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Pleased with Beta Test, TGen to Use Illumina's RapidTrack Service for Rare Disorder Sequencing

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Beta testers of Illumina’s recently announced RapidTrack sequencing service said they have been impressed with its ease and data quality and plan to continue to use it to study rare childhood diseases.

Illumina last month launched RapidTrack through its FastTrack Sequencing Services business. The new offering is based on the HiSeq 2500 and offers a whole human genome in less than two weeks at a minimum of 30x average coverage from as little as 3 µg of sample. The company claims that RapidTrack offers the fastest sample-to-data turnaround of any current whole human genome sequencing service at a price of $9,500 per individual sample or $7,600 per genome for groups of 50 or more samples.

David Craig and Matthew Huentelman, co-directors of the Center for Rare Childhood Disorders at the Translational Genomics Research Institute, are some of the first to use the service. In collaboration with Illumina, the two completed a beta test of RapidTrack using samples from two patients of the center.

According to the two directors and their clinical collaborator, Vinodh Narayanan, rare childhood disease is a great first target for such a rapid service. Though TGen has considerable experience with its own in-house sequencing capabilities, Craig and Huentelman told Clinical Sequencing News that the ease and speed of the RapidTrack service makes it an attractive alternative to avoid backlog and get quick results for patients.

"For this first test we just contributed two samples," Huentelman said. "We haven't done more samples to date, but we're definitely interested in running more and we are queuing some up now."

The group chose two cases with different clinical presentations for the first tests. Narayanan explained that one was a likely mitochondrial disorder, while the other was a child from a consanguineous marriage with an inherited ataxia.

"We sent out the samples Monday, and received the hard drive the following Tuesday," Craig said. In both cases, the RapidTrack sequencing results yielded promising candidates for the cause of the subject's symptoms, he said, though only one — the mitochondrial disorder case — was a clear match.

For that sample, Craig said, the discovery was almost immediate after examining the RapidTrack data. "We got the hard drives, and the data was on the computers around 9 at night, and by 9:15 for that one individual, there was a clear match between the clinical phenotype description and a gene that had what looked like a compound heterozygote hit," he said.

Huentelman added that for the other subject, while the genetic cause may not be as clear, there are some definite candidates that he and Craig are continuing to consider as they analyze more of the RapidTrack data.

According to the two directors, the data quality of the service exceeded what they see with their in-house sequencing using the HiSeq 2000.

"I don’t know all the specifics in terms of the chemistry," Craig said. "But my impression was that the HiSeq 2500 data that came off was equivalent to MiSeq, which basically means the read quality at length doesn't die off as soon as it [does], let's say, on the HiSeq 2000 we have."

"So it would be superior quality to what we would internally generate, and I think that has to do with the fact that there isn't a chemical reaction going on on a slide for 12 days. It's more like two days … so my impression was that it's really good data."

For example, Craig said, in the mitochondrial disorder case, the promising variant the group identified included an 11-base indel. "Seeing an 11-base indel is not always possible. But [with the RapidTrack data], indels and some of the more complex variants that require really high-quality data were reasonably good," he said. "Better than we would get [internally]."

Huentelman also stressed that there are more subtle advantages to outsourcing the nuts and bolts of sequencing, especially with such a rapid turnaround time. "We prepare samples as quickly as we can and get them on a sequencer, but … sometimes there's either not enough personnel time or there are samples prepped and not enough sequencer space and we might have to have a hard pause. That was the attractive part of being able to make use of the service," he said.

Craig and Huentelman said they have used other services, like Complete Genomics, for applications where there is less urgency. But for the rare childhood disease work, and some other potential applications, the longer time frames of other approaches are less suitable.

Complete Genomics said in its most recent quarterly earnings call that its turnaround time was around 80 days, up from a low of 62 days in the third quarter of 2011 (IS 5/8/2012). Company officials said that they are working to improve this and that they are also working toward a two-week turnaround time for clinical customers for some time after the end of this year (CSN 3/14/12).

Pricing for the Complete Genomics service varies based on the number of genomes ordered, but the average price per genome it reported for the first quarter was $4,333.

Craig said the TGen team is "definitely" interested in continuing to use the RapidTrack service and is queuing up additional samples for it now.

Illumina announced with its introduction of the service that it is working on moving RapidTrack to its CLIA-approved lab, a goal that it reiterated this week (see story, this issue). Craig said that regardless of whether the sequencing is done in the company's research or clinical lab, his group would still do its own independent CLIA validation on all samples it runs through RapidTrack. "That part of it isn't as important to us as the turnaround time aspect," he said.

"The striking aspect for us was the feeling, 'That was easy,'" Craig said. "It was just very cool that for one of [the samples], within 20 or 30 minutes it seemed very clear to us what the best candidate was."

It raises the question, he said. "How often do we really want to be doing all of this internally?"

Huentelman added, "When you … take something your lab does really well and have someone else do it for you, there are a few concerns: One, how much it's going to cost you; Two, if it's going to be as good as you can do yourself."

Craig said that the cost-benefit analysis of the RapidTrack services is compelling. "If you do the math on how much this costs and include the fact that you have a $700,000 machine with a three-year lifespan, and it's $4,000 just to buy the reagents [for a single genome], it's not too hard to get close to that $9,500" per-genome cost of the RapidTrack service, Craig continued.

Internal sequencing could end up saving only $1,000 to $2,000 per genome, "so it kind of reshapes your thinking," he said. "You could see you might want to spend your time on more complex assays like ChIP-seq, methyl-seq, RNA-seq."

The group's immediate plans for the RapidTrack treatment include sample sizes in the "tens," Craig said.

Other Users

An Illumina representative told CSN that Christopher Mason, a biomedical researcher at Weill Cornell Medical College, is also an early user of the RapidTrack service.

Another researcher, Stephen Kingsmore of Children's Mercy Hospital, has not used RapidTrack per se, but has been engaged with the company in a separate program using the HiSeq 2500 to sequence samples from infants in the hospital's neonatal intensive care unit on an even more accelerated turnaround timeline of about two days.

Kingsmore gave a webinar presentation last month discussing his experience sending samples to Illumina for sequencing on the HiSeq 2500 and using software to narrow results — a process his group has dubbed 'STAT-Seq' — which allowed his team to find the genetic cause of acute illnesses in several infants (CSN 7/18/2012).

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