My project involves screening for novel SNPs in tumor samples. I've identified a novel SNP locus in a particular gene. How can I proceed to design primers for PCR testing on a bigger tumor sample? Is there any easy to use software to do that?
Hi Jason,
If you know the coordinate of your SNP, i.e. chromosomal location, you can go Primer-Blast Tool in NCBI website and add a region upstram and downstream to your target and then choose the parameters (product size)
So it is better to add nucleotides upstream and downstream for your gene from (Change region Shown) and click (update view), so the target region now is getting bigger depending on how many nucleotides you added to it.
From (Primer Pair Specificity Checking Parameters Specificity check) You need to be sure to select the right choice depending on your application and if you are working on humans. If so please choose (Genome, reference assembly for selected organism) and the number 9606 (human) will appear for the organism.
Finally, click on GET PRIMERS.
This is a direct way so you don't need to worry about having a software.
This is a bit old paper but still good. I'm not certain if this helps but wish you the best of luck !
Hi Jason,
If you know the coordinate of your SNP, i.e. chromosomal location, you can go Primer-Blast Tool in NCBI website and add a region upstram and downstream to your target and then choose the parameters (product size)
So it is better to add nucleotides upstream and downstream for your gene from (Change region Shown) and click (update view), so the target region now is getting bigger depending on how many nucleotides you added to it.
From (Primer Pair Specificity Checking Parameters Specificity check) You need to be sure to select the right choice depending on your application and if you are working on humans. If so please choose (Genome, reference assembly for selected organism) and the number 9606 (human) will appear for the organism.
Finally, click on GET PRIMERS.
This is a direct way so you don't need to worry about having a software.
Dear Jason,
I handled this question many times. If you want me to help, please contact me through my email: [email protected]
René
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