Wednesday, 9 February 2011

1st feedback from Ion Torrent at AGBT

Definitely exciting! Wished I was there instead of reading twitter and blog reports on the event. 
During a Life Tech conference workshop, Kevin McKernan, vice president of advanced research R&D, said that PGM customers can expect a 10-fold increase in output about every six months.
Since Life Tech launched the system in December, it has announced its first chip upgrade, from the Ion 314 Chip to the Ion 316 Chip. The upgrade promises to increase the output from 10 to 100 megabases per run and will be available to early-access customers this quarter, and more generally in the second quarter (IS 1/11/2011).
The best internal run today has yielded 300,000 reads 100 base pairs in length of quality Q17, according to Maneesh Jain, Ion Torrent's vice president of marketing and business development, who spoke during a separate Ion Torrent conference workshop. He said that the company plans to "address" RNA-seq as an additional application "later in the year."
The system's read length is currently about 100 base pairs. According to information provided during the Life Tech and Ion Torrent workshops, read length is expected to increase to 200 base pairs in the fourth quarter and to 400 base pairs in 2012.
McKernan said that in a single run to sequence the E. coli genome, the system provided "uniform genome coverage regardless of GC content." Coverage of human genes has also been "very even" and has included areas that were missed by both SOLiD and Illumina sequencing, he said.
The PGM's per-base accuracy also continues to improve. According to McKernan, based on 50-base reads, it was about 98.7 percent at the end of 2010 and has since improved to 99.6 percent. In the second quarter of this year, it is projected to improve further, he added.
The company has also improved the accuracy for homopolymer regions, he said, largely based on better software. While the per base accuracy for a stretch of four identical bases was 94 percent at the end of last year, it has increased to 98 percent for five identical bases today, and is expected to go up to 99 percent during the second half of this year.

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