The simple way to test if you have contamination is sequencing your own DNA as well as one of the tubes you prepared without any saliva sample. If there is any contamination, you will find in the no-saliva tube your DNA results.

for each dna extraction you need to do the control extraction using for instance sterile water instead of your saliva sample with your buffers and reagents.

Contamination is a common problem especially with PCR amplification methods, in hybridization (microarray) should not be a problem,

for illumina snp just run your own DNA and you will know your snp profile ....

but still the amount of your DNA in the tested samples will be negligible probably below detection limit

Hi,

I would agree to the other answers especially as this will show you the accumulated background from your workflow. In general I do not expect that some individual cells will massively impact as long as your extraction yields high amounts of DNA which I would assume to be the case.

Best Sven

Personal experience, cross contamination is always possible that is why during analysis, analyst profile must be included (e.g. forensic labs have their own internal database for their analysts). We used cheek cells for STR profiling.

Thanks @Dale. That has been the practice in our lab since we routinely do STR analysis. We also use reagent blanks and PCR negative control to rule out possible contamination. Based on experience contamination from analysts is rare if the sample amount is high. I have no experience yet handling samples for NGS that's why I'm a bit concerned with contamination issues. But yes same principle, as others have advised I will have my own genome sequenced and SNP typed.