The Case for Personalized Medicine: Interview with Edward Abrahams of PMC November 25, 2011
Posted by Dr. Bertalan Meskó in Genome, Interview, Personalized medicine.1 comment so far
The third edition of The Case for Personalized Medicine (PDF) was released a week ago and I had a chance to do an interview with Edward Abrahams, Ph.D. of the Personalized Medicine Coalition. The new edition is a primer that highlights the progress in the field of personalized medicine for policymakers, researchers, and business leaders.
- How many prominent examples of personalized medicine might we have next year?
It’s impossible for us to know how many prominent examples of personalized medicine products will be available a year from now, but we project that the rapid acceleration in the number of new products coming onto the market will continue. When we published the first edition of The Case for Personalized Medicine in 2006 – there were only 13 available products; when we published the second edition in 2009, there were 37 products available, and now, in 2011, there are 72.
- Sometimes lecturers use two numbers: 7 billion and 3 billion referring to the mass sequencing of everyone’s DNA in the world. When could it happen, what is your estimation?
We understand there to be 3 billion SNPs.
- It seems now from gene expression profiling we are moving towards RNA sequencing and next generation sequencing. What do you think is the next trend in research?
Both research and clinical care will benefit as the cost of whole genome sequencing declines at a rate dramatically more quickly than Moore’s Law would predict inching towards the $1,000 mark. The $1,000 price point is critical because it will make whole genome sequencing comparable in cost to existing medical tests thereby opening up new opportunities for researchers to understand the genetic underpinnings of wellness and disease and providing clinicians with a valuable tool for assessing patient health.
- It is often written by economists that while personalized medicine costs more, it is more cost-efficient. How can we find the balance between having a well designed personalized medicine concept in healthcare and checking everyone’s samples for random biomarkers?
This is a good question. Evidence is needed to show the clinical and economic utility of anything that becomes part of the standard of care. But personalized medicine will be most successful where it makes health care more efficient by enabling the matching of treatment to patient to maximize therapeutic benefits and reduce adverse events, not where it imposes a new one-size-fits-all guideline on physicians to test the entire population for a random biomarker.
- What are the goals and planned activities of the Personalized Medicine Coalition for the next few years?
The Personalized Medicine Coalition is an education and advocacy organization comprising more than 200 member institutions. In keeping with our educational mission, we will plan conferences and develop new documents along the lines of The Case for Personalized Medicine to educate policymakers, business leaders, and others needing to understand personalized medicine and the opportunities it offers to improve patient care while making the health care system more efficient. We will also work with our members to understand and remove barriers to personalized medicine by advocating for changes to health care policy in the United States and around the world.
News from Visualizing Pharma to the Kinect Effect November 8, 2011
Posted by Dr. Bertalan Meskó in e-patient, Genome, Health, Health 2.0, Healthcare, Medicine, Medicine 2.0, Mobile, Video, Web 2.0, What's on the web?.add a comment
- Doctor heads to social media to find patients (video report)
People use their computer or phone to research places to eat, places to visit and things to buy. Sandy Hensley is part of a growing group of people finding medical needs there as well. ”I get all my other life recommendations on Twitter so I think it makes sense to me to make connections with people who you really want to trust like your health care providers on there.” Hensley said.
- This CPR training system gives feedback how you do chest compression:
The School of Medicine’s Office of Information Resources & Technology is launching this week a private, internal social-networking service, called CAP Network, that could dramatically alter communication among faculty, students, postdoctoral scholars and staff like the changes wrought on a much larger scale by Facebook and LinkedIn.
- Photo source: Bigstockphoto
Take a picture of your concern with your mobile camera. Send it as a MMS (Swedish SIM cards only) including relevant information as text in the MMS, or send your query via our iPhone app. We will respond as quickly as possible (within one day) with medical information.
23andMe Now Offers Sequencing for $999 October 2, 2011
Posted by Dr. Bertalan Meskó in 23andMe, Genetic testing, Genome, Web 2.0.1 comment so far
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
Synthetic Life: Craig Venter TED Talk July 28, 2011
Posted by Dr. Bertalan Meskó in Genome, Ted Talks, Video.add a comment
TEDMED just released the presentation of Craig J. Venter, the father of the human genome project and other interesting initiatives including the race for the synthetic life.
