Tagged Questions

Questions pertaining to genome-wide association studies.

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1
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1answer
28 views

A question on exclusion of study participants for an Exome genotyping array

I'm reading a paper that used whole exome sequencing on an African American and European populations to discover novel low frequency and rare variants associated with lipid levels & the risk of ...
1
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1answer
26 views

Investigating rare variants in ethnically different populations (European ancestry & African ancestry)

If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) ...
2
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1answer
157 views

GWAS: matched-pairs and logistic regression

Logistic regression is a common analysis tool used for GWAS when your response variable of interested is qualitative. It comes as one of the standard tools in most GWAS packages (e.g. PLINK). Most ...
1
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1answer
93 views

Interpreting SNP-in-gene associations from GWAS studies

For most SNPs identified in GWAS studies, is the underlying assumption that if it is indeed associated with a phenotype (and lets assume its associated because it affects protein function), that you ...
11
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2answers
2k views

What is the difference between naive and adjusted p-values in a GWAS study?

What is the difference between a naive p-value and an adjusted p-value in the results of a GWAS study? See from this paper: After Bonferroni adjustment, a single gene, DCTN4 (encoding dynactin 4) ...
14
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1answer
191 views

Paralogous genes in genome-wide association studies?

Has anybody tested if paralogous genes are over-represented among the genes identified by genome-wide association studies (GWAS)? For example, if a GWAS study finds 200 genes associated to the ...
2
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1answer
62 views

variation in expression accounted for a SNP — what's a usual percent?

I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the ...
6
votes
1answer
236 views

What is the relative power of GWAS studies in different species?

I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more ...