Tuberculosis kills nearly 2 million people annually, and kills more adults than malaria, AIDS, and all tropical diseases combined. TB is the cause of one in four avoidable deaths in the Third World…
Conquering TB: How Genomic Information And Tools Can Lead To New Tuberculosis Therapies That Combat Drug Resistance
March 19, 2010 — adminNew Statistical Method For Genetic Studies Could Cut Computation Time From Years To Hours
March 19, 2010 — adminIn the ongoing quest to identify the genetic factors involved in disease, scientists have increasingly turned to genome-wide association studies, or GWAS, which enable the scanning of up to a million genetic markers in thousands of individuals. These studies generally compare the frequency of genetic variants between two groups – those with a particular disease and healthy individuals…
Stanford Study: What Makes You Unique? Not Genes So Much As Surrounding Sequences
March 19, 2010 — adminThe key to human individuality may lie not in our genes, but in the sequences that surround and control them, according to new research by scientists at the Stanford University School of Medicine and Yale University…
Vastly Expanded Versatility Of Optogenetics Brain-Research Technique
March 19, 2010 — adminRecently, brain researchers have gained a powerful new way to troubleshoot neural circuits associated with depression, Parkinson’s disease and other conditions in small animals such as rats. They use an optogenetics technology, invented at Stanford University, that precisely turns select brain cells on or off with flashes of light. Although useful, the optogenetics tool set has been limited…
What Makes Us Unique? Not Only Our Genes
March 19, 2010 — adminOnce the human genome was sequenced in 2001, the hunt was on for the genes that make each of us unique. But scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and Yale and Stanford Universities in the USA, have found that we differ from each other mainly because of differences not in our genes, but in how they’re regulated turned on or off, for instance…
Adding Common Genetic Variants To Breast Cancer Risk Models Offers Only Small Benefit
March 19, 2010 — adminScientists report that breast cancer risk assessment models, which predict a woman’s chance of developing breast cancer, do not perform better when they include common inherited genetic variants recently linked to the disease. Therefore, recommendations for breast cancer screening or treatments will remain unchanged for most women…
Discovery Of Switch Mechanism For Controlling Traffic In Cells
March 19, 2010 — adminScientists have identified a mechanism that switches on an extremely important process for the proper functioning and survival of our body’s cells. Specifically, the fast-track transportation pathway of ‘cargo’ to and from the surface of the cell…
DNA Nanotechnology Breakthrough Offers Promising Applications In Medicine
March 19, 2010 — adminA team of McGill Chemistry Department researchers led by Dr. Hanadi Sleiman has achieved a major breakthrough in the development of nanotubes – tiny “magic bullets” that could one day deliver drugs to specific diseased cells. Sleiman explains that the research involves taking DNA out of its biological context…
51st Annual Drosophila Research Conference From The Genetics Society Of America
March 19, 2010 — adminMore than 1600 basic research scientists who study genetic models in Drosophila (fruit flies) are expected to attend the 51st Annual Drosophila Research Conference in Washington, DC, April 7-11, 2010. SCIENTIFIC PROGRAMFor the complete program and Schedule of Events, see http://www.drosophila-conf.org/cgi-bin/dros10-cgi/drosSOE.pl…
Fungi Can Change Quickly, Pass Along Infectious Ability
March 19, 2010 — adminFungi have significant potential for “horizontal” gene transfer, a new study has shown, similar to the mechanisms that allow bacteria to evolve so quickly, become resistant to antibiotics and cause other serious problems…
Bench To Bassinet Program Seeks Congenital Heart Disease Treatments
March 18, 2010 — adminWhat: To help speed the translation of scientific discoveries into usable treatments in congenital heart disease, the National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health launched the Bench to Bassinet Program…
UV Exposure Has Increased Over The Last 30 Years, But Stabilized Since The Mid-1990s
March 18, 2010 — adminNASA scientists analyzing 30 years of satellite data have found that the amount of ultraviolet (UV) radiation reaching Earth’s surface has increased markedly over the last three decades. Most of the increase has occurred in the mid-and-high latitudes, and there’s been little or no increase in tropical regions. The new analysis shows, for example, that at one line of latitude – 32…
