November 15, 2011 | The CEO of the Inova Translational Medicine Institute (ITMI), which recently signed a major deal to sequence the genomes of hundreds of pre-term babies, has shed light on the motivation and goals of the partnership.
The Complete Genomics deal with ITMI calls for the sequencing of 1,500 genomes—including 250 pre-term babies, their parents and an equal number of controls. Complete Genomics will begin delivering sequencing results to ITMI in the next 2-3 months and expects to finish most of the 1,500 genomes in the first quarter of 2012.
ITMI CEO John Niederhuber believes that the project will yield clues as to the genetic basis of premature births, and potentially even therapeutic targets for various obstetrical abnormalities.
ITMI is a not-for-profit research institute within the Inova Health System in Northern Virginia. Niederhuber joined ITMI one year ago following his tenure as director of the National Cancer Institute (NCI). In that role, Niederhuber had already immersed himself in the potential medical benefits of next-generation sequencing (NGS). He launched a pilot program of The Cancer Genome Atlas (TCGA) with Francis Collins, director at the National Human Genome Research Institute at the time.
“When I left the government last July , I was wondering what could I do next?” Niederhuber says. “If we all believe the future of medicine is going to be transformed by this type of technology and others including proteomics, then maybe I could have some impact by working out how one is going to use this? Not just for research but making a difference at the point of care.”
Niederhuber’s initial focus was on cancer and other adult diseases, but he concluded that he would be echoing efforts going on elsewhere. On the other hand, he realized that Inova served a huge population of patients, with dozens of babies delivered every day, not to mention one of the largest regional neonatal intensive units (NICUs) at Inova Fairfax Hospital.
“Maybe the future of medicine is about being able to do this care characterization before birth or at birth and build from there, understanding the potential targets for managing risk and having a reference point if disease develops down the road. That’s really next-gen medicine! We know very little about the causes of obstetrical diseases. We have no clue at all about what causes preterm delivery,” he says.
Niederhuber received backing from his colleagues, including Inova CEO Knox Singleton. “They said, ‘No, you’re not crazy!’” Although he wondered if physicians and patients would be receptive, the ITMI proposal sailed through IRB approval.
ITMI plans to sequence 250 pre-term babies with no known congenital abnormalities and 250 full-term newborns, along with their parents, for a total of 1,500 genomes. ITMI has been recruiting families since last June, with more than 150 entered to date. The first group of samples has already been sent to Complete Genomics for sequencing.
Niederhuber says he had a lot of confidence in Complete Genomics “because of our past work at NCI”. He considered BGI as a potential outsourcing partner, but didn’t talk to the Chinese institute about this specific project. “That was because of its pilot nature, and I suppose I wanted more control and accessibility,” he says.
The initial goal for Niederhuber and his collaborators is “to mine that data and find markers for pre-term delivery.” But that will raise many more questions: “How are we going to integrate this information with the phenotypic information of patient care? How are we going to make that useful information at the point-of-care with the physician, who may not know much about genetics?”
A huge challenge will be the medical interpretation on the sequences. Niederhuber says that “conversations with a variety of entities” are taking place, with the goal of developing new interpretation tools, either in-house or in conjunction with others. “We will work with our own people, but we’ll also contract with others in partnership to apply the tools that exist. We’re very committed to trying not only to work on the data itself but also develop the tools to fill that space on the analytics side for patient care.”
The next phase of the program will include a longitudinal cohort of 2,000 offspring and is being finalized currently. Niederhuber outlined some of the likely areas of investigation: “What if we go to the obstetrics arena in the first trimester, and we consent the mothers, and look at proteins, genetics and so on, and follow through pregnancy? What if we followed after birth? What if we expand beyond parents into grandparents? That would be interesting.” •
This article also appeared in the November-December 2011 issue of Bio-IT World magazine. Subscribe today!