Why might my gene of interest drop out during WGA if it is not near a telomere or centromere?

There are a few regions, comprising a maximum of less than 0.2% of the genome, that are not amplified well because (we believe) the secondary or tertiary structure of the DNA over hundreds to thousands of bases results in poor priming efficiency.

We have developed reaction conditions that solve locus dropout in at least one case. We would like the opportunity to test our protocol on your gene of interest. If you could send us information regarding the locus that dropped out (ie, the SNPs of interest), we would check to see if we can amplify the region with our improved protocol. Alternatively, we could amplify some samples for you and send them back to you for your own testing. Please contact QIAGEN Technical Service if you are interested in this option.