HI everyone...New to NGS and require help on interpreting the data on IONTORRENT PGM

[sushantvinarkar]

Dear All,
We in our diagnostic molecular lab are doing Sanger Sequencing for many of the gene mutation analysis and few months back we have got Iontorrent PGM. The tehnical staff has progressed and till now we have completed 4 runs. We have started analysis of the data and I require help in regards how the data needs to be analysed especially taking in consideration of panels of gene and the Iontorrent platform.
We would like to take forward Iontorrent NGS platform for diagnostic reporting of gene mutations in our lab and would like to know in detail about how to go ahead in this regards(the precautions and the points to be taken into consideration before reporting of a mutation)
Hope to get response from the members as well as would like to know there experiences.
Thank you.

[GenoMax]

Have you had training from Ion for analysis of this data? Since you are a diagnostic lab you may want to get help from your local FAS. Regulation varies from country to country and you would want to do the right thing applicable in India.

Are you using targeted capture? What kind of informatics expertise do you have in your lab? In general you are going to do some basic QC, align, call variants, annotate the variants (e.g. using snpEff). Most of this can be done in Ion Reporter itself (software that runs on the server associated with your Ion PGM).

An alternate option may be to contract with one of the several knowledge based companies that operate out of India (e.g. Strand Genomics, Ocimum Biosolutions etc) to set up a SOP.