SNP screen question - (Feb/04/2004 )
I want to screen the coding region of a gene for unknown SNPs, which method is simple and effective? sequencing or SSCP?
Thank you in advance for your answer.
There is an article on this question here
There are many techniques for SNP detection (discovery) and genotyping of known SNPs, especially high throughput technology.
If you are only interested in one gene and are not going to analyze hundreds of samples, I think sequencing and SSCP are the choice. First design several sets of primers to cover the whole region of your gene, then do PCR on a mixture of DNA from different individuals (like 20-30), and then sequence your pcr products. If there is overlapping peak at some position, you will know there will be a potential SNP.
Does it make sense? If I am wrong, pls correct me.
I agree with rassen, it all depends on the number of samples you would like to test. If 5-10 I would probably do SSCP first and thereafter sequence the interesting ones