How to start a SNP prioritization in GWAS
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7.9 years ago
kumar.vinod81 ▴ 330

I've done a GWAS where 220 rice accessions were genotyped using a 6K Illumina Genotyping array and data were used for association with a quantitative trait. I found a sharp peak around a already well known gene but the most significant SNP is not in the same gene. Even the SNP in candidate gene didn't show any association with the trait for which it is known and frequently used for introgression studies. What should I do, is it a new SNP underlying the concerned trait or something is false positive? Should I am to enrich the region with more number of SNPs or there are some other methods which can be used to further test the quality of GWAS results. how should I prioritize this region?

Please suggest...

gwas snp-prioritization • 2.5k views

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