One of the more powerful and exciting applications for benchtop sequencing platforms is targeted sequencing panels.  These panels allow sequencing of targeted regions of the genome amplified by multiplexed PCR amplicon pools.  This allows for rapid, sensitive, and specific amplification of targets and rapid sequencing of samples.  These panels allow us to deliver results to customers with our standard ten business day turnaround time for benchtop sequencers.  To check the performance of these panels we tested three of the Ion Torrent AmpliSeq Ready-to-use Panels with DNA isolated from a well characterized colon cancer cell line, CCL-225 (HCT-15).  The Inherited Disease Panel was also run on Craig Venter HuRef (NS12911) DNA.

This is a guest post contributed by Dr. Brad Chapman from the Harvard School of Public Health. Original post can be found here.

By now you have heard that Roche has submitted a hostile takeover bid for Illumina to the tune of over $5 billion USD. If you have not you can read about the particulars here.

Early speculation has it that this will turbocharge the effort to have DNA sequencing used routinely in the clinic given Roche’s distribution channels and partners in diagnostics. My question is, "Are the clinics, and the clinicians, ready for this very powerful tool to arrive on their doorstep?" Clearly it would take at least a year for Roche to fully digest the acquisition but they already have been making inroads via their 454 instrument. Having a platform like the MiSeq would only hasten their ability to deliver a truly robust system to the diagnostic marketplace.

So much for a slow journey, huh? I leave the office for a day and I miss the announcement of the improvements to Illumina’s two DNA sequencing instruments, the HiSeq and the MiSeq. In case you missed it, you can learn more here. Now it seems we have a choice of platform, should we want our whole genomes in one day, either the HiSeq® 2500 or the ion torrent Proton machine, which we covered in our previous blog post.

The cool thing about the HiSeq 2500 is that it will have dual running modes. Want a genome in a day? Switch to a mode that will deliver 120 Gb of data in 27 hours, roughly equivalent to a human whole genome at 40X coverage. Need more data? Switch to a second mode and generate 600 Gb of data over approximately 11 days.

A recent blogpost at BioLektures explains why it isn’t really fair to compare MiSeq and Ion Torrent data based on their predicted quality scores, as Ion Torrent tends to undercall quality across their reads.  Illumina’s predicted quality score algorithm, however, is more accurate in predicting the actual quality score.  In a recent application note Illumina compares predicted quality scores between their MiSe