I am planning to do NGS on human blood samples and my targets are 3 known mutations. The next step would be whole exome sequencing to look for any new variants. My question is how does NGS help in identification of novel.muations? Once we identify any variants,what next is to be done?
Are you looking for SNPs that are not in public databases? Are you looking for (known or unkown) SNPs that are associated with a phenotype (disease)? Question 1: it is likely that you will be able to identify new and private SNPs by performing whole exome sequencing several DNA samples. Question 2: you may discover SNPs associated with the phenotype if the statistical power is sufficient; If it is the case, this new result would be interesting even if the SNPs identified are registered in databases.
I did not get what do you mean by targets mutations? are you looking for known mutations? if you have a well known gene for your phenotype just sequence that gene with sanger sequencing. if you do not find mutation in known gene then you can go for whole exome/genome
sequencing.
I am looking for SNPs that are not in public databases. So I have to do whole exome sequencing of many DNA samples before I declare them as pathogenic and associated with the given disease.
ok. Thus, if you identify an unknown SNPs, you may ask the question: how does it work? how does the mutation alter a phenotype at the molecular level, at the cell level, and the organism level? Also, the next step would be to investigate the effect of your SNP on the sequence of amino acids and on the function of the protein, and its possible pathogenicity.
@Pascal Rihet Thank you. I got it now.
@Ambrin Fatima Yes im looking for known mutations.
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