Opening your genome to the public April 20, 2011
Posted by Dr. Bertalan Meskó in genetics, Genome, Web 2.0.1 comment so far
Ramūnas Janavičius, a clinical geneticist (MD) and blogger at Cancer Genetics, just made his genomic data open to the public. The Personal Genome project did the same with 10 volunteers. An excerpt from the entry of Ramunas:
Today is a good day. I can not imagine a better day than personal birthday (and forthcoming DNA Day) to share my personal genome scan information, which you can find in this blog HERE* [GenomeScan_RJv2].
This is quite low density profile generated through 23andMe v.2 genotyping on Illumina Hap550+ array while a year ago.
He shared his genomic data under Creative Commons 3.0 license. Though it would be better to see his genomic raw data, but the Excel file with the SNP variants is also very interesting.
The first commenter pointed out that he doesn’t have curly hair as indicated by a variant, but he has a strange variant:
rs17602729, a SNP located in the AMPD1 gene and also known as ‘C34T’, has at times been called the “most prevalent genetic disease mutation”, at least in Caucasians. [PMID 11331279] Perhaps up to 10% of Caucasians and African-American carry one C34T allele (i.e. carry one rs17602729(A) allele) – and actually, most of them are unaware of any medically related issues since they don’t typically have any particular symptoms that would warrant a trip to the doctor.
Feel free to discover the data and let him know if you find anything interesting.
Linked electronic medical records for genomic research February 4, 2011
Posted by Dr. Bertalan Meskó in Data, Genome, science.2 comments
I’ve just come across an interesting study on BMC Medical Genomics. Authors aim at linking electronic medical records and genomic data which is I believe a very promising approach. The Personal Genome Project did something similar but only with 10 participants.
The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome science. eMERGE also includes a special emphasis on the ethical, legal and social issues related to these endeavors.
Current progress: The primary site-specific phenotypes for which samples have undergone genome-wide association study (GWAS) genotyping are cataract and HDL, dementia, electrocardiographic QRS duration, peripheral arterial disease, and type 2 diabetes. A GWAS is also being undertaken for resistant hypertension in 2,000 additional samples identified across the network sites, to be added to data available for samples already genotyped.
Results are being posted in dbGaP. Other key eMERGE activities include evaluation of the issues associated with cross-site deployment of common algorithms to identify cases and controls in EMRs, data privacy of genomic and clinically-derived data, developing approaches for large-scale meta-analysis of GWAS data across five sites, and a community consultation and consent initiative at each site. Future activities: Plans are underway to expand the network in diversity of populations and incorporation of GWAS findings into clinical care.
Whole Genome Sequencing in Diagnostics? September 24, 2010
Posted by Dr. Bertalan Meskó in genetics, Genome, Personalized medicine.1 comment so far
Using whole genome sequencing in diagnostics has been an issue for years, and as the cost of sequencing is rapidly declining, it seems it can pave the way for personalized medicine. A new research published in Genome Biology, Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors, just proves this point:
Adenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment.
We conclude that complete genomic characterization of a rare tumor has the potential to aid in clinical decision making and identifying therapeutic approaches where no established treatment protocols exist. These results also provide direct in vivo genomic evidence for mutational evolution within a tumor under drug selection and potential mechanisms of drug resistance accrual.
Personal Genomics in the News September 16, 2010
Posted by Dr. Bertalan Meskó in Genetic testing, Genome, Personalized medicine, Video.add a comment
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.
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.
Personalized Genomics: DTC Companies are in Huge Trouble July 30, 2010
Posted by Dr. Bertalan Meskó in Genetic testing, genetics, Genome, Personalized medicine.2 comments
- Federal ‘Sting’ Slams Gene Tests (New York Times): Watch this video
Today’s US Congress Committee on Energy and Commerce hearing into the direct-to-consumer genetic testing industry was a vicious affair. Representatives from testing companies 23andMe, Navigenics and Pathway faced a barrage of questions about the accuracy and utility of their tests, made all the worse by the fact that many of the Committee’s members seemed unable to distinguish between the more responsible companies in the field and the scammers and bottom-feeders.
- Consumer Genetics Needs More Transparency, Not Excessive Regulation: Daniel MacArthur and Daniel Vorhaus provide potential solutions.
Therefore, while advertising beef, the genetics community only seems to be delivering tofu. The complexity of genetic diseases has been far greater than anticipated, and the public’s interest in learning about genetic predispositions is unexpectedly low. So, will genetics ever impact primary care? It already has and will continue to do so, but it is likely to continue in an evolutionary rather than revolutionary manner. Primary health care providers who keep current by reading the medical literature and attending professional meetings will not be left in the dust. And, in time, the benefits of genetic technology will benefit our patients.
