Seeking to test saliva samples from donors for copy number of a specific gene that is subject to duplication and deletion (and which is hypothesized to predict a specific phenotype shared by participants, who are part of a disease community). In a basic sense, what are the best practices (and alternative approaches) to testing the saliva samples? Am presuming custom assay, to be done by a sequencing provider via multiplex qPCR, comparing yield to a non-varying gene that always has exactly two copies, using a pair of primers for each -- but am unfamiliar with best platforms or even if the above is a sound approach. Seek info to source the work from a standpoint of greater knowledge than currently. Please forgive ignorance; am a nonexpert and part of the disease community that seeks answers and to help others. Advice for assuring a robust result welcome. Thank you in advance for your insights!
For this targeted, not genome-wide approach you can use TaqMan copy number assays. There are many pre designed assasy for mouse and humans available. RNaseP is the reference gene most people use.
Thank you Jimbou for your helpful reply. I will check out the link and the approach you mention.