Illumina does not recommend using WGA samples as input for the Infinium HD Assay because the first step in the protocol is a WGA step. Our scientists observed up to a 4% decrease in call rate during limited internal testing. The decrease in call rate varied depending on the specific sample and WGA method used. Additionally, any allelic bias present in the original WGA sample might be compounded by another WGA reaction.
For the Infinium Assay, we recommend fragment sizes of at least 2 kb. The GoldenGate Assay can tolerate shorter fragments (> 200 bp) and is more forgiving of degraded samples.