A View from Emily Singer
Pacific Biosciences Sequencing Machine Unveiled
The company showed off its behemoth instrument at a conference in Florida this week.
Pacific Biosciences’ highly anticipated new sequencing machine has finally arrived.
The company unveiled the instrument to attendees of the Advances in Genome Biology and Technology meeting, a swanky event that has become the place to make a splash in sequencing. With venture funding of $266 million to date and a unique technology capable of reading single DNA molecules in real-time, Pacific Biosciences has been the most talked about sequencing start-up ever since it first emerged from stealth mode at the same conference in 2008. Indeed, Pacific Biosciences was named one of our TR50, top 50 most innovative companies.
The company also announced that it has already sold ten units–with a price tag of $695,000 each–with a number of sequencing centers waiting in the wings. (Included in the first round of customers are: Baylor College of Medicine, the Broad Institute, Cold Spring Harbor Laboratory, the US Department of Energy Joint Genome Institute, the Genome Center at Washington University, Monsanto, the National Cancer Institute/SAIC-Frederick, the National Center for Genome Resources, the Ontario Institute for Cancer Research, and Stanford University.)
It was at the 2008 conference that company founder Stephen Turner first made his oft-repeated claim for an instrument capable of sequencing a human genome in just 15 minutes. According to a preview at Bio-ITWorld.com, CEO Hugh Martin updated that prediction:
Even with future upgrades, Martin says the current machine will not be the one that delivers the ‘15-minute genome,’ as PacBio founder Stephen Turner claimed two years ago. Although the number of ZMWs on a SMRT cell will be doubled to 160,000 ZMW over time, PacBio will need 1 million to get the genome. “It’s probably [capable of delivering] a 2- or 3-hour genome.” The V2 instrument will reach the 15-minute target, but that isn’t scheduled for release now until 2014.
The Bio-IT piece also notes that
Martin did not preview trace data or discuss error rates in the machine preview. However, at full release later this year, he said the average read length will be 1000-1250 bases, fractionally longer than 454 or Sanger sequencing, with 5% reads between 3-5 kb. For a targeted sequencing experiment, “you’ll get 5% of 30% [the Poisson limit] of 80,000 [ZMWs]–so you get 1,000 reads in the 3-5 kb range for $99.” Despite the lower throughput compared to the high-end second-generation machines, Martin pointed to an advantage in flexibility, for example allowing diagnostic samples to be run without having to wait until sufficient samples make it worthwhile for a run on a 2nd-gen box.
Not everyone was impressed. Geneticist and blogger Daniel MacArthur noted in a recent post,
Overall, I can’t help but be underwhelmed by everything I’ve seen from PacBio so far, especially compared to the dramatically over-hyped claims (15 minute genome, anyone?) the company has become notorious for over the last couple of years.
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