News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel

News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
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Goals are to use whole gene sequencing to develop better clinical laboratory assays in support of personalized medicine

Creating new clinical laboratory tests to support personalized medicine is one goal of a unique collaboration recently announced that involves the pathology department at Beth Israel Deaconess Medical Center (BIDMC) and GenomeQuest, Inc. (NASDAQ:GQ). The two collaborators are expanding a relationship launched several years ago that involved doing whole genome sequencing of tumors.

More specifically, the expanded relationship will be a two-year collaboration to develop whole-genome analysis (WGA) applications for personalized medicine. The move signals pathologists and clinical laboratory managers that first movers are taking steps to address the growing need for clinical genomics informatics infrastructure.

“The plummeting cost of sequencing and the increasing volume of predictive, public studies makes the clinical application of genomics not just a practicality but a healthcare imperative,” declared GenomeQuest CEO Richard Resnick. “We believe that our collaboration with a combined innovation and delivery leader like BIDMC is a major step forward in expanding genomics and its rewards from the bench to the bedside.”

Clinical Genomics Informatics Tools and Software

Harvard pathologist Mark S. Boguski, M.D., Ph.D., FACM by offered a number of observations about the partnership in an interview with GenomeWeb’s BioInform. He emphasized that personalized medicine based on next-generation sequencing technologies is driving the demand for clinical genomics informatics infrastructure.

Pictured above is Richard Resnick, CEO of GenomeQuest. His company is collaborating with the Department of Pathology and Laboratory Medicine at Beth Israel Deaconess Medical Center to use whole gene analysis (WGA) as a source of diagnostic information. Their mutual goal is to identify ways to use WGA to advance personalized medicine. This can come from improved diagnosis, as well as in helping clinicians better tailor the right therapies needed by individual patients. (Photo by GenomeQuest.)

This demand includes two basic components. The first is high-performance computing tools that incorporate genome analysis into routine clinical procedures. The second is software that can extract medically relevant data from the millions of sequences in the human genome.

Under the partnership agreement, GenomeQuest will provide the BIDMC Department of Pathology with the infrastructure and software applications it needs for its next-generation sequence-based projects. BIDMC pathologists will develop clinical-grade annotation methods and databases for diagnoses of cancers and other diseases.

“By partnering with GenomeQuest, our Department of Pathology will be able to perform genomic analyses and to collaborate with industry partners, without a heavy investment in information technology,” explained Jeffrey Saffitz, M.D., Ph.D. BIDMC Mallinckrodt Professor of Pathology. He was quoted in a statement on the partnership, which was published on GenomeQuest’s website. “The end result [of the partnership] will profoundly fine tune and improve patient diagnosis, treatment, and outcomes,” noted Saffitz.

Clinical Genomics Informatics Market Is Poised to Explode

The personalized medicine market is poised to explode. PriceWaterHouseCoopers estimates it will reach nearly $500 billion in 2015, Saffitz said.

In his interview, Boguski observed that gene sequencing and bioinformatics companies have invested significant resources into developing informatics tools. However, these tools are geared to the research market. Now, gene sequencing vendors realize that the real return on investment will come from developing informatics tools for the clinical diagnostics market.

Ironically, few sequencing vendors have taken advantage of the opportunity. Boguski offers one explanation: As yet, no one has developed a suitable business model. One goal of the GenomeQuest-BIDMC partnership is to do just that.

Yet another reason for the hesitation, Boguski noted, is the fact that the genomic research market has relied on open-source, rather than commercial tools. This shut out bioinformatics firms. Now, the rapid rise of clinical genomics is opening this opportunity for these companies.

Boguski sees the move of bioinformatics companies into the clinical informatics space as inevitable for two reasons. First is the accelerating demand for high-performance computing tools and software to handle extraction of sequenced genome data. Second is that the current market demand is too small to support the cost of creating a  viable open-source informatics infrastructure.

Boguski predicts that as sequencing costs drop, the data interpretation bottleneck will worsen and users will need “professional systems.” This is particularly true, he noted, in view of issues such as regulatory requirements for these systems.

[Genetic sequencing] centers who don’t have the expertise or who don’t want to develop their own software are going to have…to use [commercial] companies,” he stated.

Molecular Diagnostics Will Aid Pathologists in Delivering More Value

In the future, molecular diagnostics-based personalized medicine will depend on a single platform for next-generation sequencing, observed Boguski. Differentiation in the marketplace will be in the realm of high-performance computing tools and whole-genome analysis software.

“What will differentiate one molecular diagnostic test from another will be the algorithms and software filters put on whole-genome or transcriptome data,” he told BioInform.

Pathologists and clinical laboratory managers can expect that in the future, it will be the medical laboratories with computer crunch power and WGA software that thrive in the new landscape of personalized medicine.

—Pamela Scherer McLeod


Related Information:

Pathologists May Be Healthcare’s Rock Stars of Big Data in Genomic Medicine’s ’Third Wave’

Beth Israel Deaconess Medical Center and GenomeQuest Collaborate in Personalized health Care Initiative

Harvard’s Mark Boguski Outlines His Vision for a Clinical Genomics Informatics Infrastructure

Mark Buguski presented at Executive War College 2012