Questions tagged [gwas]

Questions pertaining to genome-wide association studies.

9 questions with no upvoted or accepted answers
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What are the different types of SNPs?

When I search for this online I get answers such as substitutions, deletions, insertions etc. But I mean in the sense that I have been reading different terms infront of the word SNP such as: lead SNP,...
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20 views

How many samples to run an association study on B-Cell receptors

We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/) to ...
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328 views

What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?

What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
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47 views

Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
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25 views

Simulating phenotype using gcta64 and 1000 Genomes

I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation? I'm trying to use ...
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11 views

Unlinked SNP now insignificant after conditional analysis?

I'd like to know if two of my significant GWAS loci (p < 5E-8) independently contribute to my trait. Index SNPs for these loci are approximately 2Mb apart. According to LDLink, these SNPs are in ...
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25 views

N value in a GWAS?

Just like the title says. I am reading about a GWAS but I don't know much about them. I understood most of it but I couldn't figure out what the "n" value was.
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35 views

How should I interpret a weighted genetic risk score?

I created a weighted GRS by summing the product of the dosages times their regression coefficients from the GWAS in which I found them. So GRS=sum(dosage1*coefficient1 + dosage2*coefficient2 +...). ...
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82 views

Phenotype choice for one of a MZ twin pair in a genetic association study

I was having a discussion with a colleague and this question came up... It is commonplace in molecular genetics studies to only genotype one of a pair of monozygotic twins (and then implicitly impute ...