Genomes on Facebook? Beyond Sequencing 2011


Author: 
Theral Timpson

Who owns our genomic data? This question began a panel discussion titled “When People Share Their Genome on Facebook” at the second annual Beyond Sequencing conference in San Francisco Tuesday. The panel was led by Bio-IT World’s editor-in-chief, Kevin Davies, author of The $1,000 Genome. Another panelist, Dr. Pilar Ossorio, quickly deflected the question saying “it’s not a matter of ownership.” She posed another question, could a representation of one’s genomic data be copyrighted? According to Dr. Ossorio, associate professor of law and bioethics at the University of Wisconsin School of Law, one thing is certain: when someone posts their genomic data to Facebook or any other public site, that person is giving up their rights to the data--whether they had rights to begin with or not.

A third panelist, Dr. Ken Patel from Sandia National Laboratories, admitted he didn’t know whether Facebook would be the best place to share this kind of data, but that Facebook is tremendous in size and certainly “something to be reckoned with. It’s already there.” Dr. Patel envisions the approaching day when “my doctor will follow my Facebook page and keep in touch with other health professionals on my medical info.” In 2008, Congress passed legislation called GINA (the Genetic Information Non-discrimination Act) to protect, as the name says, against discrimination by insurance companies and employers based on one’s genetic or genomic data. Dr. Jonathan Eisen, a panelist from UC Davis Genome Center, asked “just how much teeth the legislation really has.” What about informed consent for relatives? Say we ponder what it means to put our genomes out there in cyberspace, what about others --our children and parents--who are affected by our genetic data going public? What about international protection? GINA covers US residents at home, but not abroad. Eisen pointed out that Dr. George Church, founder of the Personal Genome Project which seeks to have 100,000 genomes online for public sharing, doesn’t just accept anyone. Those who are selected go through a rigorous briefing and even a class with a geneticist before being selected.

The audience, mostly made up of researchers, was eager to put in their questions. “Why is the medical community so far behind?" The panel did their best with this citing first the cost of genomic sequencing, second that doctors are not trained in genetics, and also the fact that data is so preliminary. Each of the Direct-to Consumer companies who are offering genetic information, vis., 23 and Me, Navigenics, Decode, has different algorithms for calculating risk. The results can be inconsistent from one provider to the next.

A second question from the audience came from a doctor who asked why folks would put up their genomic data online without phenotypic data. So far a lot more is learned from a person’s ancestry, lifestyle habits and past medical history than from the many gigabytes of DNA code. Will it become the norm to share our data on a site like Facebook? Kevin Davies reminded us that 23 and Me is already a sophisticated social networking site that has led to some discoveries. Whether it is their model, or one like Navigenics who works closer with doctors, or a public site like Facebook, time will tell. This discussion posed more questions than answers.

Conference Keynotes

Dr. Michael Snyder, Stanford Center for Genomics and Personalized Medicine

Beyond Sequencing is one of a quartet of conferences on sequencing put on by CHI (Cambridge Healthtech Institute). Others include the Next Generation Summit in August, a conference in September on Applying Next Generation Sequencing and the XGen Congress and Expo in March. Around 400 attended this show June 20-21 at the Hotel Kabuki in San Francisco’s Japantown. Keynote speakers were well known scientific figures from Stanford, Dr. Michael Snyder, Stanford Center for Genomics and Personalized Medicine and Dr. Ron Davis, long time director of the Stanford Genome Center. Dr. Snyder has been tracking his own ‘omics’ profile (including his genome, epigenome, transcriptome, proteome, metabolome, and microbiome) for a year now and keeping a close monitor on his health as a test project. I heard one of Dr. Snyder’s talks earlier this year and he continues to preach the gospel of quality data. In his lab they use various sequencing companies. He showed that the data from each is different. With his own data he compared Illumina’s output with that of Complete Genomics, commenting that Complete Genomics made fewer calls, but that they were more accurate. The first step when looking at one's data is to define all rare variants (only the ones in genes). Snyder then went through his one by one (this is still the only way). An unusual variant that stood out in his data was TERT, an allele associated with one’s telomeres and with anemia. Puzzled by this because he’s not anemic, he checked it out with Sanger sequencing. It was correct.

The next question to ask is whether we are hetero- or homo-zygous for an allele. To answer this, Dr. Snyder sequenced his mother’s genome. He then turned to a Disease Risk Profile developed by his colleague at Stanford, Dr. Atul Butte. Some of this report made sense, some did not. Snyder was surprised to find out that he was at high risk for Type 2 Diabetes. He’s never shown any symptoms. He got tested several times over the past year and found out that his glucose level was indeed high, at times in diabetic range. He offered that he has made some lifestyle changes, such as modifications to his diet and a more committed exercise program. Snyder is now focusing his research on ‘regulators,’ those actors in the cell which work similar to government. There are master regulators which control many processes throughout the body and those which are more local. Snyder compared the function of these two types of regulators to the work of president Obama versus a local school board official who serves part time.

Dr. Ron Davis, Stanford Genome Center

Ron Davis has been the recipient of numerous awards including this year’s Gruber Genetics Prize for 2011. He is a pioneer in the development and application of recombinant-DNA techniques and has seen technologies created in his lab become commercial successes. Dr. Davis shared with us a few of the new projects he’s currently working on at the Stanford Genome Center. He sings a different tune than many in this age of uber-sequencing. Several of the studies and projects he promotes are alternatives to sequencing such as using arrays to go after a targeted sequence. Many are arguing why not just sequence the entire genome because the price has come down so far. Then you can always go back to the data. Ron has several answers. First of all, the clinicians he’s talked to are legally concerned about the idea of going back to a patient and saying, ‘hey, we found out some new stuff about your genome the other day.’ One study he presented compared using exon expression chips as opposed to RNA Seq. Not only were the chips cheaper by about 1/10, but also the work could be done much, much faster. Working on 5,000 samples the sequencing would take 50 years whereas the samples could be processed by the chips in one year.

Perhaps the most promising of Dr. Davis’ projects are ‘Point of Care’ technologies. These will lower cost, provide higher sensitivity and most importantly all be based on electricity. An example of this is a digital antibody assay where the standard assay is used with electronics using a particle rather than fluorescence. He calls it a PLISA (particle) rather than ELISA assay. Sample collection for these technologies would be non invasive, using urine, sweat and/or breath. (One study is a TB breath test for children). In all of these, there is no need for PCR.

Look for an upcoming podcast interview with Dr. Ron Davis from Stanford's Genome Center to hear more about these Point of Care technologies.



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