ndSNPQC of 162 samples ran in triplicate across three laboratories with the Affymetrix OncoScan® assay. The inter-sample ndSNPQC variance is larger than the mean of the intra-sample ndSNPQC variances. These inter-sample ndSNPQC differences are governed by inherent properties of the samples. TSBIDs 00019-74 have a markedly lower ndSNPQC in sample-runs performed at laboratory B. Investigating the source of this difference we identified that the DNA for these samples was plated in two separate events and only laboratory B used plates from the second plating event.