SNP eQTL status and eQTL density in the adjacent region of the SNP are associated with its statistical significance in GWA studies.
Breast Neoplasms
/ genetics
Female
Gene Expression Profiling
Gene Expression Regulation
Genetic Predisposition to Disease
Genome-Wide Association Study
/ methods
Humans
Lung Neoplasms
/ genetics
Male
Models, Statistical
Organ Specificity
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Regulatory Elements, Transcriptional
Scleroderma, Systemic
/ genetics
Cancer
Expression quantitative trait loci (eQTL)
Gene expression
Genome wide association studies (GWASs)
Statistical significance
Journal
BMC genetics
ISSN: 1471-2156
Titre abrégé: BMC Genet
Pays: England
ID NLM: 100966978
Informations de publication
Date de publication:
12 11 2019
12 11 2019
Historique:
received:
18
03
2019
accepted:
18
10
2019
entrez:
14
11
2019
pubmed:
14
11
2019
medline:
19
5
2020
Statut:
epublish
Résumé
Over the relatively short history of Genome Wide Association Studies (GWASs), hundreds of GWASs have been published and thousands of disease risk-associated SNPs have been identified. Summary statistics from the conducted GWASs are often available and can be used to identify SNP features associated with the level of GWAS statistical significance. Those features could be used to select SNPs from gray zones (SNPs that are nominally significant but do not reach the genome-wide level of significance) for targeted analyses. We used summary statistics from recently published breast and lung cancer and scleroderma GWASs to explore the association between the level of the GWAS statistical significance and the expression quantitative trait loci (eQTL) status of the SNP. Data from the Genotype-Tissue Expression Project (GTEx) were used to identify eQTL SNPs. We found that SNPs reported as eQTLs were more significant in GWAS (higher -log The results of this study indicate that the SNP's eQTL status, as well as eQTL density in the adjacent region are positively associated with the level of statistical significance of the SNP in GWAS.
Sections du résumé
BACKGROUND
Over the relatively short history of Genome Wide Association Studies (GWASs), hundreds of GWASs have been published and thousands of disease risk-associated SNPs have been identified. Summary statistics from the conducted GWASs are often available and can be used to identify SNP features associated with the level of GWAS statistical significance. Those features could be used to select SNPs from gray zones (SNPs that are nominally significant but do not reach the genome-wide level of significance) for targeted analyses.
METHODS
We used summary statistics from recently published breast and lung cancer and scleroderma GWASs to explore the association between the level of the GWAS statistical significance and the expression quantitative trait loci (eQTL) status of the SNP. Data from the Genotype-Tissue Expression Project (GTEx) were used to identify eQTL SNPs.
RESULTS
We found that SNPs reported as eQTLs were more significant in GWAS (higher -log
CONCLUSIONS
The results of this study indicate that the SNP's eQTL status, as well as eQTL density in the adjacent region are positively associated with the level of statistical significance of the SNP in GWAS.
Identifiants
pubmed: 31718536
doi: 10.1186/s12863-019-0786-0
pii: 10.1186/s12863-019-0786-0
pmc: PMC6852916
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
85Subventions
Organisme : NCI NIH HHS
ID : P01 CA206980
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA148127
Pays : United States
Organisme : NLM NIH HHS
ID : R56 LM012371
Pays : United States
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