How To Get Started Learning Gwas Analysis

Question

[David_emir]

Hello All,

I have a genotyping data from Human Omni 1 Quad v1.0 DNA Bead Chip with Demographic Particulars of Cases and Controls. Since i am very new to GWAS , it would be really helpful if you please let me know the ways for Conducting a full GWAS analysis of the raw data, for arriving at SNPs with different p-value (<0.005, < 0.001) data sets, how to have an Association analysis of imputed data and also have a pathway analysis from the SNP data to chart disease relevance.

It would be really helpful if you guys please let me know the pipeline for it and related tools for this analysis !

Thanks a lot for you help !

Answer 1

[zx8754]

Following two papers with examples should get you started with GWAS QC and Analysis:

Data quality control in genetic case-control association studies

Basic statistical analysis in genetic case-control studies

EDIT: Starting point for Pathway analysis see:

Plink - Set-based tests

Plinkseq - Gene/group-based association tests

[mandar.bobade60]

These two are very good papers for starters to understand statistics and its use in GWAS QC. Thanks a lot for this suggestion. It was very useful.

[David_emir]

Thanks a lot for your help, Its really useful.. I have a doubt, Is it possible for arriving pathway-based analysis, report from the derived SNPs?

[zx8754]

See edited answer. Please avoid asking extra questions in comments.

Answer 2

[Bioch'Ti]

Hi, you may also been interested in using the Tassel Saftware that implements the Mixed Linear Model. There is some support to its use. Visit: http://www.maizegenetics.net/tassel/