Dear colleagues,
we did gene sequencing for two populations; patients and controls.
we have many results, new SNPs
how could I interpret this and what is the most effective statistical tests and method to use.
thank you
Here's a good place to start: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154648/
Dear Safia
Statistical analysis depends on the hypothesis of your study, and the goal of the experiment, for example, detect allele frequency? or detect a presence of a new mutation in a certain gene? or association of phenotypic trait ( disorder ) with certain allele?
Each case has its procedure
Good Luck
Case-Control sequencing study is classic, after you identify some new SNVs about the disease, you can make an annotation of these new SNVs, the software ANNOVAR may be useful, you can focus on the gene function and the frequency of these SNVs, the damaging(loss of function or missense variants) SNVs and rare SNVs is a good data to research, then if you find a significantly damaging genes, you can conduct experiments in cell or animal level.
Hope these methods can help you!
http://annovar.openbioinformatics.org/en/latest/
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