Early Proton Users Report Good Data, Rapid Exomes; Look Forward to Sample Prep and Automation Improvements
November 09, 2012
SAN FRANCISCO — Following the launch of its Ion Proton desktop sequencer in September, Life Technologies officials said this week that more than 7,000 runs have been completed on the system in the company's own labs and in the labs of its customers.
One such customer, Joe Boland of the National Cancer Institute, reported during a workshop at the American Society of Human Genetics conference here this week that his lab has done 50 runs on its four Proton machines and is routinely generating between 8 gigabases and 9 gigabases of data per run with read lengths of around 150 base pairs.
He said that when the machines were first installed in September, throughput was 4 to 6 gigabases and reads were 100 bases, but this rapidly increased to 8 gigabases of throughput and reads of 150 base pairs. Already, the team has had some runs over 10 gigabases and expects to routinely generate between 9 gigabases and 11 gigabases by the end of the year.
Accuracy, too, has improved, Boland said, and is around 99 percent, which is "absolutely fine for what we need."
The NCI lab also houses two Illumina HiSeq 2000 instruments, one MiSeq, and six Ion Torrent PGM machines.
Boland said he planned to use the Protons primarily for rapid exome sequencing, as well as "high-level" amplicon sequencing of between 500 and 1,000 samples, and whole transcriptome sequencing.
The bulk of NCI's sequencing is exomes, Boland said, and the lab's two HiSeq instruments produce 56 exomes per machine every six to eight days, so "our pipeline is constantly full."
The Protons will be used to both increase capacity as well as to sequence exomes for which a rapid turnaround is needed. Additionally, if there are technical difficulties with a sample on the HiSeq it can go directly to the Proton, instead of going back into the HiSeq queue.
Boland said that the center's first exome runs on the Proton using Nimblegen capture array covered about 80 percent of the exome at 20-fold coverage. As the lab continues to gain experience, he said, the percent of the exome covered is continuing to improve, and the lab is now covering just below 90 percent of the exome at 20-fold coverage. Average coverage is around 100-fold.
The team has also tested transcriptome sequencing on the Proton. Using version 2 of the Ion Total RNA Kit and between five and 500 nanograms of input poly-A RNA, he was able to generate 50 million reads from a melanoma cancer sample, compared to just 2.5 million reads using the PGM 316 chip.
Going forward, Boland said that he is looking forward to sample-prep improvements and automation with the Avalanche sample prep chemistry and the Ion Chef system, products that Life Tech is planning to launch in 2013 (IS 9/18/2012).
Avalanche is Ion's emulsion-free PCR sample prep chemistry, which it plans to launch next year. Similar to the company's Wildfire technology for its SOLiD systems, Avalanche will based on isothermal amplification. Meantime, Ion Chef is a system for automating sample prep, reducing hands-on time, and thus increasing the efficiency of chip loading.
"That consistency will be key," Boland said of the Ion Chef.
Harvard’s George Church Enters Genomics X PRIZE Competition
By Kevin Davies
October 4, 2012 | BOSTON—At the Consumer Genetics Conference (CGC)* yesterday, Harvard Medical School professor George Church announced that his group will be entering the Archon Genomics X PRIZE presented by Express Scripts.
Church and colleagues at the Wyss Institute for Biologically Inspired Engineering at Harvard University become the second team to enter the $10 million contest to sequence the genomes of 100 centenarians, following Life Technologies declaration a few months ago.
“The sequencing of exceptionally old yet healthy individuals may tell us more about health than studies focused on so-called common diseases in younger individuals,” said Church, in a statement. “The importance of what types of DNA can protect against human ailments hasn’t been studied enough, and the availability of open-access genomic data on such individuals will be invaluable.”
The contest itself will be held in September 2013. Teams have until May next year to officially register for the competition.
During his keynote at CGC, however, Church said the field of next-generation sequencing was moving so fast that he would not commit to which particular technology his team would be entering until nearer the competition date.
Ironically Church has good relations with the first company to enter the X PRIZE contest, Life Technologies, as his prolific group has developed concepts or technologies that have been involved to some degree or other in the technologies underlying Life Technologies’ SOLiD sequencing system, the Ion Torrent platform, as well as nanopore sequencing favored by start-ups such as Genia Technologies (Life has invested in Genia).
Church paid tribute to the promise of the Ion Proton desktop sequencer, which has just started shipping from Life Technologies. The mark 3 version, he said, would have a total of 1.2 billion pixels, while noting that the key enzyme, DNA polymerase, had the ability to go some 60,000 times faster.
Church also pointed to immense potential for nanopore sequencing, as well as new work in his lab and others on in situ sequencing.
In another announcement, Church noted that his group had entered into three-way collaboration with scientists at Columbia University to leverage Genia Technology’s nanopore system, which utilizes a CMOS (complementary metal-oxide semiconductor) device, to accelerate the use of DNA sequencing in the clinic.
Your assumption is that he needs/wants more money. He has so much money he can never spend it all. I am sure he has more interesting things to do with his time, like visit his house in Vail. This is a poor indicator of the health of a stock. Are you a fear monger?