Crowdsource and crowdfunding are everywhere these days.
Jimmy Lin, a medical student at Johns Hopkins University, and other young scientists created the Rare Genomics Institute, a non-profit that leverages falling DNA sequencing costs and rising online giving to support medical research. Great idea!
In mid-July, the institute announced that it had completed its first crowdfunded gene sequencing and discovered what it believes is the root cause afflicting 4-year-old Bronx resident Maya Nieder. The girl can’t speak, and doctors are unsure whether she can hear. They had likewise failed to determine why she has missed so many developmental milestones. Lin’s team posted Nieder’s story online, and within hours donors had given the $3,500 needed to sequence key slices of the Nieder family’s DNA. (Yale University covered the rest of the costs.) The results, RGI says, point to a flaw in a gene crucial to fetal development.
Moreover, my friend, Lucien Engelen just published the results of his genomic analysis at 23andme. He aims at crowdsourcing potentially underlying genetic consequences of his genome.
What do you think? Was it a good idea? Would you make such information public?
Years ago, I wrote about how 23andMe analyzed someone’s genes for $999 (only a few gene variations were used for predicting disease risks). And now they offer exome sequencing for the same price.
What 23andMe is offering is to make people’s exomes available to them, and the DNA sequencer will go over their DNA 80 times (known as 80-fold coverage) to make sure that the genetic code is accurate. This is stunning because a year ago this would have cost ten times as much or more. 23andMe isn’t the first company to offer consumers exomes — that would be Knome, of Cambridge, Mass. — but still the low price is eye-popping. It’s also a lot more data than the DNA chips 23andMe has used up until now, which capture single-letter changes in genetic code scattered across the genome.
What is an exome? Your exome is the 50 million DNA bases of your genome containing the information necessary to encode all your proteins
While 23andMe brings down the price of consumer genetic tests and builds up relations with big pharma (doesn’t share individual data though), it seems the DTC genetic testing is neither accurate in predictions nor beneficial to individuals according to a study described on Medical News Today.
Working under the supervision of Associate Professor Cecile Janssens, together with researchers from Leiden, The Netherlands, and Boston, USA, Ms Kalf examined the risk predictions supplied by two large DTC companies, deCODEme (Iceland) and 23andMe (USA). They simulated genotype data for 100,000 individuals based on established genotype frequencies and then used the formulas and risk data provided by the companies to obtain predicted risks for eight common multi-factorial diseases – age-related macular degeneration (AMD), atrial fibrillation, celiac disease, Crohn’s disease, heart attack, prostate cancer, and Type 1 and Type 2 diabetes (T2D).
Although the predictive ability of the DTC tests in the study was moderate for all diseases, both companies assigned an increased risk to a substantial part of the group. Yet the risk of disease in this group was often not substantially higher than the risk in the rest of the population studied. For AMD, the disease with the highest predictive ability, both companies assumed that the risk in the population was around 8%. Of all subjects designated as having an increased risk, 16% using the 23andMe risk estimations and 19% using deCODEme’s estimations would develop AMD, compared to the 4% found in the rest of the population studied.
When I had a free test at Navigenics and Pathway Genomics, I had a chance to visit the Navigenics HQ as well in San Francisco. Now Daniel MacArthur visited the 23andMe and Complete Genomics HQs.
I was graciously received by Shirley Wu, who gave me the grand tour, and various members of the 23andMe science team (especially Nick Eriksson and Tom Do) then uncomplainingly put up with my questions for what must have seemed like hours. The visit reinforced my overall impression of the company: this is a group of very smart people working with an increasingly impressive customer data-set on some seriously interesting problems. Their recently announced discovery of two novel genetic regions associated with Parkinson’s disease (due for publication in the near future) is a taste of what’s to come.
Direct-to-consumer genetic testing is becoming more and more apparent even though its clinical validity and utility are pretty questionable regarding medical decisions. Eric Topol and his team now studied over 2000 patients who had genomic tests (Navigenics) and reported if there was any changes in symptoms of anxiety, intake of dietary fat, and exercise behavior. The results are not surprising therefore they raise the question whether these tests can be used for anything at all. The study was published in NEJM.
From a cohort of 3639 enrolled subjects, 2037 completed follow-up. Primary analyses showed no significant differences between baseline and follow-up in anxiety symptoms (P=0.80), dietary fat intake (P=0.89), or exercise behavior (P=0.61). Secondary analyses revealed that test-related distress was positively correlated with the average estimated lifetime risk among all the assessed conditions (β=0.117, P<0.001). However, 90.3% of subjects who completed follow-up had scores indicating no test-related distress. There was no significant increase in the rate of use of screening tests associated with genomewide profiling, most of which are not considered appropriate for screening asymptomatic persons in any case.
