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Next-Gen Genomic Testing a Focal Point for Precision Medicine

Next-generation genomic testing strategies are turning into promising tools for precision medicine across the national research community.

By Jennifer Bresnick

- Precision medicine brings the promise of laser-focused treatments custom crafted for each individual based on their unique genetic makeup. 

Precision medicine and next-generation genomic testing

As researchers unlock more and more insights into conditions ranging from Alzheimer’s and cancer to diabetes and autism, it is becoming increasingly clear that a patient’s genes play a major role in the development of diseases and the effectiveness of available therapies.

Genome sequencing has become a vital weapon in the battle to create a working roadmap towards curing cancer, crafting new treatments for neurodegenerative diseases, and vastly reducing the burden of a wide range of other life-limiting conditions. 

In just a few short years, the process of sequencing the human genome has moved from a multi-million dollar effort to a simple test so cheap and easy that the results are available for a few thousand dollars in just a couple of days.

At the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC), which focuses on diagnosing and treating one of the deadliest pediatric cancers, fast and affordable DNA sequencing has made the difference between life and death for hundreds of children.

READ MORE: Precision Medicine Summit Brings Big Data, EHR Ideas Together

“The depth of the analysis that can be done now is staggering,” said NMTRC Chair Dr. Giselle Sholler to HealthITAnalytics.com.  “When we first started [using genetic sequencing for precision medicine applications], it would have taken over two months, but now we can do it in near real-time for our patients. 

“The sequencing that’s done by our partners at the Translational and Genomic Institute takes ten days,” she added.  “These are patients who just can’t wait more than a few weeks before having a treatment ready for them, so it’s a huge step forward.”

Patients can now have their tumors sequenced before starting expensive and arduous therapies that may or may not work for their particular type of cancer, and individuals at high risk of being impacted by genetic conditions can plan ahead for more eventualities or investigate treatments that may reduce the likelihood of future complications.

These advances in patient care have been fueled in part by the development of next-generation genomic sequencing techniques, which take advantage of the sheer volume of genetic data available to the research community.

Using a DNA library, next-generation genomic sequencing allows scientists to compare relatively small segments of a patient’s genome to standardized samples and extrapolating the results based on how well the two datasets align.  

READ MORE: NIH, Pharma Orgs Launch $215M Precision Medicine, Cancer Project

This method allows researchers to more quickly and efficiently discover new biomarkers for targeted conditions by comparing and contrasting new data with existing references, and may help geneticists tackle more precision medicine problems faster than ever before.

But a bioengineer at Rice University believes that current sequencing techniques are only scratching the surface of what is possible with next-generation technologies. 

With the help of $5.5 million in grant funding from the National Institutes of Health and the National Cancer Institute, researcher David Zhang plans to refine the way researchers comb through mostly healthy DNA to find the one or two sections that may contain items of interest.

Comparing the process of sequencing to finding a single colored bead in a large jar of white ones, he thinks his technique can help to clear the unremarkable data from view and make it more likely that researchers will hit upon the colored bead.

"In cancer, for example, most of your DNA are healthy," Zhang explained. "You only have a very small fraction that's cancer DNA.  We need a way to enrich DNA of interest by removing the vast majority of healthy DNA that does not provide meaningful scientific or clinical information.  If you're doing random sampling, chances are you'll only see the white [beads].  We can get rid of them to reveal all the unusual ones."

READ MORE: How Precision Medicine Will Shift from Research to Clinical Care

If successful, this strategy may help to form the foundation for rapid diagnostic tools available at the point of care.  The grant money will allow Rice University to purchase a next-generation sequencing machine.  Researchers at Texas Medical Center will also be able to use the machine, which Zhang hopes will encourage collaboration across the two organizations.

Next-generation sequencing has also shown promising results at UCLA, where researchers from the Jonsson Comprehensive Cancer Center were able to predict which patients with a certain type of brain cancer are more likely to benefit from specific treatments.

By tracking how T-cell levels changed throughout treatment for glioblastoma tumors, Dr. Robert Prins and Dr. Linda Liau were able to gauge the effectiveness of a personalized immune therapy treatment.

“We found that when there were elevated levels of T-cells initially present inside the glioblastoma tumor, the patients lived longer following immunotherapy compared to those without T-cell infiltration into their tumors, said Prins. “We also found that when there was a significant overlap of T-cells with the same T cell receptors in the tumor and in the blood, survival was also extended.”

As these and other precision medicine research projects spur new breakthroughs, the entire healthcare community is looking for ways to leverage the excitement around next-generation sequencing technologies.  Pharmaceutical companies, sequencing and testing facilities, data analysts, and other life science experts are eager to grab a portion of a staggeringly huge market opportunity.

A recent market report projects that that the next-generation sequencing market will be worth more than $27 billion by 2022, expanding at a compound annual growth rate of 40.1 percent.  The next-generation cancer diagnostics market, which is likely to rely heavily on advancements in genomic sequencing, may hit $20.25 billion by the start of the next decade.

Oncology, along with infectious diseases, have thus far driven a great deal of growth in this segment, and are likely to continue to push the market upward as researchers delve deeper into the development of more effective and efficient therapies for hard-to-treat cancers and other conditions.

Some researchers are even looking beyond the use of pharmaceuticals to treat the issues uncovered by genetic testing.  They intend to go straight back to the source.

Genome editing is the next logical step in precision medicine, although it is an area fraught with ethical debates.  This emerging area of science focuses on slicing out damaged sections of DNA and replacing the information with artificially engineered nucleases.

It may seem like science fiction, but explorations into this region of treatment and prevention are already bringing hundreds of millions of dollars in investments and spending. 

A BCC Research report estimates that the global genome editing market totaled more than $206 million in 2015 and close to $400 million in 2015.  The marketplace is likely to reach a whopping $2 billion by the end of the decade as scientists continue to refine the genome editing technology known as “CRISPR/Cas9,” said BCC Research analyst Mike Fan.

"Due to its wide range of potential applications, CRISPR/Cas9 has become not only a 'hot' research and development area, but also a hot topic of public discussion and debate, particularly because it may one day be used to make edits to human germ lines, which could pass to next generations,” he said. “In the pharmaceutical industry, drug makers are collaborating closely with genome editing specialized companies to speed the technology forward to clinic use."

As research centers, laboratories, vendors, and healthcare organizations continue to develop these and other precision medicine techniques, patients may soon find that DNA sequencing will become a routine aspect of care for many conditions. 

Plummeting costs and more familiarity with the potential benefits of next-generation technologies are likely to produce significant benefits for the development of personalized treatments as providers continue to seek innovative strategies for bringing the best possible care to those who need it most.

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