Pathway Genomics Responds To Medco, Mayo Clinic Study Revealing Gene Testing Reduces Hospitalization Rates For Warfarin Patients
March 18, 2010 — adminPathway Genomics Inc., a U.S. based genetic testing company, responded to research released at the American College of Cardiology annual meeting that found that the number of hospitalizations for heart patients taking warfarin, the world’s most-prescribed blood thinner, dropped by approximately 30 percent when genetic information for the patient was available to doctors prescribing the drug…
The Winner Of The 2010 Szent-Gyorgyi Prize For Progress In Cancer Research
March 18, 2010 — adminThe National Foundation for Cancer Research has announced that renowned scientist Peter K. Vogt, Ph.D., Professor in the Department of Molecular and Experimental Medicine at The Scripps Research Institute, La Jolla, California, is the recipient of the 5th Annual Szent-Gyorgyi Prize for Progress in Cancer Research. Dr…
Disabling Skp2 Gene Helps Shut Down Cancer Growth
March 18, 2010 — adminIncreased understanding of the Skp2 gene and its relation to cellular senescence may lead to the development of novel agents that can suppress tumor development in common types of cancer, researchers from The University of Texas M. D. Anderson Cancer Center and Memorial Sloan-Kettering Cancer Center report in the journal Nature…
NIH’s Genetic Testing Registry to Launch in 2011, But Will Dx Firms, Labs Voluntarily Participate? (GenomeWeb News)
March 18, 2010 — adminAfter much urging from personalized medicine stakeholders for the federal government to create a registry of clinical and analytical specifications for marketed genetic tests, the National Institutes of Health announced this week that it would develop such a database.
NIH’s Genetic Testing Registry to Launch in 2011, But Will Dx Firms, Labs Voluntarily Participate? (GenomeWeb News)
March 18, 2010 — adminAfter much urging from personalized medicine stakeholders for the federal government to create a registry of clinical and analytical specifications for marketed genetic tests, the National Institutes of Health announced this week that it would develop such a database.
Newer Genetic Info Adds Little to Predicting Breast Cancer (MedicineNet.com)
March 18, 2010 — adminTitle: Newer Genetic Info Adds Little to Predicting Breast Cancer Category: Health News Created: 3/17/2010 6:10:00 PM Last Editorial Review: 3/18/2010
Newer Genetic Info Adds Little to Predicting Breast Cancer (MedicineNet.com)
March 18, 2010 — adminTitle: Newer Genetic Info Adds Little to Predicting Breast Cancer Category: Health News Created: 3/17/2010 6:10:00 PM Last Editorial Review: 3/18/2010
A moment of Clarity. Some DTCG is not bad.
March 18, 2010 — admin
Ok,
Here is the G-d’s honest truth. Not all SNP/DTCG companies are bad. What do I mean by bad?
Not all SNP/DTCG companies misrepresented that which is not medically useful as medically useful.
I look at Pathway and Counsyl for example. Fast followers looking to say what they do and mean what they say.
Some of these DTCG tests could be clinically relevant and useful. The problem I have, is that there is no point at which I can say, “Hey I just want the clinically relevant stuff!” No ear wax please.
I need that as a clinician. If I want a huge panel of say CYP450 tests, where do I go? there are some labs that do this and charge and arm and a leg. One company, who I used charged the patient thousands of dollars because insurance wouldn’t pick it up.
That cannot ever happen again.
With the addition of these tests with some clinical value, there must be a value add of inexpensive and RAPID TAT (Turn Around time)
A classic example is my last post. Provided these tests become validated clinically, in a patient who can’t give me her Gail risk information (tough not to, but it could be a real case) I would use that other panel
The same is true for BRCA founder mutations. Provided you won’t drop it in some google database that they get served up mastectomy ads, some patients are afraid of needles and that is a barrier.
There are some very good things here. These good things are getting drowned out by some very bad things.
We can work together if you are willing to bend.
Keith Grimaldi said it best on his blog
“The lack of really effective clinical utility and the existence of commercial interests increases the confusion though. It’s hard to sell something that is interesting, “fun”(?), quite expensive, but not actually that useful to the majority right now. Hard to sell means sometimes over the top marketing.”
