Trends in Biotechnology

There's been a mini-furor over how a recent Cold Spring Harbor Conference triggered a complaint by the magazine Genome Technology about how their journalists were under restrictions that bloggers and twitterers weren't. Here's another blog entry to catch you up.

Personalized medicine and next-gen sequencing are the most exciting, and most hyped, things happening in the field. The presence of both was felt at the conference because both require lots of informatics/IT support. As realists, we want to dampen our excitement somewhat because the flood of data (as you'll read about below) doesn't always lead to more knowledge. As optimists, however, we believe that the promise of personalized medicine and the potential illumination yielded by next-gen sequencing are real, not hype alone.

There was a panel discussion at Bio-IT World that focused on personalized medicine. It included people from Navigenics, Knome, the 1000 Genomes Project, and Complete Genomics, among others. It's clear that genotype data, and soon complete genomic sequence data, will be available for a large number of people. However, you do have to make the distinction between genetic risk data that is useful for the scientific community for research purposes, and that which is useful for a particular individual. There's no doubt that the results of genome-wide association studies (GWAS) are providing a lot of interesting data for researchers and informaticians, but the leap to say that this data is useful for the individual is less obvious. Most genetic risk factors are relatively weak by themselves, and often provide a prediction of increased risk that is very modest. Additionally, such risk factors as APOE for Alzheimer's don't come with any preventative treatment options so it's unclear what benefit they have for the individual.

I was fortunate enough to attend the American Association of Cancer Researchers (AACR) meeting in Denver the week before Bio-IT World. Bio-IT World was filled with talks and discussions about how technologies such as next-generation sequencing, which have the potential to generate huge amounts of data, are requiring changes in IT and informatics. But a theme at AACR, from several speakers, was that data itself does not solve the problems of understanding the underlying biology of disease. And understanding the biology is how new therapeutics and diagnostics are going to come about.

Gathering clinical trial information rapidly, and acting on it, allows research to react flexibly to its own outcomes, saving time and money. Technology allows researchers to view genomic data in a systematic way (as a system), revealing new insights. The BIO IT World conference attendees are a biased crowd, believers that software can help, witnessed by the provocatively titled session about how technology "...will Help Clinical Investigators Reduce Their Paperwork and Get Back to their Real Work."

Georgetown's Lombardi Cancer Center is attempting to bring together disparate systems so they can better make sense of their information and treat patients. NCI's Ken Beutow spoke of cycling between clinical care, research, and back. Integration is more than ETL, it requires understanding the business purpose of different systems or databases, and finding the right way to integrate information to provide the right pathways and answers.

And share "freely and generously," as Benjamin Franklin put it - that idea was echoed by many. Notionally, it's simple; technically...a bit more complicated. The standards debate will continue. That said, the appeal of the benefits that standards provide - access to information - can be outweighed by their implementation cost. Standards can help information be shared and used in ways its originators hadn't imagined...as Eric Schadt put it, "We're not going to make progress by publishing papers" - understanding results, and having access to data, spurs progress.

Does the format of the information matter, or does access to the information matter? Is a large infrastructure required to support sharing? Somewhere between an emailed spreadsheet and a complex interoperable infrastructure lies a way to get information in a meaningful way, easily. That's all we need to do to speed the pace of progress, huh? Guess that's why most of us are here.