Catalog of human variation

Applied Biosystems, TGen team up to hasten advent of personalized medicine

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PHOENIX—In another application of its SOLiD 3 system, Applied Biosystems, a division of Life Technologies Corp., and the Translational Genomics Research Institute (TGen) will cooperate in a strategic alliance designed to accelerate research into complex diseases and medical conditions aimed at progressing toward the goal of personalized medicine.

The SOLiD 3 System, Applied Biosystems' next-generation genomic analysis platform, will be used to sequence DNA from thousands of patients with a variety of diseases. The SOLiD trademark is the acronym for "Sequencing by Oligonucleotide Ligation and Detection."

Using methodology that focuses on selective amplification of a set of genes applied to a specific patient, TGen researchers will apply SOLiD sequencing technology across a broad spectrum of research efforts that focus on developing a more personalized approach to medicine that is specific to an individual's unique genetic makeup. The research will begin with three pilot phases, says Dr. Jeffrey Trent, president and scientific director of TGen, which aim to producing a catalog of human variation.

"By surveying a few people with high coverage, many people with low coverage and a third selective group, we'll determine how easy it is to discover genetic variation," Trent explains. "The SOPs we're developing will result in cost reductions that will help make genome sequencing a routine diagnostic tool in medical care," he says, but adds that cost reduction is not the stated goal of TGen.

In a related development, study results were released last month at the 100th annual meeting of the American Association for Cancer Research (AACR) in Denver by Dr. Daniel Von Hoff, TGen physician-in-chief, indicating that some cancer patients can experience longer periods when their tumors do not progress under treatments based on their individual genetic profiles.

The study shows that molecular profiling of patients can identify specific treatments for individuals, helping keep their cancer in check for significantly longer periods, and in some cases even shrinking tumors. The study included 66 patients at nine centers across the United States, all of whom had previously experienced growth of their tumors while undergoing as many as six prior cancer treatments, including conventional chemotherapy.

However, after molecular profiling identified precise targets, new treatments were administered that resulted in patients experiencing significant periods of time when there was no progression of their cancer, providing tantalizing evidence that personalized treatment holds exciting potential.

Using five SOLiD systems, Trent and other investigators will partner with Applied Biosystems scientists to perform six different projects focused on comprehensive characterization of genetic and molecular changes occurring within clinical cohorts for a variety of diseases, including cancer and autoimmune and neurological disorders. The scientists at TGen chose the SOLiD technology for this project, due to its inherent scalability, high-throughput and better than 99.94 percent data accuracy. TGen believes these attributes make the SOLiD system uniquely suited for translational research of complex diseases by enabling the detection of single nucleotide polymorphisms and other structural variations across the genome in large numbers of samples.

"Consistent with TGen's mission of developing the next generation of diagnostics and therapeutics, the alliance with Applied Biosystems forges ties with a key industry partner whose technologies align seamlessly with our research objectives and should produce accelerated progress in our efforts to better understand the genetic underpinnings of many diseases, with a particular emphasis on cancer," Trent says.

Lauren Lum, senior public relations manager for Life Technologies, says the anticipated impact for individuals with cancer, autoimmune and neurological disorders is that scientists will be able to characterize the genetic etiology of the disease.

"First, this can, as has been demonstrated for cancer, reveal potential intervention points that could be used to guide patient management and treatment," Lum says. "Second, the genetic variants that are implicated as being potentially causative of disease can feed target pipelines for drug discovery. In addition, these genetic markers have the potential to be used as diagnostic markers to determine risk and propensity for disease onset and recurrence. Early examples of these efforts are seen in instances where genomic and transcriptomic information from tumors have been used together with other clinical information about tumors to determine if tumors are responding to treatment. Beyond these areas, is the potential for these genetic biomarkers to be used to classify and stage diseases to harmonize the genetic profile of patients entering clinical trials. It is anticipated that this has the potential to improve R&D productivity in drug discovery efforts for these diseases."

Lum adds that Life Technologies anticipates that the SOLiD technology will be able to achieve up to 100Gb a run by the end of 2009 at a cost-per-run that is below $10,000. 

"Naturally, we are projecting that the costs per human genome will be substantially below that cost, and we will continue to decline to very affordable levels as improvements in throughput, bioinformatics and optimization to chemistries are made," Lum says. "In the potential eventuality that complete human sequencing can be performed for $1,000 or less, we would anticipate that the deployment of SOLiD for routine diagnostics could happen; however, this would require advances in bioinformatics, computational biology and interpretive software to enable clinical utility of genomics data."

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