Predictive Genomic Risks Are Too Divergent

“Companies that offer analyses of future health risks based on basic genetic tests should be more transparent about the limitations of their predictions” Craig Venter.

In the recent New Scientist, Venter and four colleagues have proposed guidelines for the industry after assessing the results of scans of their own personal genomes as provided by the Californian firms 23andMe and Navigenics.. They found the companies recorded the genetic markers consistently at least 99.7 per cent of the time, but diverged on their assessment of the associated health risks. That’s similar to New Scientist’s comparison earlier this year of the results of scans from 23andMe and a third company, , Decode Genetics of Reykjavik, Iceland. In this case the genetic markers were consistently recorded 99.996 per cent of the time.

International Business Machines Goes Personal Genome

“One of the oldest names in computing is joining the race to sequence the genome for $1,000. On Tuesday, I.B.M. plans to give technical details of its effort to reach and surpass that goal, ultimately bringing the cost to as low as $100, making a personal genome cheaper than a ticket to a Broadway play. The project places IBM. squarely in the middle of an international race to drive down the cost of gene sequencing to help move toward an era of personalized medicine. The hope is that tailored genomic medicine would offer significant improvements in diagnosis and treatment.”

via NYTimes

The Edge Synthetic Biology MasterClass

George and Craig

I am currently watching and listening to “A Short Course on Synthetic Genetics”. Being as it is all the rage now to be masterclassed by the super elite in science and technology, (see The Singularity University at NASA AMES post) The Edge recently ran a SynBio masterclass in Hollywood. Presented in July this year by Craig Venter (Founder of Synthetic Genomics, Inc. and President of the J. Craig Venter Institute and the J. Craig Venter Science Foundation) and George Church( Professor of Genetics at Harvard Medical School and Director, Center for Computational Genetics, and Science Advisor to 23 and Me) it was organized by John Brockman who publishes the website forum www.edge.org dedicated to scientists & technologists and their ideas.

This masterclass consisting of six hours of lectures discussed synthetic biology and “how the world will be changed by the ability to routinely read genetic sequences into computing systems and then store, replicate, alter and insert them back into living cells.” Topics included “What is life, origins of life, in vitro synthetic life, mirror-life, metabolic engineering for hydrocarbons & pharmaceuticals, computational tools, electronic-biological interfaces, nanotech-molecular-manufacturing, biosensors, accelerated lab evolution, engineered personal stem cells, multi-virus-resistant cells, humanized-mice, bringing back extinct species, safety/security policy.

Those present to listen and absorb all they could about the emerging potential of the synbio age were there by invite and included many members of America’s technological/intellectual/cultural/scientific/economical elite, including:

Stewart Brand, Biologist, Long Now Foundation; Whole Earth Discipline
Larry Brilliant, M.D. Epidemiologist, Skoll Urgent Threats Fund
John Brockman, Publisher & Editor, Edge
Max Brockman, Literary Agent, Brockman, Inc.; What’s Next: Dispatches on the Future of Science
Jason Calacanis, Internet Entrepreneur, Mahalo
George Dyson, Science Historian; Darwin Among the Machines
Jesse Dylan, Film-Maker, Form.tv, FreeForm.tv
Arie Emanuel, William Morris Endeavor Entertainment
Sam Harris, Neuroscientist, UCLA; The End of Faith
W. Daniel Hillis, Computer Scientist, Applied Minds; Pattern On The Stone
Thomas Kalil, Deputy Director for Policy for the White House Office of Science and Technology Policy
Salar Kamangar, Vice President, Product Management, Google
Lawrence Krauss, Physicist, Origins Initiative, ASU; Hiding In The Mirror
John Markoff, Journalist, The New York Times; What The Dormouse Said
Katinka Matson, Cofounder, Edge; Artist, katinkamatson.com
Elon Musk, Physicist, SpaceX, Tesla Motors
Nathan Myhrvold, Physicist, CEO, Intellectual Ventures, LLC, The Road Ahead
Tim O’Reilly, Founder, O’Reilly Media, O’Reilly Radar
Larry Page, CoFounder, Google
Lucy Page Southworth, Biomedical Informatics Researcher, Stanford
Sean Parker, The Founders Fund; CoFounder Napster & Facebook
Ryan Phelan, Founder, DNA Direct
Nick Pritzker, Hyatt Development Corporation
Ed Regis, Writer; What Is Life
Terrence Sejnowski, Computational Neurobiologist, Salk; The Computational Brain
Maria Spiropulu, Physicist, Cern & Caltech
Victoria Stodden, Computational Legal Scholar, Yale Law School
Nassim Taleb, Essayist & Risk Engineer, The Black Swan
Richard Thaler, Behavioral Economist, U. Chicago; Nudge
Craig Venter, Genomics Researcher; CEO, Synthetic Genomics, A Life Decoded
Nathan Wolfe, Biologist, Global Virus Forecasting Initiative
Alexandra Zukerman, Edge

