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A Single Man: Stephen Quake Q&A


By Kevin Davies

September 15, 2009 | Working on a single HeliScope instrument, Norma Neff, a research associate in the lab of Stanford professor Stephen Quake, generated the first single-molecule human genome sequence in just four runs in a month while Ph.D. student Dmitry Pushkarev handled the informatics. According to Quake, a.k.a. “patient zero” and co-founder of Helicos Biosciences, his group’s success—published in Nature Biotechnology in August—is proof of the growing democratization of genomics. “Literally three people did this work,” says Helicos president Steve Lombardi. “That’s a real harbinger of what we see the direction of this market going. It’ll be very interesting to see what Francis Collins, in his officially appointed role [as NIH Director], does with that!” Kevin Davies asked Quake about his landmark personal genome publication.

Bio•IT World: You talk a lot in the paper about the democratization of gene sequencing.  
Quake: There’s a table in the supplement which indicates the effort that’s been needed to sequence human genomes up until now. Our work is important at this time in that this is the first case [in which] you haven’t needed a genome center to sequence a human genome. What we’ve shown is that you can do it with a pretty modest set of resources—a single professor’s lab, one person doing the sequencing, one instrument, lower cost. Those are all order-of-magnitude improvements over what’s been published recently.

That being said, the DNA sequencing industry is certainly competitive. Everything is moving fast, very much in flux. All the manufacturers are improving their platform by a factor of two per year. I’m just saying, at this point in time, Helicos is the best platform, and they’re going to be in a dogfight to try to keep that title—which is good for the scientific community.

There’s very little mention of Helicos in the paper. Did you deliberately keep this a separate effort?
Yeah, it’s complicated. One of the reasons is the conflict-of-interest rules of my institutions… Stanford and the Howard Hughes Medical Institute. They have almost orthogonal, non-overlapping conflict-of-interest rules, very constraining. One upshot of that is I’m not allowed to collaborate with a company… It’s much more strict on the Hughes side; it’s like one of the Ten Commandments.

You didn’t buy the HeliScope, you collaborated with Stanford faculty?
Exactly. The machine was purchased by the stem cell institute at Stanford. The purchasing process was very transparent... The reason they bought it was not to sequence my genome, but to sequence cancer, tumor stem cell genomes. That’s what’s up next. Mine was just to practice, to show that we could do it and to get the informatics into place.

The supplementary information put the price of your genome at $48,000. Can you elaborate?
Those were just the reagent costs. The amortized machine cost is about another $10-20,000.

Why didn’t you name yourself in the paper as Patient Zero?
Well, you know, we wanted to retain some semblance of dignity for the scientific literature! It’s really irrelevant for the purposes of the paper.

Did your grad student write the variant calling algorithm out of necessity?
Helicos wrote a mapper, but not a base caller. We used their mapper, which is tuned to the error profile of the instrument. All the mapping softwares have been written with particular instrument performance in mind. For example, MAQ and ELAND are written basically for the Illumina platform, where the dominant error is substitution. For Helicos, the dominant error is deletion, and that has consequences for how you do the algorithm. We used the Helicos mapper [IndexDP], but then, all the base callers are tied to the mapping software. So ELAND and MAQ will call the bases, but it’s all linked into how they do the mapping. So we ended up writing our own base caller.

The genome coverage was 90%. Would you get higher coverage with more reads?
There are very repetitive parts of the genome that don’t map well. Most people aren’t mapping to the whole thing. The Chinese one was also 91-92%, something like that.

The paper notes the frequency of deletion errors...
Yeah, that’s the primary source of error—deletions due to these ‘dark bases.’ One of the reasons this is an interesting result for the academic literature is: Is it possible to sequence the human genome with reads that are a little shorter and different dominant error mode than you have on other platforms? We show that it’s definitely possible.

You’ve done some preliminary analysis of genetic conditions. Did you use Trait-o-matic?
That’s right. George [Church] was very kind, and ran it through Trait-o-matic. That’s where we got a preliminary annotation… We’re preparing another paper on the annotation. In fact, my medical colleagues have gotten really interested in this. There’s a small army doing a hand annotation for things that aren’t covered in Trait-o-matic yet, like pharmacogenomics. That’s going to be quite a lot of fun.

What other research uses do you foresee using the HeliScope?
We already have three more genomes in the can related to leukemia and cancer. We’re neck deep trying to analyze those and understand what they mean.

After a tough 2008 for Helicos, this must be a very timely publication?
It’s hard to say whether there will be any impact. It’s kind of a David vs. Goliath battle. There are four commercial platforms out there right now, and three of them are billion-dollar companies. The fourth is Helicos, which is a scrappy little bunch—they’re trying to hang on! I think they’re fantastic, and I’m hoping they’re going to end up at the top of the heap.  


This article also appeared in the September-October 2009 issue of Bio-IT World Magazine.
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