Personalized Genomics News: From Virtuality to the Streets June 8, 2010
Posted by Dr. Bertalan Meskó in 1000$ Genome, 23andMe, DNA, e-patient, Genetic screening, Genetic testing, genetics, Genome, Medicine, Personalized medicine, Video.add a comment
- 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.”
- Breaking: Congress to Investigate DTC Genetic Testing (Genomics Law Report): A really detailed and interesting review.
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.
- Technology to Print Ingredients Onto Pharma Tablets (Medgadget): Printing of pharmaceutical ingredients directly onto tablets is becoming a reality.
- 23andme: A detailed review of the data the blogger just received from 23andMe.
- Family Spends $200,000 To Have Their Entire Genome Mapped (The Medical Quack)
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.
A patient analyzes her own 23andMe data:
- Sequencing your genome just got cheaper (Genetic Future): The $1000 era is coming fast…
Pathway Genomics: Let’s see my genes March 19, 2010
Posted by Dr. Bertalan Meskó in Genetic screening, Genetic testing, genetics, Genome, Health, Health 2.0, Medicine, Medicine 2.0, Personalized medicine, Web 2.0.6 comments
As I’m doing PhD in clinical genomics and I’m really interested in the connection between internet and medicine, so I was very happy when Pathway Genomics, one of the newest direct-to-consumer genetic companies, offered me a free genetic test. After an interview I did with them, I sent my saliva sample back and 3-4 weeks later, I received an e-mail that my results were ready. This is just an entry about my experience and the things I found interesting. As I got a free test from Navigenics a year ago, I plan to compare these services in a future entry.
The reason why I was very interested in the service of Pathway Genomics is what they analyze:
1) Sampling: It was quite an easy process with only a few papers to fill (though it’s always hard to solve FedEX issues from Europe) and clear instructions. A video about a patient showing the whole process in 1-2 minutes including salive collection and filling papers would be useful.
2) Preparations: I liked that I had to fill a questionnaire focusing on my lifestyle and patient history (Your Environment and Lifestyle, The Shape You’re In and You and Your Family). As family history is the best genetic test out there, it’s important to use that data while analyzing genetic results. Though, I couldn’t calculate my BMI (couldn’t use kg and centimeter) and the Family history app has never been working for me.
3) Results: I still think that predicting risk of diseases based on a few SNPs cannot be accurate enough and we cannot base a medical decision on that. But drug responses and carrier status are totally different. For example, now I know I’m not a carrier for any of the disease they analyze, and I’m a slow metabolizer of caffeine (I never drink coffee as it has quite a negative effect on my work maybe due to this slow rate of metabolization).
4) Health conditions: Based on your genetic profile, it creates different groups for conditions such as Immediate Action, Take action, Be proactive, Learn More and Live a healthy lifestyle. It’s also shown whether the risk is based on validated or preliminary study results. It seems to me it creates a score for diseases based on SNPs and elevates the score by the number of questionnaire answers that proved to be risk factors. That’s where a genetic counselor is very important. For example, just because I’m 25 years old and Caucasian, I’m in the risk group for ulcerative colitis. I would love to see the combined risk (genetic + lifestyle) and would love to download the raw data in order to analyze it again with Prometheus and SNPedia.
Also I’m not sure whether an SNP with 1.07 odds ratio can really elevate my risk for anything.
Anyway, it’s easy to navigate among the results and I like that there is no percentage of risk which makes it easier to understand for laypeople. I plan to contact one of their genetic counselors next week.
5) Ancestry: I’m in the same maternal haplogroup as Benjamin Franklin or Marie Antoinette (see migration map below on which we can adjust the migration pattern with the timline). The descriptions are detailed and full of references information. I particularly liked the numerous Pubmed links. My paternal haplogroups is quite interesting and is the same as Thomas Jefferson’s.
My friend, Blaine Bettinger also commented on this test.
6) To sum it up: I liked the service mostly because of the carrier status and drug responses features. It helped me analyze the results, find more information in peer-reviewed journals and maybe make lifestyle decisions.
Pros:
- The 100% Moneyback Guarantee is still fantastic.
- It analyzes not only disease risks but carrier status and drug responses.
- No percentage of health risks, but a clear score system.
Cons:
- Charging for the genetic counseling is not a good idea ($40 for a call up to twenty minutes, or a full hour for $99). It costs almost as much as the service itself. (Update: It turns out it was an old page and genetic counseling actually is for free)
- The blog and Twitter account are not too active. There is no significant social media activity which would be crucial.
- Obviously USA-focused
- Raw data is not available for download.
In the next entry, I will compare my experiences with Navigenics and Pathway Genomics.
Whole-Genome Sequencing: Any Useful Data? July 26, 2009
Posted by Dr. Bertalan Meskó in 1000$ Genome, Genetic screening, Genome, Personalized medicine, Scifoo.3 comments
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.
Genetic Counselors: Unite! May 28, 2009
Posted by Dr. Bertalan Meskó in Blogging, Genetic screening, genetics, Web 2.0.3 comments
I’ve come across a new site, The DNA Exchange, that seems to be a really promising project.
We are a group of genetic counselors with an interest in public discussion of genetics-related issues. This is a place for GCs to express opinions and comment on personal, clinical, and professional issues in genetics through a centralized and public forum. We hope to engage the genetic counseling community as well as other health professionals and stakeholders. We encourage your feedback, and always appreciate a good debate!
And if we are talking about genetic counselors, here is another article from Scientificblogging.com.
AccessDNA: Know Your Genetics January 10, 2009
Posted by Dr. Bertalan Meskó in DNA, Genetic screening, Genetic testing, genetics, Genome, Web 2.0.Tags: Genetic testing, genetics, Genome
13 comments
I’ve recently discovered AccessDNA on Twitter and I thought I should give it a try. On the main page, it says I should create my personalized report. Well, let’s do so.
It asked me about the medical conditions that occurred in my family; environmental factors I have to face; tests I would be interested in, etc. And then I received the personalized genetic report; actually a list of genetic tests that might be useful for me.
What can I do with that information? Yes, of course I want full genome scanning. But should this be my decision? Not the decision of my doctor? Just beacuse I reported to be of Caucasian descent, I should order genetic tests that cost several thousands of dollars?
You know what? I would love to hear the opinion of Steve Murphy here. And yours!
Personalized Genetics: Are we ready? April 18, 2008
Posted by Dr. Bertalan Meskó in Genetic screening, Genetic testing, genetics, Genome, Health, Medical education, Medicine, Personalized medicine, Policy and Law, science.6 comments
As me and others have already stated for several times before, we are not. It was so good to read the opinion of Joel Burrill as I felt like we’re on the right way. Some excerpts from the interview made by Wired:
Currently there are some major barriers that need attention before companies like 23andMe will be incredibly successful. An incredibly steep barrier that needs immediate attention is the education of doctors. For doctors to actually use this type of information they need to understand the concepts and the principles that are at the heart of this type of technology, but currently the amount of education they receive in medical school is slim to none.
As for the nature of predictive medicine and companies that will offer predictive tests, I think it is a good idea, but there is going to be a gap between the patient and the doctor if these companies are marketed directly to the patient. If they are marketed to the patient, then the doctor will 1) have no knowledge of the outcome of the test, 2) have no basis to make any decisions off of other than the word of the patient and 3) no medical basis for prescribing medication.
In Hungary, medical education consists of 6 years and we have to study genetics for only 6 months (!). While the majority of the medical conditions we learn about have genetic basis, they try to introduce us to the world of genetics and genomics in just 6 months… How is the genetic education at your university or your clinic?
One of the best genetic bloggers out there these days is probably Daniel Macarthur at Genetic Future, who always comes up with some interesting posts and raises some important points:
However, the Navigenics model is also deeply regressive:… Where 23andMe talks about guiding customers through their own journey of genetic discovery, Navigenics appears to be more about giving clients the information that Navigenics thinks is medically relevant, and protecting them from all the non-essential details that might overwhelm or confuse them.
Los Angeles Times published this fascinating article, Genome scans go deep into your DNA:
Some researchers say it’s unclear whether people will understand the genetic risk data and what they will do with it. Is this just a bit of harmless fun? Will it improve long-term health outcomes? Or will hypochondriacal patients march to their doctors and demand truckloads of unnecessary tests, harming themselves and the healthcare bottom line — while others incorrectly see their results as destiny and adopt worse lifestyle habits?
At last, but not least, have you recognized that the genome of Watson was sequenced at high speed? As a commenter expressed, I guess this DNA sequencing paper would be rejected right away by Nature if it is not on DNA of James Watson. However, in today’s science, it is not the KNOWLEDGE but the SUBJECT that matters most in weighing the “significance” of a manuscript for publication.
So some major points for today:
- education of medical professionals about personalized genetics should get a much bigger attention
- closing the gap between patients and doctors in the aspect of analyzing genetic data is becoming important
- have to be cautious with these new genetic companies and we should avoid “overhyping” their importance
- papers should focus on the scientific value of the articles as selling the papers should not be the #1 objective for them
Stay tuned for more about individualized genetics.
What you have to know about personalized genetics March 31, 2008
Posted by Dr. Bertalan Meskó in 1000$ Genome, 23andMe, DNA, Genetic screening, Genetic testing, genetics, Genome, Health, Innovation, Knome, Medicine, Personalized medicine, Policy and Law, science.16 comments
Genes load the gun. Lifestyle pulls the trigger.
By Dr. Elliot Joslin
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.
All right, here is an even shorter one.
…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.
Navigenics: Will launch the service in days. My review is here.
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 $10,000 per genome.
The aim is the 1000$ genome.
Craig Venter’s genome that was published in September, 2007.
Who and what should you follow to know everything about personalized medicine?
Personalized Genetics: Back in Business March 5, 2008
Posted by Dr. Bertalan Meskó in Genetic screening, genetics, Genome, Personalized medicine.add a comment
It’s been a long time I haven’t written about the hypest field of medicine. So from now, I’ll get back to posting 2-4 times a week about individualized medicine. If you know nothing about it, check out my page dedicated to the subject.
- Let’s start with a perfect introduction to personalized medicine presented by John D. Halamka at Life as a Healthcare CIO.
- How Smartdust, Souveillance, Web 3.0, and Personalized Genetics Will Transform the Future of Medical Diagnostics (Docinthemachine)
Similarly, such technology will lead to individual genetic screening for disease risk using chipe that interact with the tiny bits f DNA we shed every time we touch something. Companies commercializing this approach also already exist and have products.
While reading these two blogposts, listen to the presentation of Kathy Giacomini (University of California): How Drugs May Be Tailored to Your Genetic Makeup
- UK controversy over 23AndMe (Genetic Future): The Human Genetics Commission (and the Gene Sherpa) have already condemned 23andMe as a dangerous waste of money and called for regulations to control their marketing.
- GEN2PHEN web based project to capture health & disease genetic knowledge (Genetics and Health)
- Don’t forget to check out the online tutorials and on-site training of OpenHelix. They focus on genetics and some tools devoted to genomics.
Global Awakening in Genetic Counseling February 23, 2008
Posted by Dr. Bertalan Meskó in Education, Genetic screening, genetics, Health.1 comment so far
I’ve recently come across this article at Nature Precedings written by Janice Edwards, Jacquie Greenberg and Margaret Sahhar. Check out these excerpts:
According to the National Society of Genetic Counselors in the USA “ To offer an optimum genetic service in a country it has been estimated that approximately 2 genetic counsellors per 1 million of the population would be the minimum number required.” Yet, the number of trained genetic counselors is estimated at less than 3000 worldwide.
Wow, we would need even more! Genetic counselors should play an important role in those genetic companies.
As global awakening in genetics continues, the Transnational Alliance for Genetic Counseling will promote transnational collaborations in genetic counselor education and research, stimulating international understanding of the role of genetics on human lives.
I wish I could promote more efficiently projects like this one.
Here is an other great example from Scientificblogging.com. The Clinical Genetics column is maintained by Prof. Camillo Di Cicco (University of Rome/Medicine) and you can find dozens of well-structured and valuable articles about genetic conditions there. I’ll definitely follow the RSS of his page.
And we shouldn’t forget about some open notebook projects. Stew at Flags and Lollipops asked a question:
Is there a super-semantic-web-enabled phenotype database out there*? I want to ask a question like ‘give a list of monogenic disorders whose locus has been confirmed by at least two labs, broken down by type of causative mutation type’ and get an answer.
So, I really believe we’re moving forward. Let me know please if you happen to know more similar methods to promote genetic conditions and the science of genetics.
Newborn Screening for “Bubble Boy Disease”: Interview January 8, 2008
Posted by Dr. Bertalan Meskó in Genetic condition, Genetic screening, Health, Healthcare, Hospital, Invention, Medicine, Newborn screening.7 comments
On the 1st of January, the state of Wisconsin made a major step in the field of newborn screening. The collaboration of Wisconsin State Laboratory of Hygiene, Children’s Hospital of Wisconsin and the Jeffrey Modell Foundation resulted in screening newborns for Severe Combined Immune Deficiency (SCID). According to the Wikipedia article this is:
…a genetic disorder in which both B and T cells of the adaptive immune system are crippled, due to a defect in one of several possible genes. SCID is a severe form of heritable immunodeficiency. It is also known as the “bubble boy” disease because its victims are extremely vulnerable to infectious diseases.
I’ve already presented The Jeffrey Modell Foundation (headquarters in New York) to you in June. Now, to know more about this medical breakthrough, Dr. Jack Routes from the Children’s Hospital of Wisconsin answered some of my questions:
- How common is the so-called “Bubble Boy Disease” in the US and in your hospital?
There is no good data on the actual incidence of the disease in the US. It is estimated that at least 1:100,000 newborns have SCID. Our newborn screening program will better ascertain the true incidence of SCID in Wisconsin.
- Is a blood sample taken from a newborn enough for the screening process?
All newborn screening tests are performed from blood spotted on a newborn screening card—the newborn gets a heel stick and blood is put on a special filter paper on the newborn screening card. A small punch is taken from the filter paper and the SCID screening test is performed.
- Please tell us some more details of the screening of SCID! How sensitive and predictive is the test?
Please see the article ( J Allergy Clin Immunol. 2005 Feb;115(2):391-8.) for a discussion of the assay. These are the only published data to date. The assay is a real time, quantitative PCR that measures the number of T cell receptor excision circles (TRECs) in the punch from a newborn screening card. TRECs are a surrogate marker for functional, naïve T cells, which will be reduced in most, but not all causes of SCID. Our group has improved the TREC assay (false positive rate is <0.01%) over the results reported in the JACI paper. There is no data on sensitivity and positive predictive value of the test—-this issue will be addressed by the WI SCID screening program.
- Do you plan to add new medical conditions to the newborn screening program?
Wisconsin constantly evaluates other genetic diseases to add for newborn screening. The WI Newborn Screening Umbrella Committee addresses this issue and I am not a member of this committee and do not know if other tests are being considered in the near future.
(Source)
I’m thankful to Dr. John Routes for the answers. This is a great example of how to construct a successful newborn screening program. Just to show you the difference, in Hungary, they screen newborns for only 4 (while they screen for 47 in Wisconsin) genetic conditions (galactosaemia, congenital hypothyreosis, biotinidase deficiency and phenylketonuria)
