Sequencing Seattle: An Idea for the Future of the Northwest
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of genome sequencing is not the outlay for the sequences but rather the costs of storing, analyzing, annotating and communicating the results of the raw data. A commitment to sequence everyone in Seattle would require an additional, greater outlay of funds for analysis, and that money could funnel into our local institutions.
Few places in this country have comparable skill in genome analysis as the UW Genome Sciences Department, and none is better. The UW Genome Sciences Department would be the logical and (I expect) willing partner for building and maintaining the analysis pipeline. Likewise, the Seattle area is home to several companies, including Microsoft and Amazon, that would make natural and highly interested parties for storing data, assisting in the annotation, and providing platforms to help standardize and democratize giving data back to Seattle’s residents in easy to use, easy to understand, and portable online tools. Imagine the cocktail party chatter when you whip out your genome app.
A commitment to sequencing Seattle would also provide an irresistible draw to all kinds of smart, innovative, ambitious professionals, such as bioinformaticists, genetic counselors, database and internet security specialists, clinicians, project managers, biomedical researchers, and public health administrators, as well as people who will create the occupations we don’t even know of yet, that will be needed to deal with this kind of data and infrastructure. Economies aren’t driven solely by commodities and resources. Intellectual and human capital will only grow in importance.
Seattle is already one of the more popular destinations for people looking nationally for where to live and have a career, and it’s not just because of our great weather. They come because. Seattle has a reputation as a forward looking, progressive city with a keen technological edge and an investment in the future. Sequencing Seattle will enhance our reputation and strengthen our draw for the kinds of innovative, risk-taking, technologically-savvy people that keep a city and a culture from becoming as stale as a week-old baguette.
And let’s not overlook the financial implications of a sequenced population. The incredible resource of a large population of sequenced individuals will draw in public and private funding from the government, non-profit agencies, and pharmaceutical companies. ‘Applications by our researchers to the NIH will have an incredible advantage because the groundwork will already have been done for cutting edge genomic research. Given the push for evidence based medical treatments following healthcare reform, pharmaceutical companies are under increasing pressure to tailor their new drugs towards defined responding subpopulations. They could pay to have every person in their clinical trials sequenced. Or they can choose to hold their clinical trials in a place like Seattle where that hurdle will have already been cleared.
Here’s another benefit: cost savings for diagnostic and preventive medicine. No one needs to be told how health care costs are rising. Seattle can be on the forefront of taking genomic information and doing prospective studies on how that information can help guide medication, treatment, diagnosis, prognosis. We have one of the strongest concentrations in public health knowledge in the nation and can leverage that expertise to learn how genome information will make people healthier in the coming century. In addition, in just one area, oncology, we are already seeing the benefits of rapid tumor genome sequencing to identify cancer-promoting mutations. In this form of treatment, the baseline genome is compared to the tumor genome to look for changes. Having the baseline genome already in the database speeds analysis and amortizes the cost.
Seattle can also be on the forefront of figuring out how can genome data be best used ethically and effectively. This year the Presidential Commission for the Study of Bioethical Issues delivered their report on “Privacy and Progress in Whole Genome Sequencing.” We can play a key role in leading and shaping the ethics of genome sequencing.
Last, I want to touch on what could possibly be the most amazing outcome: citizen science, in which people are able to create their own research programs on the fly to answer questions. Imagine that all participants are in a database with their own preferences on what kinds of queries (health, phenotype, behavior, etc.) that they’d be willing to participate in. Someone comes up with a query and broadcasts it to the group: “Is there a genetic element to coffee preferences?” Anyone interested gets a text, chooses yes or no to participate, provides their feeling about vanilla lattes, and immediately the cohort is assembled, curated and QC’d by hard-coded heuristics developed by UW Genome Sciences and hosted on Amazon’s Web Services.
Within minutes, specific findings are reported back in whatever way you’ve selected. At the same time, ghostwriting software automatically generates an academic paper that is immediately submitted to an open-source journal and posted online. Maybe everyone contributes a dollar when they join in, to defray processing costs. And that’s how you empower people to use this infrastructure to do novel science.
These might seem like great benefits, but … Next Page »