By Allison Proffitt
June 6, 2013 | Today’s biotech grail is surely genomics in the clinic—using sequencing to inform care, treatment, and disease prevention. Implementation is easier said than done, but Partners Healthcare has been doing it since 2005. Its GeneInsight suite of applications was awarded the 2013 Bio-IT World Best Practices Editors’ Prize.
Heidi Rehm of Brigham and Women’s Hospital and Director of the Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine (PCPGM) in Boston has been running a clinical genetics lab for over 10 years. For years the lab used Sanger sequencing, Rehm said, but was able to make major leaps in the volume of testing when it shifted to next generation sequencing a few years ago.
Thankfully, Rehm had been working closely with an IT team led by Sandy Aronson, Executive Director of IT of PCPGM to develop a platform designed to assist labs in, “storing genetic knowledge across genes and diseases and variants and tests in a way that allows data to be structured more efficiently,” Rehm says.
The problem isn’t a new one, and GeneInsight isn’t a new solution.
GeneInsight has been in, “full production clinical use since 2005,” says Aronson. “Our Laboratory for Molecular Medicine—[Rehm’s lab]—began providing sequence-based tests very quickly after it opened,” he says. “When you do sequencing-based tests you start finding these variants of unknown significance on a regular basis and you need mechanisms for dealing with that, and that really was the impetus for building GeneInsight and tracking the data and the knowledge lifecycle around each one of these variants.”
The platform has grown with the genetic data. The goal, Rehm says, has always been a platform that can effectively analyze data and automatically generate patient reports. Her lab has been using GeneInsight for over eight years and has generated 30,000 reports.
Two Sides, One Solution
The clinical genomics problem has always been two-sided, says Aronson.
“You have a physician that is treating patients, and you need to be able to both communicate results effectively to them, give them the ability to manage those results, and then also keep those clinicians up to date as more is learned about their patients over time,” he explains.
“From the laboratory perspective, what goes into that is you begin running genetic tests on patients, you start sequencing genes, and you find more and more variants of uncertain significance in those genes. And one of your objectives becomes to do as good a job as possible at re-classifying those variants… into pathogenic categories or benign categories.”
Building a platform to address those challenges needed to be multi-faceted.
“GeneInsight consists of a clinician-facing application that can be integrated with electronic health records or stand alone, a laboratory-focused application that manages knowledge, and facilitates reporting. Those applications can be federated either lab- to-clinic or lab-to-lab,” Aronson says.
The clinician-facing application—GeneInsight Clinic—simplifies genetic testing reports, while also staying dynamic. GeneInsight, “uses a lot of sophisticated rules-based logic to enable the auto-drafting of patient reports using patient-specific and disease-specific information,” explained Rehm. The platform delivers Web-based reports to physicians and can be integrated into several electronic health records (EHRs). But keeping the reports connected to the system, “allows the variant database to be connected to patient reports, so if knowledge changes in variants, it can be delivered in real time to physicians,” Rehm says.
Early on, Partners Healthcare knew that this wasn’t a task to tackle alone. “Even a place with the scope of Partners will not be able to curate the genome by themselves for every indication that could be seen in one of our patients. Achieving our goal required working with others,” Aronson said.
First, GeneInsight was registered as a Class 1 exempt medical device with FDA, so it could be shared with other labs and clinics across the country. Later, GeneInsight LLC was set up to facilitate that distribution.
Aronson says Partners is working with Mount Sinai Medical Center, the New York Genome Center, Illumina’s CLiA laboratory, Rehm’s lab, and ARUP Laboratories in Utah to define how “share and share alike” networks could work and what the governance surrounding that should be.
Aronson wants to encourage, “more and more places to operate under a model where in exchange for contributing your data… [labs] can benefit from the data that are contributed by other places.”
Rehm agrees that interpretation is the major bottleneck in clinical sequencing, and believes that as a community, “[we] can evolve and improve that process over time through widespread data sharing.”
Even after almost eight years, Aronson still has a GeneInsight wishlist. He plans to provide deeper support for kinds of variants that are becoming more and more important, such as structural variants and other types of omics data. He also hopes to develop deeper integration with clinical process to take advantage of the “clinical context” that clinicians can bring.
Editor’s Note: Heidi Rehm will be keynoting the 2nd annual The Clinical Genome Conference in San Francisco later this month, where she will address the evolution of clinical sequencing from targeting disease testing into whole genome and exome approaches, and compare and contrast and the benefits of one vs another. For more information, see http://www.clinicalgenomeconference.com/.