My question is based on conducting a meta-analysis on the association of multiple variants in a single gene with a complex disorder using published case-control studies.
For my study, around 5 well-studied SNPs in a single gene have been widely reported to be associated with a disorder as single SNPs or as haplotypes (two up to five SNPs in LD varying between different studies).
If I wish to explore associations of a 3-SNP haplotype with the disorder between studies, can I extract data from studies that only report 5- or 4-SNP haplotypes (that include the 3 SNPs) in association with the disease?
Edit: Thank you for your answers.
It's not a common way to do the meta-analysis. But it should work if you can extract the sample numbers for each condition (your target haplotyes and phenotype).
I have only a limited experience with that subject, but SNP alleles could be found associated in LD in such a way as to suppress the main phenotypic effects of only one of them (and YES, thay could be in HW equilibrium, at least in ancient populations). I would be very careful about extracting data of three out of five SNPs if no validation is possible by any experimental approach. Try estimating MAF for each of them could be of help.
- Badges
- Science topic
- Similar topics
- Biological Science
- Genetics