As a follow-up to a study where we analyzed several tag-SNPs in candidate genes, we sequenced the genomic areas around the tag-SNPs associated with the disease. The sequencing was done in pooled samples. But now we have trouble finding a good method to determine the allele frequencies in these pooled samples. Anyone with experience with this type of problem?
The main problem in these types of analysis is the possibility of unequal pooling. On a data level this can be assessed to some extend by evaluating informative SNPs, if available. Some useful experiments and comparisons are described in these papers;
http://nar.oxfordjournals.org/content/33/3/e25.long
http://www.clinchem.org/content/48/9/1605.full
http://www.biomedcentral.com/1471-2164/13/16
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