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

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

Hosted by Robert Michel
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Smaller, more affordable sequencers and genome sequence interpretation computers are catching the interest of pathologists and medical laboratory scientists

In the field of whole human genome sequencing, the technology continues to improve at a remarkable pace. Products now entering the research and clinical marketplace offer speedier, more accurate gene sequencing capabilities at prices that are within the budget reach of many clinical laboratories and anatomic pathology group practices.

Miniaturization and lower cost is driving genomic medicine ever closer to the routine clinical setting. The combination of next generation gene sequencers with a smaller footprint and advances in genomic data analysis technology mean that genomic testing will increasingly migrate to smaller lab settings. Dark Daily offers its readers a look at some of the latest gene sequencing products and what their manufacturers say about the capabilities of these gene-sequencing systems.

Whole Human Genome Sequencing and Analysis

Until recently, the combination of time required to run a whole human genome sequence  and high instrument cost ($500,000-$750,000) have confined human genome sequencing to relatively few research laboratories. That is now changing in ways that promise increased genetic testing at the clinical level.

ion proton sequencer machine

Pictured here is the Ion Proton Sequencer, manufactured by Life Technologies. According to the company, this benchtop instrument can produce a whole human genome sequence in one day at a cost of $1,000. This system shows how next-generation gene sequencing technology is reaching the point where it offers clinical laboratories the necessary combination of accuracy, speed, and a low-enough cost to use this technology in clinical diagnostics. (Photo by Life Technologies Corporation)

Earlier this year, Life Technologies Corporation (NASDAQ: LIFE) started taking orders for a new benchtop sequencer, according to a company press release. The device, called the Ion Proton Sequencer, sequences the entire genome in one day at a cost of $1,000. This compares to the weeks or months and $5,000-$10,000 previously required to sequence a human genome, the release pointed out. The unit costs $149,000.

New Data Analysis Technology Offers Numerous Advantages

Meanwhile, in Cambridge, Massachusetts, Knome, Inc. (NYSE:HYB) has developed a powerful, file cabinet-sized computer to interpret sequencer data within the confines of a research or medical laboratory. Previously, accessing results required use of the Internet or distant servers.

knome knosys100

Pictured is Knome co-founder Jorge Conde with Knome, Inc.’s knoSYS100, a file cabinet-sized computer with enough storage and processing power to analyze a whole human genome in one day. As DNA sequencing gets faster and more affordable, new services and tools such as this are emerging to help researchers and clinical laboratory scientists utilize advances in genome sequencing. Such technological advances will help move genomic medicine into the hands of clinicians eager to use DNA sequencing to inform diagnosis and treatment. (Photo copyright Bio IT World.)

The appliance represents a significant advantage for patients concerned about privacy issues. “You have control over [the data] physically within your walls and logically within your network,” stated Lee Watkins, Jr., Director of Informatics at the Center for Inherited Disease Research at Johns Hopkins University, in a story in The New York Times. “Everyone’s DNA is a very personal thing.”

“When you would like to get genetic information quickly interpreted, and take it to the patient, this machine is right there” added Stephen B. Liggett, M.D., Director of the Center for Personalized Medicine and Genomics at the University of South Florida, in the Times.

Other advantages of genomic data interpretation technology include lower overhead for facilities and less personnel.

“Normally you need a slew of people to maintain a center to process this data,” observed Peter Nagy, M.D., Ph.D., Assistant Professor of Pathology and Cell Biology at Columbia University. “Basically this machine removes the need to maintain an expensive computational facility and a group of people who make sure the operating system is working and keep the reference data.”

The appliance is called the knoSYS100 and sells for $125,000. Technical support and regular updates of the software are available for $25,000 per year.

Machine Results Still Require Human Analysis

The machine downloads raw DNA sequencing data from sequencing companies, such as Illumina, Inc. (NASDAQ: ILMN) and Complete Genomics, Inc. (NASDAQ: GNOM), to a hard disk. The computer’s software algorithms then look for medically significant variances based on the investigator’s search criteria.

“You might filter down to the variants that matter for mutations known to be causative or associated with a disease,” Knome co-founder Jorge Conde explained. The data will help researchers investigate the genetic basis for cancer, rare diseases and drug response.

Baylor College of Medicine, Yale School of Medicine, and The Broad Institute are among the early adopters of the new technology, according to the press release issued by Life Technologies.

Larger labs, such as Cold Spring Harbor Laboratory (CSHL) on Long Island, may be less likely to benefit. “We have large clusters of equipment so that we can do analysis on site,” stated Michael C. Schatz, Ph.D., Assistant Professor at CSHL. “But a smaller institution might find value in a preconfigured unit that’s alive and ready to go.” Schatz was quoted in the Time piece.

The process still requires personnel highly trained in molecular biology and genetics. “We have to validate the items, confirming or rejecting the interpretations,” observed Nagy.

This migration of genomic sequencing and data analysis to smaller lab settings is a positive trend for clinical laboratories and pathology groups. As systems for sequencing whole human genome sequences become faster, more accurate, and cheaper, it will be feasible for medical laboratories in community hospitals to acquire and use these systems in ways that advance clinical care and allow labs to deliver greater value to physicians, patients, and payers.

Finally, alert Dark Daily readers may recall that a deal is on the table for Thermo Fisher Scientific (NYSE: TMO) of Waltham, Massachusetts, to acquire Life Technologies. This merger agreement was announced on April 15, 2013 and the purchase price is approximately $13.6 billion plus the assumption of about $2.2 billion in debt. The transaction is expected to close in 2014. (See Dark Daily, “Thermo Fisher to Buy Life Technologies for $13.6 Billion in Bid to Beef Up Its Share of Next-Generation Genetic Testing Market,”  April 17, 2013.)

—Pamela Scherer McLeod

Related Information:

Insight: New DNA Reader to Bring Promise

Life Technologies, Inc. press release

Knome Launches knoSYS 100 Genome Supercomputer to Enhance Interpretation

Genomic Analysis, the Office Edition

Thermo Fisher Scientific to Acquire Life Technologies Corporation

Thermo Fisher to Buy Life Technologies for $13.6 Billion in Bid to Beef Up Its Share of Next-Generation Genetic Testing Market