Sequencing Seattle: An Idea for the Future of the Northwest

4/3/13

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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.

How?

These might seem like great benefits, but … Next Page »

Kyle Serikawa works as a Senior Research Scientist in Genomics for Novo Nordisk. He is a recent graduate and current board member for Leadership Tomorrow in Seattle. The views expressed on this post are his and do not necessarily reflect the views of Novo Nordisk. Follow @

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  • Me

    I think it’s an excellent idea. A few caveats, though, and one warning. One of the caveats is that many of the benefits of sequencing a large population will be reaped by the world as a whole, and not particularly by the Seatlleites (is that the word? Are children there ‘microseattleites’ – I digress). This is of course no bad thing and will boost Seattle’s profile, but beware of assuming a tight linkage between local outlay and local returns in a project like this. In particular, the sequencing (and analysis) will only be a small part of the outlay if an aim is to feed back into healthcare for the local community.

    Another caveat, at least from the perspective of improving the understanding of genome/phenome links, is that the best data won’t necessarily come from sequencing one community. On the other hand, the idea of “sequencing Seattle” is an attractive and accessible one, far more so than (say) phenotype-targetted national or international programs.

    Finally, a warning would be that each new round of technology has its day and its big projects, only to be superseded when the next technology comes along. Few people can now remember much about the big SNP surveys, for example, which were going to give us rich data and answer all questions. And where are all those CEPH families now? The same will happen with whole genome sequencing – it will be superseded by massively parallel surveys that include methylation or chromatin patterning in respect to gene expression; or it will be realized that the most stubborn genome-based problems are accessible only in the context of somatic variation; or something will come along that we haven’t yet dreamt of.

    But, as a rallying cry, “sequence Seattle” isn’t a bad starting point.

  • LJStewartTweet

    Great Idea. Seattle has the big data crunchers and sharing mentality to make this a reality. And also people could donate their brain’s to research in case of death too.

  • Kyle Serikawa

    Those are excellent caveats, and its true there’s no guarantee that most or even a majority of benefits would accrue specifically to Seattle. As I think about this, however, I

  • Kyle Serikawa

    (whoops, clicked too soon) hope the benefit would come from building an integrated public/private partnership that would allow everyone to make progress faster and better, which would provide a long term business and social benefit advantage to Seattle. Application builders would interact closely with both producers and users of the genetic information to create more efficiently. I’d also hope that as new technologies arise, people will keep up with them, and if we can continue to attract good people to our area, that probability goes up. When we talk about the key attributes of knowledge workers in the 21st century, I think the most important one will be adaptability.