I performed the genotyping of breast cancer patients. I am willing to analyze the data for haplotypes analysis, cluster view and phylogenetic tree. In pyrosequencing the results comes in the form of pyrogram (attachment page 1), but I am still confused to find out the minor allele frequency (MAF) in samples and what allele (major or minor) I should used to calculate this (attachment page 2).
Secondly, I will be grateful if someone guide me any other test/analysis that I could performed by using this data.
Thanks
Dear Faisal!
There are export functions in the PyroMark software, which can be used to export the data. These data is easily imported into Excel or any other software were you can calculate the MAF. Concerning the allele to use, will depend on the variant. A general rule might b to use the reference allele in HG19 och HG20 as the wild type.
Dear Faisal
The purpose of Henrik is very excellent as approach so you can complete also your litterature by reading manuscript entitled : Pyrosequencing in genotyping and epigenetic Studies. Gerald Schock. 2012.Direct link : http://cgs.hku.hk/portal/files/GRC/Events/Seminars/2012/20120328/pyrosequencing%20in%20genotyping%20%20epigentic%20studies.pdf
Another interesting link: https://icmb.utexas.edu/images/ICMB/Facilities/Pyrosequencing-and-its-applications.pdf
Hoping it will be helpful
Marius
Dear Henrik Gréen and Marius K. Somda
Thanks for your reply and kind guidance. Actually, I performed the pyrosequencing at the end of last year in Bordeaux, France. Due to lack of guidance I take the hard copies of pyrogram and prepare the excel file and came back to Pakistan. Now I am willing to know which allele is major or minor, but I don't know how to perform know about MAF. I try to contact the person Institute Bergonie but they are not replying the email. Time is going on and I am still confused in analysis of data.
Is there any other way that I can calculate the MAF from Pygrogram (peaks etc).
Kindly guide me in this regard.
Thanks
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