What medicine cannot tolerate is Over the Top Marketing. It leads to inaccurate statements. This is something extremely forbidden in certain states. In fact, some states don’t allow advertising to patients at all, or there laws are so strict you couldn’t say anything than
“Dr Murphy, accepting new patients, take insurance”
Why is this? It is to prevent false claims and promises. Doctors can’t make money back guarantees. They can’t make statements which are not based on fact in advertising. A lot of companies in a rush to get out young science and feed the hype cycle for grants and whatever have been all too guilty of this hype.
So when I get a comment from one of my readers who says (paraphrased)
“Hey all this bashing you do on DTCG is making us in the science end of the SNP reseach look bad”
It prompted me to say, hey, I wouldn’t have to throw so much cold water on it if it weren’t being hyped so much by DTCG…….
So I guess my point is simple.
Hey DTCG, your opportunity is to leverage your amazing platforms to launch medical services, TO and WITH physicians.
Keep the nonmedical exactly that, NONMEDICAL
Keep the Medical EXACTLY that, MEDICAL
People can benefit by knowing their 2D6/2C19/2C9/VKORC1.
But there are some hurdles to be overcome
1. How can I trust your results?
You have started by enlisting or creating CLIA certified labs, that is a good start. Maybe FDA cert would be nice. Not needed, but nice. There currently is only AmpliChip that is FDA approved….Would like others.
2. How can I know your interpretation is correct?
By using board certified molecular pathologists, I can get a comfortable feel for the fact that the results have been vetted by your specialist. This is muy importante!
3. How can I integrate the results into my EMR/PHR/etc.?
This is going to be super important. How can I save these results linked to patient care? Sure, some would pull paper and put it in the chart, others would prefer a pull in and link. You have to think how to do this.
4. What if the interpretation changes?
Will you take responsibility to contact Either the ordering physician or patient when a result changed? This will be important as we learn more about the nature of these genetic changes.
Doctor’s rely on these 4 things from most labs that they use. The depend on these services to be provided professionally and accurately.
These 4 things are EXTREMELY hard to do. But NEED to be done if you really want to be a part of the medical community. But even if you don’t, I think your customers deserve this sort of validation and service. Don’t you?
Take the jump, create a medical arm. Work with us.
The Sherpa Says: This is what is needed. Medicinally used DTCG that is “Allowed” to be of clinical use. A new Terms of Service, just for doctors, with a validation process that is transparent. And a Marketing process which is truthful.
GenVault Provides GenTegra(TM) DNA To Support Cardiovascular Genetic Testing At Berkeley HeartLab
March 18, 2010 — adminGenVault Corporation announced that Berkeley HeartLab, a subsidiary of Celera Corporation (Nasdaq: CRA), has adopted GenTegra DNA to preserve and store diagnostic samples for genetic testing related to the management of cardiovascular disease…
SNPs for breast cancer risk? It Depends.
March 18, 2010 — admin
I hold in my hot little hands a copy of the NEJM, March 18th edition. In it there is an article which isn’t even released yet.
Entitled
“Performance of Common Genetic Variants in Breast-Cancer Risk Models”
Remember when we did this for heart disease risk? FAIL WHALE…..
Do you think it will happen again?
The Study
10 common genetic variants
I had to create a couple of pages on SNPedia for this list FYI…..
The Methods:
Cases and controls-WHI, ACS CPSII Nutrition Cohort, Nurses Health Study, Prostate/Lung/Colorectal/Ovarian Cancer Screening Trial, and Polish Breast Cancer Study.
Cases-Woman who had received diagnosis of invasive breast cancer.
Risk Models Used-A hybrid of the Gail model…..I.E. Not exactly the Gail Model.
1. First degree relatives with breast cancer
2. Age at Menarche
3. Age at first live birth
4. Number of Breast Biopsies
They acknowledge that they were unable to get atypical hyperplasia and Mammographic density. Both of which have improved Gail.
So, This Gail is a little hobbled and not the best predictive model…….
The studied models- 5 logistic regression models
I don’t have the supplementary tables and methods yet.
The nongenetic model-Gail Model
The Demographic/Genetic Variant Count Model-included number of alleles.
