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Next-Gen Tools Have Near-Term Applications in the Clinic, Companies Say

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Next-generation sequencing and related tools are inching closer to the clinic. At the International Congress of Human Genetics meeting held last month in Montreal, Quebec, representatives from next-gen technology companies discussed near-term applications of their tools, including how they may be used in the clinic. "Right now, [sequencing] cost declined so fast in the last 12 months, it surprised us," said Martin Reese, co-founder and CEO of Omicia.

There have been some successes in applying next-generation sequencing approaches to clinical problems, like childhood genetic disorders or cancer. For example, Reese points out that researchers at Omicia and the University of Utah used the company's Variant Annotation, Analysis, and Selection Tool, or VAAST, to identify a gene variant associated with a lethal X-linked disorder in infants. Further, sequencing is finding many applications in cancer to match up mutations in patients' tumors to the drugs that target those mutations. "Cancer is undergoing an amazing revolution," said Roopom Banerjee, president and CEO of RainDance Technologies.

Other clinical applications are falling right in line. Eric Schadt from Pacific Biosciences and Mount Sinai School of Medicine in New York said that Mount Sinai's newborn screening facility is moving toward using next-gen approaches to search for variants related to diseases like Tay-Sachs. Such applications, he said, are likely to be the first to obtain regulatory approval for clinical use.

Another use for next-gen sequencing approaches in the hospital environment is to track hospital-acquired infections like MRSA. As sequencing becomes even faster, samples could be taken from different spots throughout any given hospital at different times and sequenced the same day to monitor the spread of nosocomial infections. Such hospital-acquired infections are a top contributor to the cost of hospital stays, Schadt added. Indeed, according to an Archives of Internal Medicine study from last year, health care-associated sepsis and pneumonia led to $8.1 billion of in-hospital costs in the US in 2006.

As next-gen sequencing data flows into the clinic, physicians have to be ready to make use of it. "Traditionally, genetic counselors and medical geneticists have lagged two to three years behind" academia in adopting new methods, Banerjee said, adding that his company is investing in targeted sequencing to get clinical-grade sequence information to healthcare professionals.

In addition, patient privacy is also a concern. "It is extremely important," said Andreas Sundquist, co-founder, president, and CEO of DNAnexus. Rules like the US Health Insurance Portability and Accountability Act can guide the process. However, he said, just because data is in the cloud does not mean that it is public — most data centers have good security in place. In the longer term, "the days of being anonymous are over," Schadt said.

"We are at the age of genomic medicine today," Omicia's Reese added, "but it is only the beginning."

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