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SNP basics - New to SNP, mol bio, etc (Sep/18/2006 )

I am trying to do fine mapping of an area of a chromosome using SNPs to further do linkage analysis. The area is about 10 cM. I have genomic DNA. Do you usually check the DNA by running some of it on a gel? How much do you run? Then do you check its compatability with regular PCR using primers to something easy like GAPDH?

Now the tougher questions...
I would like to examine SNPs in this 10cM region. I have limited funding. Would anyone care to comment on doing a SNP chip from Affymetrix that would be more whole genome association but still has good coverage in my area (about 100 Kbp inter SNP distance) or doing the TaqMan SNP genotyping assays and setting up a SNP to check every 1 Kbp? No good candidate genes in this region of interest.



I don't think DNA quality is that much critical for genotyping, but it helps to have similar concentration for all DNA samples. You can test your DNA by doing a genomic PCR and running a gel with the resulting product.
I don't know anything about SNP microarray assay, but I know taqman SNP genotyping should be more cost-effective than RFLP if you have many samples to analyze.
For reference SNP, HapMap site is a good resource if you are working on human samples. You can actually obtain haplotypes for any region of the human genome for 4 populations (YRI: Yoruba in Ibadan, Nigeria, JPT: Japanese in Tokyo, Japan, CHB: Han Chinese in Beijing, China, CEU: CEPH (Utah residents with ancestry from northern and western Europe). Once you find the regions of your interest, you can then pick some reference SNPs.
Good luck!