The Demographic/Genetic Individual Variant-Accounted for individual effects of each SNP
The Inclusive Model-Gail, Genetics Demographics
The Demographic Model
And Random….
When we do these sorts of statistical analyses we look for a couple of things.
A. Number of people reclassified and how?
B. The Area Under the ROC Curve
The AUC is a good way of seeing whether a model or test is worthless or useful. And how much MORE useful than another test.
Results-
1. The Inclusive Model Yielded and AUC of 61.8%
2. The Nongenetic Model yielded an AUC of 58%
3. The Genetic Individual Variant Yielded an AUC of 59.7%
4. The Genetic Variant Count Yielded an AUC of 58.8%
5. Breast Biopsy BY ITSELF Yielded an AUC of 56.2%
That is a 3.8% difference in Yield from Genes and without Genes integrated into the weaker Gail Model.
Lastly, they asked. Well, does this Inclusive Model do a good job of discrimination of High risk vs. low risk.
The Answer- It determines lower risk better than Gail. It does not determine higher risk better.
The authors of this study have stated that
“As in Diabetes and cardiovascular disease, the addition of the common SNPs added little to the predictive value of the clinical models. On the basis of theoretical models, Gail has shown that increases in the AUC similar to those observed here and not sufficiently large to improve meaningfully the identification of women who might benefit from tamoxifen prophylaxis or screening mammography”
Take Home
The addition of these factors only creates a minimal statistical increase that is of no useful clinical benefit.
The Sherpa Says: If the press says “gene tests fail to improve risk assessment” You can be assured that the DTCG industry is no longer the darlings. If instead they say “Improvement in risk model” well, then you have chance to woo them back! It Depends…….
How can MDVIP use Navigenics Test for Medicine?
March 18, 2010 — adminI have been harping on this say what you mean. Say what you do. Theme lately.
I am a board certified doctor who practices personalized medicine. I see patients and apply the principles or pharmacogenomics, risk prediction and prevention tailored to each individual patient. I do this by taking a 3 generation pedigree, using current clinical risk models and pharmacogenomic or other genetic tests when indicated. That’s me.
I have this nagging pain about MDVIP, Ed Goldman and Navigenics.
Some MDVIP members are using Navigenics tests for medical risk prediction. Navigenics is ok with this because hey, they’re doctors.
The contents of our Site, including any risk estimates or other reports generated by the Services (collectively, “Your Report“) and any other information, data, analyses, editorial content, images, audio and video clips, hyperlinks and references (collectively, “Content“), are for informational purposes only and are not intended to substitute for professional medical advice, diagnosis, or treatment.
The part I want to focus on is “Are for informational purposes only and are not intended to substitute for professional medical advice, diagnosis or treatment”
It seems to me that this will be the more popular language in a Terms of Service for DTCG.
Notice that nowhere does it say, “This report is not intended to diagnose or treat”
I think that while it is nice to not say that, when in fact people are using it to diagnose, it is even goofier to say that it is not intended to substitute for a professional’s diagnosis. Ok, so are you saying
1. This is not to be used for diagnosis/medical advice
2. This is to be used for diagnosis, but the professional’s diagnosis trumps ours
3. This test is meant to be used by professionals to aid them in diagnosis and treatment
I am really confused here. Is this a medical test or not. Just come right out and say it!
The Sherpa Says: Say what you do, do what you say you do. Isn’t that what the Common Framework of Principles is About?
Hand Bacteria May One Day Aid Forensic Identification, Study
March 18, 2010 — adminNext time you leave your computer station or close the lid of your laptop think about this: your mouse and keyboard are covered in hand bacteria that could be traced back to you, according to a new US study that suggests the unique bacterial communities we leave behind on objects we have handled may one day sit alongside DNA and fingerprints as part of the forensic tool…
Gene Expression-Based Prognostic Signatures In Lung Cancer Not Ready For Clinical Use
March 18, 2010 — adminA review of published articles on gene expression-based prognostic signatures in lung cancer revealed little evidence that any of the signatures are ready for clinical use. Serious problems in the design and analysis of the studies were also found. The review was published online March 16, 2010 in the Journal of the National Cancer Institute…