Gene Sequencing, Watson and Computerized Medicine

Last week at the advances in Genome Biology and Technology meeting in Florida, Eric Schadt, CSO of Pacific Biosciences in Menlo Park touted a radically new procedure for sequencing. A much faster process, last week Schadt and his team traced the source of the Cholera in Haiti, sequencing five strains of cholera in less than an hour. It would have previously taken a week or more. Uniquely, the Pacific Bioscience machine sequences single molecules of DNA by adding fluorescent labelled bases that flash a defining color as they are added to the DNA strand.1 This technique eliminates averaging and amplification. The company projects a human genome in fifteen minutes by 2013. However, limitations of high cost, lower accuracy, 85%, and the number of sequences that they can read per run all require further evolution.

The genome and molecular biology in general will add vast amounts of raw data to the patient medical record. The implications of this vast database will be largely unknown. The challenge will be to correlate that data with the patient’s outcome as a means of advancing medical knowledge. The computer will correlate the data on an individual, clinical, regional, and presumably national level. Obviously, as the numbers grow with accumulated data over time and collated by region, the certainty of the observations will increase. On the clinic level, a simple statistical correlation over time will add knowledge, but on a regional or National scale, the studies will lead to data mining, unexpected surprises and statistical certainty.

Enter Watson. “IBM and Nuance Communications announced Thursday a research agreement to explore, develop and commercialize the Watson computing system’s advanced analytics capabilities in the health care industry.” --- “Columbia University Medical Center and the University of Maryland School of Medicine will contribute their medical expertise and research to the collaborative effort.”2

If Watson can come to understand medical narrative, language and terminology, such would obviate the necessity of converting doctor speak into a database format. By comparing patient data with the totality of medical information, Watson can write the book on diagnosis and treatment by its massive correlation between cause and effect. Watson is a game changer, perhaps as significant as the genome. Like the computer, Hal, in Carl Sagan’s 2001, the computer takes on omnipotence in answering the question – any question.

The larger challenge, however, might be in applying the technology. Who can ask, and how much does it cost? Will we continue to bank information behind the walls of the Digital Millennium Copyright Act (DMCA) or sequester knowledge with high cost, professional- access-only? Will clinicians and thus the patients pay dearly for access from the government, the Exchange, an insurance company, the hospital, a drug company or IBM? How many hands will be in this trough? The cost of current medical information drives the cost of patient care to no small measure. It could get worse. If on the other hand, we make Watson’s memory base affordable to all physicians and associated providers, the positive impact on quality healthcare will be immeasurable.

In a not too distant time, might Watson 2.0’s massive parallel circuitry answer all 300 million of our questions simultaneously? Could not everyone have access to appropriate medical information? One-viewpoint demands free Information, like free speech for all. Another view argues for professional interpretation. There may be more to Watson than meets the eye, and a hope that IBM will get it right.

1. Nature 470 10Feb 2011 p155
2. http://www.healthcareitnews.com/news/ibm-nuance-apply-watson-analytics-healthcare%E2%80%A8