In a selected sample of subjects who completed follow-up after undergoing consumer genomewide testing, such testing did not result in any measurable short-term changes in psychological health, diet or exercise behavior, or use of screening tests. Potential effects of this type of genetic testing on the population at large are not known.
(Hat tip: Medgadget)
There are 4 articles focusing on personalized medicine I would like to share with you today.
Personal Genotyping Course Progress Report
At the Stanford School of Medicine’s Scope blog, Lia Steakley recounts student participation in the school’s summer elective course that offered the physicians-in-training the option to study their own genotype data. “Overall, 33 students in the class of 60 … opted for personal genotyping. Ten others analyzed their genetic background using commercial services before the class,” Steakley reports, adding that a Stanford task force will deliberate to determine whether to offer the course again. Our sister publication Genome Technology spoke with Stuart Kim, one of the course organizers, and professors at other medical schools who’ve incorporated genotyping components into classes they offer for its September issue.
Focus on biomedical art
Despite continued doubts about the clinical utility of direct-to-consumer genetic tests, tens of thousands of people have sent away tubes full of their saliva to learn more about their genetic profiles. Armed with such DNA data, a number of early adopters are showing how empowering—and beneficial to science—personal genetic information can be. Elie Dolgin reports on one company’s plans to make medical genetics more participatory.
Next Generation Sequencing viewers reviewed
I gathered up some of the recent free next generation sequence viewers that were capabale of viewing BAM files – and put each through the motions with a few BAM files and reference sequences of various sizes. While there are some great ideas and several choices to be found along the feature spectrum, I think we are still in the dark ages with this stuff. No viewer has really been able to entirely combine usability with performance and analysis capabilities, let alone extensibility and web connectivity.
I would like to share three papers, articles that focus on the personalized genomics market with you. Almost 3 years ago, I wrote about that FDA had suggested two genetic markers to be used to determine the minimal starting dose of Coumadin. Later, in a paper, Rosove et al. said that “The value and cost-effectiveness of genetic testing to reduce bleeding or thrombosis rates remain unknown.”
Well, now it seems there is the answer.
Patients who received a test of two genes connected to warfarin sensitivity were 28 percent less likely to be hospitalized for a bleeding episode or blood clot than those whose safe and effective warfarin dosing was determined by traditional trial and error method.
Also researchers have provided the first published example of genome-scale RNA and DNA sequencing of a tumour to aid in clinical decision making and therapeutic choice.
“Utilizing a complete map of the molecular changes within a tumour in a clinical setting represents a world first in the application of this technology,” says Dr. Steven Jones, associate director of the Genome Sciences Centre and professor, Simon Fraser University. “It ushers in the era of personalized medicine in oncology, whereby therapies will be tailored precisely to the genetic make-up of the tumour. I anticipate that in the not too distant future nearly all patient tumours will be characterized in this way as a matter of course.”
And Health Populi reported a very interesting correlation between DTC ads, genetic pre-disposition, and healthy decisions:
A team of researchers now finds that DTC can play an important, positive role in motivating health consumers to adopt healthy behaviors. “The intention to engage in healthy lifestyles was strengthened by exposure to familial risk cues in DTC ads and this effect was mediated through enhanced efficacy to take healthy actions,” the paper concludes. Familial risk cues engendered positive self-efficacy.
When preparing for this year’s Researchers’ Night (details below), I was trying to collect some information and updates about the consumer genomics market for my presentation and found great slideshows. Enjoy!
If you thought that research was all about lab coats and Bunsen burners, think again. Like everyone else, researchers come from numerous backgrounds, have diverse interests and pursue a spectrum of hopes and dreams.
One thing they all have in common is a passion for research – and they want to share it with you. The European Commission’s ‘Researchers in Europe’ (RIE) initiative allows citizens to get closer to our researchers and gives a face to European research.
Mary Carmichael at Newsweek had a great series of articles focusing on direct-to-consumer genetic testing. An excerpt:
I’ve been following DTC genetics since 2007, when wide scanning first became available to the public. Since then, a number of writers have gotten wide-scale genetic tests and expounded on the results. Indeed, I sometimes wonder if I’m the last science reporter on earth with virgin genes. (Technical virgin: My doctor gave me a cystic fibrosis carrier test when I was pregnant.) Initially, I put off getting a full-genome scan because I wasn’t sure how useful such a test would be. I had no particular reason to take one, save curiosity. I wouldn’t expect to find anything serious and potentially life-altering like the Huntington’s disease gene in my results, because my family medical history is thankfully rather boring. The data most likely to be medically relevant to me would concern the genetics of common diseases, and at the time, many comprehensive and well-designed studies of those were still getting underway. I decided to wait a few years and see how research progressed. But here I am, three years later, still unsure.