Grid Computing in Medical Research

Oxford University announced in a press release the Integrative Biology Project.  Excerpt:

"[The project] aims to build a giant computing grid to support the modelling of complex biological systems, which will use advanced computer simulations to help understand and treat disease. The international, multi-institutional and cross-disciplinary project team includes world experts on the modelling of heart disease and cancer.  The intention is to use computing power to bring together knowledge at all the different levels of biological understanding – from gene function to physiology – in order to provide a coherent theory of biology which can be applied to disease."

The Integrative Biology Project homepage is here.

Further description of the project can be found in this Vnunet article.

7 Trends in 2 Newsletters

Disease Management News, a subscription based newsletter (here), recently published an article describing 7 key trends in disease management in 2004.  The article has been reprinted (pdf) at the Better Health Technologies webpage.  Here are the seven trends:

1) Cost Management Will Continue to Be the Primary Driver of DM Technology Adoption
2) Predictive Modeling Technologies Will Focus on “Impactability”
3) Information and Communication Technologies Will Enable DM Assembling as a Viable Business Strategy
4) Consumer Electronics Giants Will Bring DM into the Living Room
5) Remote Patient Monitoring and Wireless Technologies Will Enable “Healthcare Unbound”
6) Personalization Technologies Will Allow Patients to “Have It Your Way”
7) The Electronic Health Record Will Break From the Pack

Thanks to Matthew Holt for the pointer.


SALVATORE SALAMONE, LSID: An Informatics Lifesaver, Bio-IT World, Jan 12 2004.

The vast array of informatics data available today makes it difficult to automate data access and sharing, which in turn makes it difficult to set up production-quality workflows in the research environment.

The Interoperable Informatics Infrastructure Consortium (I3C) is trying to tackle such issues with a new naming standard and data access protocol called the Life Science Identifier (LSID). At its core, LSID provides a uniform way to name and locate specific pieces of informatics data over the Internet.

…Similar to a URL, LSID uses a uniform resource name (URN) to locate data. The URN contains five parameters…that uniquely identify the data of interest.

…To take advantage of the URN in an informatics application requires two pieces of software: a client piece within an informatics application, and a server piece associated with the actual data.

…With LSID, an organization continues to use its normal routines for generating and storing informatics data. The only thing that changes when using LSID is that there is an alternative access route.

ABI’s SNPlex Genotyping System

Malorye A. Branca, ABI Enters High-Throughput Genotyping Market with SNPlex, Bio-IT World. Jan 16 2004.

The SNPlex System makes use of ABI’s 3730xl and 3730 instruments, which are already popular DNA analyzers. It combines the company’s Oligonucleotide Ligation Assays with capillary electrophoresis for detection, ABI GeneMapper software for allele-calling and quality control, and a new data-mining program called BioTrekker.

SNPlex can process up to 48 SNPs (single nucleotide polymorphisms) from a single sample at once. With the 95-capillary system, it can analyze more than 4,500 SNPs, in about 15 minutes, or 400,000 in 24 hours. The company hopes to have the system up to 192 SNPs per sample soon. That would allow one million genotypes, per instrument, per day…

…large-scale studies… [of] diseases like diabetes, schizophrenia, or stroke…require millions of SNPs in hundreds to thousands of patient samples.

Nutritional Genomics Reviewed

Jim Kaput and Raymond L. Rodriguez, Nutritional genomics: the next frontier in the postgenomic era, Physiol. Genomics 16: 166-177, 2004.  (only abstract available free) (UPDATE: now full-text available online for free here)

"The interface between the nutritional environment and cellular/genetic processes is being referred to as "nutrigenomics." Nutrigenomics seeks to provide a molecular genetic understanding for how common dietary chemicals (i.e., nutrition) affect health by altering the _expression and/or structure of an individual’s genetic makeup. The fundamental concepts of the field are that the progression from a healthy phenotype to a chronic disease phenotype must occur by changes in gene _expression or by differences in activities of proteins and enzymes and that dietary chemicals directly or indirectly regulate the _expression of genomic information. We present a conceptual basis and specific examples for this new branch of genomic research that focuses on the tenets of nutritional genomics: 1) common dietary chemicals act on the human genome, either directly or indirectly, to alter gene _expression or structure; 2) under certain circumstances and in some individuals, diet can be a serious risk factor for a number of diseases; 3) some diet-regulated genes (and their normal, common variants) are likely to play a role in the onset, incidence, progression, and/or severity of chronic diseases; 4) the degree to which diet influences the balance between healthy and disease states may depend on an individual’s genetic makeup; and 5) dietary intervention based on knowledge of nutritional requirement, nutritional status, and genotype (i.e., "individualized nutrition") can be used to prevent, mitigate, or cure chronic disease."

