I have some samples (cancer tissues) analyzed with OncoScan FFPE array platform. I saw that there are 96 signature SNPs which are used by the Chromosome Analysis Suite (ChAs) for checking that the AT and GC channel CEL files are correctly matched and classified. I was wondering whether is possible to get the genotype calls for other SNPs/positions. And if yes, how can one do that. I need to check if samples that are labelled as coming from the same patient (normal tissue - primary tumor - relapse) are correctly matched and classified. Some samples are analyzed using the CytoScanHD platform, for which I have the genotype calls (from ChAs) and other with OncoScan FFPE. Basically I selected a list of SNPs that are really well able to maximize the distance (computed using SPIAssay R package, https://cran.r-project.org/web/packages/SPIAssay/index.html) between two unrelated samples, at least among CytoScanHD samples, and I need to do the same also for the other (OncoScan FFPE) samples.
Thank you in advance!