I understand that comparing own sequence data with unselected controls from ancestry-matched population examined by projects such as the 1000 Genomes and HapMap can give an indication as to whether there is any variation in allele frequencies, provided that the disease is rare and these populations can be considered as unselected controls. Does anyone have any recommendation on how to carry out this comparison? At the moment I have allele frequencies and functional prediction (e.g. synonymous or nonsynonymous). When does one decide to sequence a set of controls? What are the considerations one has to keep in mind when comparing own data for cases with publicly available control data as opposed to own genotyped controls?
Can you elaborate on your question. Is your data coming from SNP arrays or Exome sequencing?
Thank you for your reply. I genotype my cases by Sanger sequencing, so I can identify both rare and common variants in the coding regions of a gene of interest