Predictive Genome Scientist Face Off

Mapping the Epigenome

Mapping the Human ‘Diseasome’

Lewis Wolpert
“I have entered into this wager with Rupert Sheldrake because of my interest in the details of how embryos develop, and how our understanding of this process will progress. In my latest book, How We Live and Why We Die, I suggest that it will one day be possible to predict from an embryo’s genome how it will develop, and I believe it is possible for this to happen in the next 20 years.”

Rupert Sheldrake
“Lewis Wolpert’s faith in the predictive power of the genome is misplaced. Genes enable organisms to make proteins, but do not contain programs or blueprints, or explain the development of embryos.”

Lewis Wolpert (developmental biologist) & Rupert Sheldrake (parapsycholgist) have set themselvesa a face-off challenge via the RS  that “By 1 May 2029, given the genome of a fertilised egg of an animal or plant, we will be able to predict in at least one case all the details of the organism that develops from it, including any abnormalities.”

——

The Diagrams: (top) This radial diagram produced by The New York Times and Martin Krzywinski, the developer of Circos, represents the number of small molecules, called methyl groups, attached to segments of chromosome 22 across seven different types of human tissue. Methyl groups are one part of the epigenome, which controls how genes are expressed in different types of cells. (bottom) Dr. Butte, an assistant professor of medicine at Stanford, is trying to redefine how diseases are classified by looking not at their symptoms or physiological measurements, but at their genetic underpinnings. This map links different diseases, represented by circles, to the genes they have in common, represented by squares. Each circle represents a disease or disorder and is scaled in proportion to the number of genes associated with that disease.

Crowdsourcing/Opensource genomics

This past September, Silicon Valley startup 23andMe took another step in its self-described mission of “democratizing personal genetics” when it slashed the price of its gene-scanning service from $999 to $399. Increasing its user base is part of the company’s goal of becoming a robust platform for web-based genetic research. And by starting to collect, compile, and compare phenotypic and environmental data from these users, 23andMe is catalyzing DNA’s move from labs to Facebook tabs.

23andMe.com has the feel of a social-networking website, but its users are sharing genetic information rather than photographs. For $399, you don’t get a full genome scan, but rather a look at 580,000 different single nucleotide polymorphisms (SNPs): the genetic variants most often tied to distinctive personal traits. Users can elect to share this information with family and friends via their site-based profiles. 23andMe’s competitors, deCODEme and Navigenics, have different price structures and focus on different selections of SNPs, but the basic premise of their services is the same.

via Seed

Open Personal Genomics versus the sales pitch

To [George] Church, open consent isn’t just a philosophical consideration; it’s also a practical one. If the PGP (Personal Genome Project)were locked down, it would be far less valuable as a data source for research — and the pace of research would accordingly be much slower. By making the information open and available, Church hopes to draw curious scientists to the data to pursue their own questions and reach their own insights. The potential fields of inquiry range from medicine to genealogy, forensics, and general biology.

And the openness doesn’t serve just researchers alone. PGP members will be seen as not only subjects, but as participants. So, for instance, if a researcher uses a volunteer’s information to establish a link between some genetic sequence and a risk of disease, the volunteer would have that information communicated to them.

This is precisely what makes the PGP controversial in genetics circles. Though Church talks about it as the logical successor to the Human Genome Project, other geneticists see it as a risky proposition, not for its privacy policy but for its presumption that the emerging science of genomics already has implications for individual cases. The National Human Genome Research Institute, for example, has cautioned that the burgeoning personal-genomics industry, which includes research-oriented projects like the PGP as well as straight-to-consumer companies like Navigenics and 23andMe and whole-genome-sequencing shops like Knome, puts the sales pitch ahead of the science. “A lot of people would like to rapidly capitalize on this science,” says Gregory Feero, a senior adviser at the NHGRI. “But for an individual venturing into this now, it’s a risk to start making any judgments or decisions based on current knowledge. At some point, we’ll cross over into a time when that’s more sensible.”