Workshop on SNP Genotyping: Strategies & Applications in Human Genetics

Posted by: aftabac Posts: 271 :: 11-03-2011 :: | Reply to this Message

Re: Workshop on SNP Genotyping: Strategies & Applications in Human Genetics

The major impediment will be cost. Depending upon which platform is used for genotyping (illumina or Affy) and how many samples are run, the cost of a GWAS will vary from 200-400 dollars. Any GWAS study needs 1000s of patients; the cost is simply prohibitive.
Lets say that we want to do cadidate-gene or candidate SNP analysis, which will need a much smaller sample size and cost of genptyping one SNP is less than one dollar, we will still need to have a 'hypothesis' which is not possible without a good understanding of underlying biology at molecular level.
Perhaps, the only thing we can do is 'me too' studies in which already identidied loci can be looked at in Pakistani population. Again, sample size will need to be quite large and we are not sure whether the reported SNPs from other populations are in linkage disequilibrium with the causal SNP in our population. Unfortuantely, the HapMap project doesnt contain any individuals from South Asia so we have to wait for completion of 1000 Genome project results.
Ok, now lets see that we have few SNPs genotyped in few hundred people and we know their disease status (or have information on the quantitative trait) the statistical analysis is straight forward as one can use usual biostatistical methods; unless study participants are related. Even if they are related, linear mixed models are pretty good in taking into account the complex correlation matrix.
No, I am not discouraging, I am only stating the obvious; this needs serious money. If some one has money to get genotyping done, I can analyze their data for free.

Posted by: rqayyum Posts: 199 :: 20-03-2011 :: | Reply to this Message