Bio-Info-Tech: The Cyborg Baby of Cheap Genomes and Cloud Data

By Razib Khan | March 8, 2012 9:00 am

By now you may have heard about Oxford Nanopore’s new whole-genome sequencing technology, which has the promise of taking the enterprise of sequencing an individual’s genome out of the basic science laboratory, and out to the consumer mass market. From what I gather the hype is not just vaporware; it’s a foretaste of what’s to come. But at the end of the day, this particular device is not the important point in any case. Do you know which firm popularized television? Probably not. When technology goes mainstream, it ceases to be buzzworthy. Rather, it becomes seamlessly integrated into our lives and disappears into the fabric of our daily background humdrum. The banality of what was innovation is a testament to its success. We’re on the cusp of the age when genomics becomes banal, and cutting-edge science becomes everyday utility.

Granted, the short-term impact of mass personal genomics is still going to be exceedingly technical. Scientific genealogy nuts will purchase the latest software, and argue over the esoteric aspects of “coverage,” (the redundancy of the sequence data, which correlates with accuracy) and the necessity of supplementing the genome with the epigenome. Physicians and other health professionals will add genomic information to the arsenal of their diagnostic toolkit, and an alphabet soup of new genome-related terms will wash over you as you visit a doctor’s office. Your genome is not you, but it certainly informs who you are. Your individual genome will become ever more important to your health care.

But this is all incremental change on the margins. Genetics has already been bleeding into daily life inexorably over the past generation. Who even thinks to note the battery of screening tests which newborns are put through now? The real revolution in our lives will be the merging of personal genomics with the information cloud more generally. Large corporations already have detailed data on your purchasing habits. Now imagine that every morning and evening you perform a biomarker assay at the cost of a pin prick. Consider the possibility that in ten years, millions—perhaps tens of millions—of individuals may trace their own biomarkers daily. Now imagine that all these data pour into the cloud, along with genomic information, age and sex, and purchasing habits. Additionally, position tracking will also generate a spatial profile of individuals over time.

Today correlation between cancer and location is the stuff of class-action lawsuits. But this sort of correlational science is often weak tea, and will seem pathetic in comparison to what is to come. Biological information technology will hyper-charge correlational science. From the cloud one can extract out patterns of elevated cancer risk, conditional on genetics, location, and lifestyle. Correlations of particular genomic features with purchasing habits will naturally fall out of the information stream. Data will reveal your risk based on exactly where you live, while controlling for genetic background. Currently medical trials runs into thousands of individuals, with coarse assessments of confounding variables. The new information cloud will increase the sample size to millions, and instead of self-reports it will be able to track confounds in real time!

You may wonder what this has specifically to do with the $1,000 genome. In many ways, modern genomics has been one of the first fields where such mass agglomerations have data have become the norm. Many techniques out of genomic science will be leveraged more generally across our lives. The Human Genome Project will be less relevant over the long term than the broader set of skills and methodologies that emerged out of it, and which became necessary for a whole generation of biologists. The $1,000 dollar genome will arrive within the next year or two, but the milestone will be forgotten soon enough. Rather, it will be a flag which heralds the birth of a new information age, when gray silicon and red goo merge together, as as the prefix bio on biotechnology starts to become archaic.

CATEGORIZED UNDER: Technology, Top Posts
  • http://community.jax.org/genetics_health/b/weblog/default.aspx Mark Wanner

    This is an interesting post, particularly with all the skepticism about genomic medicine being projected by the media today in the wake of the latest “cancer is complex” research study.

    I think your premise is valid on the technological level. On the other hand, I strongly doubt that the integration of genomic data with everyday life will be an easy or seamless process. Even after the obvious data bottlenecks and analysis challenges are effectively addressed, barriers await. An entrenched and genome-ignorant medical establishment–at all levels, from insurers to doctors–will be one. Ethical issues and privacy concerns will be another. To borrow Dr. Eric Topol’s phrase, the medical system will need to be creatively destroyed in order to fully benefit from advances in genomic and other technologies.

    Finally, regarding society’s tolerance for widespread genetic testing, is it really true that no one thinks about newborn screening? Parents of newborns in Minnesota might disagree!

  • Pingback: Not just genomics: the creeping future | Genetics Source()

  • http://www.documentroot.com doc

    I saw this and thought… this is the “cloud computing killer”. case-and-poit of why it’s impossible to drive biological computing to the cloud. 10 times the current data stream per sample with lower fidelity and far more local processing requirements. i suspect this trend will continue… data generation in biological computing vastly outstrips internet bandwith – especially in a laboratory setting. cloud computing becomes impossible, but fortunately the cost of the kind of multicore processing required has been plummetting, so standalone, local compute devicees for diagnostics will be doable

  • Pingback: Your Accessible Genome – Bridge8()

  • http://agctsequencing.wordpress.com Doug

    I think that some concerns that have been raised is that insurance companies will use genetic data to determine high risk for disease. Of course we are also beginning to understand that predisposition for disease in genetic terms does not include external factors currently studied in epigenetics.

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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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