Patrick J. Stover, Nutritional genomics, Physiol. Genomics 16: 161-165, 2004. (only abstract available free)

"The integration of genomics into nutritional sciences has illuminated the complexity of genome responses to nutritional exposures while offering opportunities to increase the effectiveness of nutritional interventions, both clinical and population based. Nutrients elicit multiple physiological responses that affect genome stability, imprinting, expression, and viability. These effects confer both health benefits and risks, some of which may not become apparent until later in life. Nutritional genomics challenges us to understand the reciprocal and complex interactions among the human genome and dietary components in normal physiology and pathophysiology. Understanding these interactions will refine current definitions of benefit and risk and lead to the establishment of dietary recommendations that have a high predictive value, minimize the risk of unintended consequences, and account for the modifying effects of human genetic variation. Furthermore, nutritional genomics will enable the design of effective dietary regimens for the prevention and management of complex chronic disease. This review focuses on new perspectives that have been presented to the nutritional sciences by the advent of genomics, and new challenges that demand attention because of their potential impact on, and immediate translation into, current public health nutrition recommendations and interventions."



DNA series on PBS.  Check your local listings here.


IT and Evidence-Based Medicine

Bill Briggs, Working Together: I.T. and Evidence-based Medicine. Health Data Management, Jan 15 2004.

"Until very recently, the most reliable source clinicians had for current best practices was the medical textbook…

"Today…clinicians striving to practice evidence-based medicine gain instant access to a mountain of information on best practices through information technology. And provider organizations are using I.T. to mine their own data and access external clinical evidence-based guidelines from a range of data sources. Their goal is to get current information into the hands of clinicians where they need it most: at the point of care, where patient treatment decisions are made. The payoffs, many experts say, include reduced medical errors, greater operating efficiency and improved patient care. Sooner or later, higher reimbursement levels might be tied to evidence-based medicine as well.

"…Data on best practices and other research is being mined internally and accessed externally via the Internet from many sites. The challenge for provider organizations is how to put global data in context and apply it to the individual patient."

"…Evidence-based medicine requires merging data from external sources along with that of patient-specific data residing locally in multiple information systems, including electronic medical records and computerized physician order entry. All are necessary to feed information on a given situation to hardwired or mobile computers to support clinicians’ decisions at—or near—the point of care."

The article looks at a couple early adopters of evidence-based medicine, including Vanderbilt University Medical Center.  William Stead, M.D., the associate vice chancellor for health affairs and director of the Informatics Center at Vanderbilt is quoted toward the end of the article:  “I don’t think the average physician here or elsewhere really knows when they are following the evidence and when they are not…Nor are they aware of the frequency at which they are not following the evidence. I don’t think Vanderbilt or anyone else is practicing evidence-based medicine to the degree we need to.”

UPDATE: A little back-and-forth on IT and Evidenced-Based Medicine (EBM) over at Matthew Holt.


Another information thepary oriented product, this one from InterMap Systems is called the HealthMap Platform.  Check out this page to download a flash demo.

IBM and Information-Based Medicine

Nancy Weil, New IBM Unit Integrates Drug Research, Healthcare. HealthIT World. Jan 13 2004.

"IBM has started a new business unit focused on medicine within its life science division, promising to help customers integrate healthcare data, including research, genetic tests, patient medical records, clinical trials records, and medical images…IBM has coined the phrase ‘information-based medicine’ to describe its approach to integrating, mining, analyzing, and managing medical data from a variety of sources."

"…’What we see happening is the convergence between life sciences, healthcare, and IT,’ [VP Mike] Svinte said. ‘The thought is that convergence really has the ability to change the way healthcare is delivered, to change the diagnosis and treatment.’"

"…The field of information-based medicine is so new that a successful business model has not yet been clearly defined…The key question is who will pay for such data-integration systems."


Read more

Going to Church on Personal Genomes

Patricia Thomas, DNA as Data, Harvard Magazine Jan-Feb 2004.

"I am convinced that we will want our personal genome possibly more than we want a personal computer," [George] Church says. Although obtaining such information is extremely expensive at present, he anticipates that "the same kind of people who pay to go into space" will soon be having their genetic code deciphered. As for making personal genomes as affordable as personal computers, he says, "I don’t know what year that will be, but it will probably happen so fast that people will be amazed."

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