Data Yearning to Become Expensive Information

Posted by Pete Shanks August 6, 2014
Biopolitical Times
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Several initiatives have surfaced recently that hope to move genomics more effectively toward medical applications. They are trying to link genomic and phenotypic data, establish baselines for health, and use computational techniques to move the science forward. Some seem more promising than others; even discounting for self-promotion, Craig Venter may be leading the pack.

The highest-profile and clearly most political announcement was made in the UK by Prime Minister David Cameron on August 1. It firms up the proposals for Genomics England, which plans to sequence 100,000 genomes — 40,000 from patients suffering from cancer and other rare diseases; 35,000 from their relatives; and 25,000 from the cancer cells themselves. 

The broad outlines of this are not new, and were cogently critiqued by Helen Wallace of GeneWatch UK a couple of months ago, on grounds of effectiveness (dubious) and privacy (very worrying, and addressed even by The Observer). Commercial exploitation is also a concern. The project is a partnership between the government, the Wellcome Trust, and Illumina, which will perform the sequencing. Cameron is pushing it hard:

This agreement will see the UK lead the world in genetic research within years. As our plan becomes a reality, I believe we will be able to transform how devastating diseases are diagnosed and treated in the NHS and across the world.

In the US, there has been a more surprising, though much smaller-scale, development: The embattled direct-to-consumer testing company 23andMe has scored a $1.4 million grant from the National Institutes of Health. It’s pin money to the Googleplex, of course, but some kind of validation. This will help them refine web-based surveys, collect phenotypic data, dip the company’s toes into whole-genome screening, and accomplish the:

Enablement of external non-23andMe researchers to access aggregate de-identified data from the 23andMe database to further accelerate the pace of human genetic research.

Back at the mothership, Google X (the “semi-secret" research arm that works on everything from self-driving cars to Glass) has had another bright idea: They will work out what is normal for humans. The Baseline Study is in its early days but involves "70-to-100 experts from fields including physiology, biochemistry, optics, imaging and molecular biology.” They’ll study 175 (and, later, more) people in great detail (partly using wearable devices, including glucose-monitoring contact lenses), and of course they are being, that is, will be, careful:

Baseline will be monitored by institutional review boards, which oversee all medical research involving humans. Once the full study gets going, boards run by the medical schools at Duke University and Stanford University will control how the information is used.

The genomics research establishment is somewhat skeptical, it seems. Yaniv Erlich of the Whitehead Lab at MIT tweeted:

Breaking: Google moonshot study (that does exactly what has been done in genomics for years) 

Daniel MacArthur, who has been working in the field for a long time, and is currently based at Harvard, the Broad Institute and Massachusetts General Hospital, took an even less charitable view in several tweets, including:

Late to this, but calling this Google study a moonshot just absurdly devalues that term …

I confidently expect Google to be AT LEAST as successful in life sciences as they have been in social media

Ouch. For more nuanced commentary, see George Dvorsky at io9 and Kenrick Vezina at the Genetic Literacy Project, among others.

But Craig Venter is ahead of them all, at least in his own analysis. And he has hired one of Google’s hot shots, Frank Ochs, who basically made Google Translate work. According to MIT Technology Review:

Venter says that he’s sequenced 500 people’s genomes so far, and that volunteers are starting to also undergo a battery of tests measuring their strength, brain size, how much blood their hearts pump, and, says Venter, “just about everything that can be measured about a person, without cutting them open.” This information will be fed into a database that can be used to discover links between genes and these traits, as well as disease.

That’s only the start. The goal is a million human genomes sequenced by the end of the decade. Venter remains absolutely committed to the DNA-programming view of humanity, but appropriately humble about the lack of advances over the last decade or so:

I’ve had my genome for 15 years, and there’s not much I can learn because there are not that many others to compare it to.

That is going to change.

Previously on Biopolitical Times: