DNA As Crystal Ball: Buyer Beware (Newsweek): A genome-wide association study identified a new gene variant associated with Alzheimer’s disease but it turned out clinically it’s not useful.
“Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction” of whether someone will develop Alzheimer’s, she told me. “Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction.”
The United States House of Representatives Committee on Energy and Commerce today launched an investigation into direct-to-consumer (DTC) genetic testing, sending letters to three prominent DTC companies: 23andMe, Pathway Genomics and Navigenics.
The family said they received no medical counseling here and are making their own conclusions. One comment made is that the parents stated they will probably be using more pharmaceuticals, interesting.
I met George Church at this year’s Scifoo event in San Francisco and we talked about how useful the data is that was obtained from whole genome sequencing methods. There are almost 50 people in the world right now whose genomes were sequenced like that but the number of useful genomes is very low (e.g. who made it public) . That’s one reason why the ClinSeq project is really promosing.
ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicine, including the exploration of issues related to the genetic architecture of disease, implementation of genomic technology, informed consent, disclosure of genetic information, and archiving, analyzing, and displaying sequence data.
In the initial phase of ClinSeq, we are enrolling roughly 1,000 participants; the evaluation of each includes obtaining a detailed family and medical history as well as a clinical evaluation. The participants are being consented broadly for research on many traits and for whole-genome sequencing. Initially, Sanger-based sequencing of 300-400 genes thought to be relevant to atherosclerosis is being performed, with the resulting data analyzed for rare, high-penetrance variants associated with specific clinical traits.
He also mentioned the 1000$ genome project and the unofficial estimation is that now it’s possible to sequence a person’s genome for under 5000$ and the 1000$ aim can become a reality at the end of this year.
Gene Genie is the blog carnival of clinical genetics and personalized medicine. I’ve received more than 25 submissions for this edition which is dedicated to the human genome and videos in clinical genetics.
Using genetic information to disparage opponents has no placein presidential campaigns. Nonetheless, the threat of geneticMcCarthyism provides us with an opportunity to engage in a publicdialogue about the limitations and complexities of using genomicinformation for decisions about life and health — includingvoting for our president.
“DNA is not an issue in this campaign, but in the next campaign it will be bigger,” says George Annas, a leading authority on bioethics and human rights at Boston University. “It’s coming.”
If you want to host an issue of Gene Genie in 2009, let me know (berci.mesko [at] gmail.com). Don’t forget to submit your articles (berci.mesko [at] gmail.com).
I’ve got a huge backlog now, but will try to keep sharing interesting genetic articles and posts with you regularly. So here is this week’s collection:
One of the main issues in the blogosphere is the 1000$ genome, the aim is to let everyone access their genomic data for 1000$. We thought we could reach that goal in the next couple of years, but according to Blaine Bettinger’s post, it might be done by the end of 2009.
The Genomic Revolution and the Future of Medicine and Health: A nice lecture about an essential subject
Do you have any idea how much your genome will cost? Mailund on the Internet has a great post with graphs.
Do you remember the post Steve Murphy wrote and my thoughts on how Brin helped promoting his wife’s genetic service? Sergey Brin just misanalysed his genomic data. Now Sandra Porter tells us more about the molecular details.
The world of personalized medicine must be much more than a crystal ball. Here are some new articles about the steps that have to be made and some aspects that might help us :
Young person goes to 23andME/Navigenics/ETC (They just may add this immediately)….gets predictive testing indicating that he is at a 300 fold increased risk of herniating a disc in his back. Avoids manual labor (plays video games all day) never herniates the disc. Did we do society a service? Some would argue yes….I say no.
Very soon, the cost for routine whole human genome sequencing will become cheaper, and some day will be offered during routine clinical testing along with the CBC, blood count and chemistry panel. Also, we will very soon have a greater understanding of gene variation and disease risk, which will hopefully allow intelligent and useful interpretation of the routine clinical sequencing of the entire human genome. As of May 2008, we are not quite there yet.
Of the specific proposals, one team suggested a prize for a major milestone in dealing with the problem of TB, which remains endemic in 22 nations and costs 1.7 million lives every year. Effective treatments exist, but the testing is relatively expensive and often misses active cases. So they proposed a $10 million prize for a new cheap, fast and accurate diagnostic system that could reach most of the 50 percent of cases that now go undiagnosed. Winning the prize would require not just laboratory demonstrations but field tests on 1,000 patients to show that it really works under difficult conditions.
