Comparison Between Seq Platforms.pdfVIP

Comparison Between Seq Platforms 12-11-26 8:13 PM Ion Proton vs MiSeq: any suggestion which platform is better? Our main application is targeted sequencing of cancer panel for clinical diagnosis. Shawn Baker ? Allen, as of right now Id say the MiSeq is the better bet. Its a more established technology than the Proton (which has just been released) and it seems to be producing higher quality data. But of the Ion Torrent systems, I would thought the PGM would be a better match than the Proton for targeted sequencing. Will you need the output of the PI chip (~10Gb)? Dale Yuzuki ? Im unafraid admit my bias - Im involved with Marketing the Ion Proton, for crying out loud - but will chime in here for the case that the Proton does represent the future, and that depending on the kinds of cancer panels you are looking at, the future of cancer clinical dx (i.e. whether whole exomes of tumor/normal pairs become routine), and the sample volume / turnaround time requirement, it isnt an easy which one is better answer, rather than which one is better for my present and expected future needs. A few examples will suffice. Say you want a comprehensive set of cancer- related genes for a wide-net screening project, a total of over 400 genes (represented by 16,000 amplicons). (Heres a link to the product flyer for reference:/content/sfs/brochures/Ion_CompCan cerPanel_Flyer.pdf) A 318 run can do about 350x coverage of a single sample, but a PI chip on the Proton could do multiple samples in a single 4- hour run. The MiSeq, by comparison, would have about the same coverage (doing 2x150bp reads) on the same target size (say using their TruSeq Custom Amplicon as they dont have an equivalent panel).2x250 reads wont help, as the insert size of the targets are too small, and would take about 27h for the run to finish. If you would then price out the relative sequencing costs, for the PGM 318 that would be a bit over $1,000 for a single sample, the MiSeq