We are thinking of working on candidate genes involved incleftlip/palate. Since it is a complex multifactorial disease it is difficult to zero in on certain specific genes. I was wondering if anyone has any experience in this area?
In case of doing a gene association study what methods can be used?

We are both looking for candidate genes and develop a diagnostic test for adolescent idiopathic scoliosis, a very complex genetic disease. We used Affymetrix 6.0 chips with nearly 1 million SNPs. from there we ran association studies on cases v controls to get candidate markers.

Now we are looking at the haplotypes for both associated genes and finding the best marker in that haplotype for a diagnostic test.

Let me know if you have quesions