Which of the plasmid copy number detection protocol can help? Protocols on net ? Can anyone specify any ideal protocol? Please send some recent reviews or papers even in animal system if you have..A good statistical explanation is what I am also looking for..
I think it is a good and reliable method for the detection of copy number if you have information about the copy number of the reference gene, One can carry out the analysis using the genomic DNA
There are different ways CNVs can be detected or validated, but the method you choose will depend on what you are trying to find.
- If you want to detect CNVs in multiple genes or regions of a genome (other than by WGS) you can use arrayCGH (aCGH, as mentioned above) or by SNP arrays such as (Affymetrix SNP 6.0 or CytoScanHD)
- If you want to detect CNV in a specific gene then real time PCR (qPCR, as mentioned above) or digital droplet PCR (ddPCR) approach could be used.
in my opinion, i can suggest you to use DDPCR, Digital PCR, an end-point PCR method, does not rely on assumptions of perfect amplification efficiency or on reference standards to reach high precision in copy number enumeration.
for the statistical part it's better to used R software and specially you can use CNVtools ( A package to test genetic association with CNV data ) or matlab bioinformatic toolbox.
for the protocol and how to use you can read this protocol
Chapter Copy Number Variation Analysis by Droplet Digital PCR
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