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Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. However, existing methods are computationally demanding and infeasible to handle biobank-scale data.
17p
viarchimedes
26-01-2022
11
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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The development of sequencing technologies has promoted the survey of genomewide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a challenge.
27p
viarchimedes
26-01-2022
10
0
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