By Monica Heger
Marking one of the first examples of a healthcare system adopting next-generation sequencing, Inova Translational Medicine Institute recently signed an agreement with Complete Genomics for the sequencing of 1,500 genomes, including those of 250 babies born prematurely, 250 normal babies, and both parents of all 500 children.
The project, which aims to identify prognostic, diagnostic, and therapeutic targets for preterm birth, is serving as a pilot for evaluating how whole-genome sequencing could be implemented within a healthcare setting and is the first step toward broader adoption of sequencing within Inova, John Niederhuber, CEO of Inova Translational Medicine Institute, told Clinical Sequencing News.
Niederhuber said that Inova would like to expand to a larger cohort of 2,000 babies by 2012 and "follow that cohort longitudinally" to study not only perinatal disease and preterm birth, but also to see if markers of childhood obesity, developmental disorders, or childhood diabetes can be identified. Additionally, "we're in the planning stages for similar types of projects for adult chronic disease," he said.
While Complete Genomics announced the deal with Inova in an August conference call to discuss its second-quarter earnings (CSN 8/9/2011), neither partner disclosed details about the project at the time.
Niderhuber said this week that Inova has already enrolled "well over" 150 families and has received enormous interest from patients and physicians. "We have had tremendous cooperation and patient acceptance," he said. "The rate at which we've been accumulating families is only limited by the number of personnel we have."
Complete Genomics will do the sequencing and will provide initial, basic analysis, but the majority of the interpretation will be done by Inova. Niederhuber said the institute aims to develop additional partnerships for analysis and interpretation of the data.
He said the team chose to start with preterm birth because Inova is home to one of the largest neonatal units in the country and has a large obstetrics program — around 19,000 births per year are in the Inova healthcare system.
Additionally, "we don't really know anything at all about the causes of some obstetric diseases that women have — preeclampsia, the delivery of a preterm birth of unknown cause — let alone all the congenital defects that occur in the process of embryonic development and birth," he said.
Because the team is sequencing whole genomes, it is likely that they will stumble upon other clinically relevant variants not related to preterm birth. How exactly the team plans to deal with those findings is still being worked out, said Niederhuber.
"From an ethical standpoint, if something came up that we felt was very unusual or important to a family or patient, we would certainly look at that information very carefully, and suggest to the physicians who are responsible for caring for that family that further testing be done," he said.
At the same time, though, "the project is not set up and designed to make a specific informative impact on the patient or patient's family," and the consent forms are set up in such a way that all of the patient are aware of that.
[ pagebreak ]
Aside from looking for markers of preterm birth, the project will serve as a model for a broader implementation of whole-genome sequencing in a healthcare setting.
Niederhuber said that the Inova team is already in the planning stages of a larger project, which will sequence 2,000 babies at birth and follow them longitudinally.
The details of that project have not all been ironed out, but he said the goal would be to create a database of genomes, which "will be a powerful information resource to look for all kinds of things." Additionally, the team plans to study how the genomic information could be used later in life for predicting disease risk.
"As you get older, if you have [your genome] as a reference basis, is that important? If I develop a malignancy or asthma or congestive heart failure, is it helpful to be able to refer back to that early, at-birth genomic information?" These are all questions Niederhuber said he hopes to address in the larger study.
While the project is one of the first examples of whole-genome sequencing being applied in a healthcare setting, it is also a shift for Complete Genomics from research-oriented projects to clinically oriented projects.
Complete's CEO Clifford Reid told CSN that he expects the company to sign increasingly more clinically focused deals. "Up to now, the market has been largely limited to the research market," he said. "But, we're seeing more customers like Inova who are interested in doing clinical sequencing.
Complete Genomics is currently pursuing CLIA certification in order to tap into the clinical market, and Reid said he expects to be CLIA certified by the middle of next year. "It's a very high priority," he said.
The Inova contract is one of the first examples or a sequencing project of this scale — 1,500 genomes — "that is not funded by the government or a disease foundation, but by a healthcare system," Reid added. He predicted that other large healthcare systems would follow suit.
Whether healthcare systems looking to implement next-gen sequencing will use the outsourcing model, like Inova, or purchase their own sequencers remains to be seen, but Niederhuber said it made sense to outsource the sequencing.
"For us to build our own sequencing farm would not make a great deal of sense. The technology is continually changing and we'd be constantly trying to catch up," he said. Rather, he said, Invoa looked for partners that could "be on the cutting edge of the technology, and provide the service and the early tier 1 and tier 2 analysis."
Niederhuber added that the time is right to start implementing these types of large, clinically focused sequencing projects. "The technology is rapidly approaching the point in time when it is economically feasible," he said. The main remaining challenges are in the analysis and interpretation of the data and figuring out how genomic information can be applied broadly to impact individual health, in terms of predicting disease risk, diagnostics, and knowing what drugs will or will not be effective.
"At Inova we're trying to see if we can lead in terms of beginning to make this available to physicians and their patients, initially in a very targeted way and only where it seems to be very relevant and important information, but I think we're certainly moving in that direction," Niederhuber said.
Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.