We have done in-silico analysis on SNPs (pathogenicity analysis, stability analysis, etc), which has given us the deleterious SNPs that were affecting protein structure. Now that we want 2 to 4 SNPs for experimental validation in a particular population using ARMS-PCR, my question is: how do we select the SNPs?
What if there is no literature on the SNPs but they are marked as deleterious?
How do we deal with such SNPs in the experiment?
Hi Waqas
a deleterious SNP doest not mean that it is retrieved in the literature, it depends on the population you're testing and what has been published on, since ssome SNP are specific to populations. Deleterious means that it's predicted to be on the future protein, it's just bioinformatics prediction without literature based knowledge.
try to see on the UCSC website (https://genome.ucsc.edu) with the OMIM optional track in the genome browser if you get more informations to run further.
all the best
fred
1. Filtering: Apply filters based on minor allele frequency(MAF), genotype quality and SNP location.
2. Functional prediction: use tools like SIFT, polyphen or mutatation taster to predict the functional impact of SNPs on protein function or gene regulation.
3.primer design: Design primers for PCR or sequencing assays to validate the selected SNPs.
4. Validation: perform experimental assays like Sanger sequencing or genotyping arrays to confirm the presence of the selected SNPs.
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