Supercomputer analyses patient's genetic fingerprint to individualise cancer treatment

Atlanta 03 May 2001Researchers at the Winship Cancer Institute at Emory University are teaming with NuTec Sciences Inc. and IBM to develop an integrated information system which will enable physicians to tailor cancer treatments based on a patient's specific genetic makeup. NuTec and IBM have combined disparate technologies to create GenesysSI, a new generation of information system for the onco-pharmaceutical environment. This integrated genomics-based information management system incorporates technologies for storing, retrieving, processing, and analysing patient genetic and clinical data.


Bringing the genomics revolution out of the laboratory and much closer to the patient, this system is designed for use directly by physicians to provide timely information to support the day-to-day treatment decisions of cancer patients. When fully deployed later this year, the system will pinpoint genes and gene combinations which cause cancer in individual patients, as well as highlight genetic risk factors which would suggest the need for early screenings of cancer. It will eliminate much of the guesswork involved with prescribing cancer treatments which today are often ineffective or lead to harmful side effects. Determining the genetic "fingerprint" of a patient's cancer will allow physicians to select the specific treatment which has been proven most effective against similar tumours.

"Armed with genomic information and the computational power of the NuTec/IBM system, we can identify, with exact precision and speed, novel drug targets to treat individual patients' tumours", said Dr. Jonathan W. Simons, director, Winship Cancer Institute, Emory University. "The ability to quickly get complex target analyses for tens of thousands of genes, as well as clinical data, in the same time frame that it takes to get CT scans today is a monumental step in personalised medicine for cancer."

Another major benefit of the system will be the ability for pharmaceutical companies to load clinical trials with patients who have been identified with the genetically-specific cancers for which their drugs are being tested, greatly decreasing the time it takes to bring those drugs to market. According to the American Cancer Society, more than one million people are diagnosed with cancer each year. Every day, more than 1500 Americans die from cancer, which has become the second leading cause of death in the United States.

The new GenesysSI (Seamless Informatics) system will combine leading-edge NuTec Sciences software for searching and analysing gene expression and the gene combinations behind complex and often fatal diseases with the processing power of the world's fastest commercial supercomputer. NuTec Sciences' supercluster of 1250 IBM eServer systems disposes of a processing capacity of 7.5 trillion calculations per second, which ranks among the top 10 of the world's 500 largest supercomputers. This is the fastest computer system installed outside a governmental agency. IBM disk storage systems and software for Web application serving, portals for information, and data management and integration will augment the system, enabling NuTec to transmit timely results to doctors, who can then consult with their patients using desktop and handheld computers.

The GenesysSI system will work by comparing a consenting patient's genetic "fingerprint" to thousands of different genetic profiles from the various public and private databases. Before, gene data was only compared on a one-to-one basis, a time-consuming and tedious process. The genetic fingerprint of the cancer patient will be analysed from blood and tissue samples that are computerised and charted using micro-array chips. These images will be transmitted electronically to the NuTec supercomputer, where algorithms will be run to analyse disease-causing gene combinations and determine the most effective treatments available, including new drugs being tested in clinical trials.

The results, which in most cases will be returned within hours instead of weeks or months, will be sent via the Internet to Emory, where doctors can review the reports with their patients and make treatment recommendations. "The GenesysSI system was designed with the goal of improving patient care", commented Dr. Michael S. Keehan, chairman of NuTec Sciences. "Our ability to quickly scan thousands of genes at the same time to determine differences in gene expression between normal and diseased cells will lead to improved cancer care. Working hand in hand, Emory University researchers, NuTec Sciences and IBM have designed a system that will help accelerate the diagnostic process and provide the clinician with the kind of time-relevant information needed for customised medicine."

Emory expects the system will be fully operational by the end of 2001. Emory researchers are focused initially on the four most common forms of cancer, which are breast, colorectal, lung, and prostate cancers. Hospitals around the country will be able to subscribe to the GenesysSI system on an annual basis. "This system will showcase how information technology can advance medical research and patient care", stated Dr. Caroline Kovac, vice president, IBM Life Sciences Solutions. "Right now, although there are many excellent drugs in the pipeline for treating cancer, selecting the right one for a particular patient is a trial-and-error process."

The Winship Cancer Institute is the co-ordinating centre for clinical cancer treatment programmes and research throughout Emory University, including medical, surgical, and radiation oncology, diagnostic imaging and the sub-specialities of cancer care, ranging from blood and bone marrow stem cell transplantation to internationally recognised breast reconstruction. The Winship Cancer Institute offers new therapies usually not available outside university-affiliated medical centres, including more than 200 clinical trials for all tumour types and stages of cancer.

NuTec Sciences' Life Sciences Division provides time-sensitive solutions to help pharmaceutical, biotechnology and academic clients compress their basic research and drug discovery timelines. NuTec Sciences' offerings include search and analysis tools for gene expression, gene combinatorics and proteomics, as well as database management and visualisation solutions for the integration of clinical and genetic data. IBM Life Sciences Solutions brings together IBM resources, from research and e-business expertise to data and storage management and high-performance computing, to deliver new solutions to the life sciences market, including biotechnology, genomic, e-health, pharmaceutical and agri-business companies.

Leslie Versweyveld

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