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Genetic Pioneers GET a Taste of the Science's Imaginative Future


By Aaron Krol 

May 5, 2014 | While the Bio-IT World Conference and Expo convened last week in downtown Boston*, drawing thousands of attendees to discuss cutting-edge developments in the computational life sciences, a more intimate event was taking place just a few miles away in Cambridge. The fifth annual GET (Genomes Environments Traits) Conference, which took place on Wednesday, April 30, has many of the same interests as Bio-IT World – genome interpretation, interconnected health networks, melding together diverse streams of data. But the GET attendees’ focus tends to slide a few years further into the future. 

The GET Conference first met in 2010 as an offshoot of the Personal Genome Project (PGP), and was intended to bring together the select handful of people whose whole genomes had been sequenced as part of the PGP or other initiatives. As George Church, the PGP’s founder and first fully-sequenced member, observed in the opening address of this year’s GET Conference, the 2010 event was likely the last time in history it would be feasible to gather every genetically characterized person in the world in one room. (The event fell short by a few individuals unaffiliated with the PGP.)

GET remains largely the province of the owners of whole genome or exome sequences, and the event is geared to their interests. The conference is preceded by GET Labs, a gathering where PGP participants offer data and samples to various research groups; this year’s cohort donated swabs of armpit microbes, facial mites, and detailed limb characterizations. The conference itself also provides opportunities to share and explore personal genetic data. Nathan Pearson of Ingenuity presented the Empowered Genome Community, an online portal where PGP members, participants in Illumina’s Understand Your Genome program, and others can upload and share their sequences and make use of the Ingenuity Variant Analysis software at no cost. In an address from a key sponsor, Google’s Jonathan Bingham talked up the newly-formed Google Genomics, which houses a copy of each PGP genome in the cloud and is building an API in which analytics can be run on genetic datasets.

While speakers like Diana Bianchi, a renowned prenatal diagnostics expert at Tufts Medical Center, and Robert Green, an investigator of the psychological effects of genetic testing at Brigham and Women’s, addressed a few fields where advances in genetics are making a real impact today, the GET Conference did not neglect the highly speculative and ambitious ideas that draw the “genetic pioneers” in attendance to projects like the PGP. This is, after all, an event in the orbit of George Church, whose work in areas like nanopore sequencing and CRISPR gene editing once seemed fanciful before rapidly spawning frenzies of discovery, and whose lab is now inserting woolly mammoth-like genes into elephant cells. Church himself presented on a potential new sequencing method – the third he has had a hand in, after sequencing-by-synthesis and nanopores – that involves digital imaging of RNA molecules, a technique his lab has validated on a 9-kilobase RNA sequence.

It was in this spirit that Randy Buckner of Harvard’s Cognitive Neuroscience Laboratory, who has voluntarily undergone hundreds of brain scans through MRI and other methods and introduced himself as “the world’s best characterized head,” described efforts to build a “brain connectome” showing the degree and directions of connectivity between areas of the brain. Among other absorbing images, Buckner showed a slide of brain tissue from a transgenic mouse engineered such that different neuron cell lines express different fluorescent proteins. Through projects like this, he said, researchers today “can track, in exquisite detail, the connections between different neurons,” a level of detail that he believes is now becoming fine enough to correlate features of the connectome with genetic variants.

Ting Wu, also of Harvard, presented an unproven, but undeniably compelling, theory about certain genetic elements she labels “ultra-conserved elements” (UCEs). UCEs are sequences that have undergone almost no change for hundreds of millions of years, in some cases since the common ancestor of all amniotes. Based on evidence that UCEs cluster near chromosomal regions that do not undergo rearrangements, Wu suggests that UCEs in fact trigger cell death if they detect that the maternal and paternal chromosomes no longer align in these areas, a state that is tested periodically during temporary chromosome pairings. “The idea is that these UCEs somehow can detect a mistake, a rearrangement of the genome that is deleterious, and get rid of the cell that carries that rearrangement,” said Wu. While she admits the theory is speculative, she is already envisioning applications of UCE therapy that can correct or protect against new mutations. For an encore, Wu proposed that this UCE therapy will be particularly useful to protect against radiation during space travel.

Genetics is not the only big data interest of GET participants. Perhaps the most ambitious project proposal at the conference came from Esther Dyson, a 23andMe board member and the founder of the Health Initiative Coordinating Council. Dyson’s organization is launching The Way to Wellville, a program that plans to enroll five enclosed communities across the United States in a longitudinal health study with massive license to alter health incentives. In Dyson’s vision, volunteer communities will compete with each other to realize the greatest population-wide shifts in five basic health metrics, enforcing changes in advertising practices for unhealthy food, store layouts, public health amenities, and anything else they can think of to move the needle on behavior. Along the way, copious data will be collected, and Dyson even hopes to promote the effort with a reality TV show.

The GET attendees are a gregarious group, sharing ideas and their personal histories of data tracking in between presentations, and not afraid to volunteer sensitive information like dire disease risk variants during Q&A sessions. Though the conference is not restricted to PGP members, they still make up the bulk of the audience – and while the crowd is generous with its data, they also expect big results. This annual get-together is a rare opportunity to see some of the open genetic data community’s wildest dreams collected on one stage.

 

 

  

* For more on the Bio-IT World Conference, see our Notes from the Expo Floor, and our coverage of the Best Practices Awards and Best of Show Awards.

 


 

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