The second proposal was for a simple, portable system that could be used by community health workers to carry out initial diagnostic evaluations for the 10 most widespread fatal, transmissible diseases. Such screening could lead to prescriptions of drugs or treatment for some conditions or referral to a doctor or nurse for conditions that require skilled care or more difficult diagnosis.
What do you think? An X Prize for Health and Medicine would be a good idea? Which medical specialty would be your choice?
Please don’t forget to contribute to the database of real clinical examples I’m currently working on. Anyway, I should create something like an RSS feed for all the interesting news and announcement I usually find in the field of individualized medicine. But now I’m going to try to share some of them with you:
What makes the sequencing of Watson’s genome different from that of Venter’s? It’s the technology. Watson’s genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn’t a $1000 genome, but it’s a step in that direction.
The current study involves a much larger sample number of 120,000, which will allow researchers to gain a better understanding of 25 diseases through examining single nucleotide polymorphisms (SNPs) and a comprehensive number of copy number variants (CNVs).
I’ve written at least a hundred times about personalized medicine so it’s the perfect time to come up with a short description of what individualized medicine is about. In this new world of medicine, you get a treatment that is not only based on the epidemiological data of your population, but your own genetic background. But let’s start with a more appropriate definition:
Personalized medicine is use of information and data from a patient’s genotype, level of gene expression and/or other clinical information to stratify disease, select a medication, provide a therapy, or initiate a preventative measure that is particularly suited to that patient at the time of administration. Personalized medicine makes it possible to give: “the appropriate drug, at the appropriate dose, to the appropriate patient, at the appropriate time”. The benefits of this approach are in its accuracy, efficacy, safety and speed.
…turning genetic variations associated with population-level risks of disease into medically advice useful for a single person sitting in an exam room.
We can also watch it on video:
Who are the key players?
23andMe: Single Nucleotide Polymorphism and genealogy analysis for 1000$. Check out my review or the demo account I created.
Knome: Whole-genome sequencing for 350,000$. Check out my review.
Helix Health: A New York company founded by our gene sherpa, Steve Murphy, who answered my questions some months ago. Helix Health focuses on the family history of the patient and their genetic background as well. Genetic counselors discuss the disease-specific risks with the patients.
DecodeMe: It analyzes over one million variants in our genomes; calculates genetic risk for 23 diseases and finds our ancestors for $985.
Who and what do stand behind the whole concept?
Archon X PRIZE for Genomics: The $10 million X PRIZE for Genomics prize purse will be awarded to the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.
As personalized genetics is still rising, users start to write more and more posts about these genetic services. And this user aspect should and will play a major role in the future of genomic medicine.
Do not trust any genetic testing company that does not make it clear what genetic variants they are analyzing. Never let anyone take your DNA unless they are clear about what they plan to do with it, what information they will give you from the analysis, and what they’ll do with the DNA after all the testing is complete. You are the consumer. You have the right to choose and the right to say no.
Steve Murphy asks an interesting questions. So what if we have a 1000 USD genome? What would we have? I guess only one thing would change: we would have our genomes on a USB drive. That’s all. The medical aspect couldn’t change in such a short period of time. We still need years of research to be able to use properly that amount of genomic data.
While writing your answer in the comment section, listen to a presentation about Decision Making in the Genomic Era:
When I started to share the most recent news and improvements of personalized genetics or genomic medicine, it wasn’t an easy job to find 4-5 articles a week. Now, my bookmark is totally full and I have to write posts focusing on different aspects of this special field of medicine. This time, while a whole genome sequencing costs less than 60,000$, genomic research should be in the focus:
Consumers also lack confidence and knowledge about genetic testing. They are generally concerned with privacy and the possibility of discrimination in health insurance and employment. However, consumers were interested in the genomic technology that can lead to better diagnosis and care for certain diseases – the ones for which they and their family members are at increased risk.
These genomic companies have taken a huge financial and clinical risk in bringing these tests to the market. The tests are in their infancy and each of these companies are transparent in advising their customers of this fact. That said, massive scientific research continues to take place to build on the knowledge base of these tests, so that they may be refined. This process will never end.
After gathering extensive experimental information on the metabolic networks of three different single-celled organisms, the researchers built a general quantitative model that can be used to control and restore biological function to cells impaired by a genetic defect or by other factors that compromise gene activity. Their network-based method does this by targeted deletion of genes, forcing the cell to either bypass the functions affected by the defective gene or to compensate for the lost function.
