Monday, July 30, 2012

Tests you can do at home: for diabetes and cardiovascular health


When I first started I have no idea these things are all available at home.   So I'm sharing these products as I discover them.   I'm like a kid in candy shop, very happy but I have not tried or calibrated any of them yet.   So read the reviews before you buy:
Cholesterol checks 
A1c monitors 
Uralysis tests

http://www.amazon.com/STANBIO-STAT-SITE-Hemoglobin-Test-Cards/dp/B001DLS87W
Hemoglobin test

Someone on another thread is saying things like "it's not accurate", "overdiagnosis", "your conclusion is not sound", blah blah blah.   I'm like:  come on, I know you are a certified health care professional.   But, have some imagination.   Here is the future:
http://www.qualcommtricorderxprize.org/



more details in my blog http://killerboob.blogspot.com
Dx 8/29/2011, IDC, 2cm, Grade 3, 1/1 nodes, ER+/PR+, HER2-

Monday, July 16, 2012

Magic Bullet for Lung Cancer and its Drug Resistance Problem

http://cenblog.org/the-haystack/2012/06/asco12-data-digest-combating-resistance-in-lung-cancer/

Magic Bullet for Melanoma and How scientist overcome drug resistance



Very good blog talking about the same story:

Not long ago, metastatic melanoma was considered a graveyard for clinical research. But last year brought a major breakthrough in treating skin cancer: the approval of Roche's Zelboraf (vemurafenib), a small molecule that has proven highly effective at treating the roughly 50% of the patient population that carry the BRAFV600E mutation.
However, Zelboraf has limitations. Patients' disease eventually becomes resistant to the drug and the lesions caused by the skin cancer tend to return after 6 to 9 months.
In the backstory, it's the full genome sequencing that has become cheaper to $4000 that will help development of both targetted drugs like anti-BRAF and understanding drug resistance further.   I think the Broad institute is a customer of Complete Genomics.   I have no financial interest btw.   


More quotes:
An amazing thing about current melanoma research is that several physician-scientists involved in the clinical trials are also actively involved in translational research-this is sadly the exception rather than the rule, in oncology. But the connection between basic science and bedside has meant new targets are being identified and quickly tested in the clinic. 
How they pulled off this trick on melanoma is what is important.   Cancer is smart, but people are smarter.
An impressive waterfall plot of tumor shrinkage for patients (n=77) with the BRAFV600K mutation drew gasps from the audience - only four patients failed to respond to the combination, while the majority had a response of 30% or better. This isn't something you see every day in cancer research! Unlike the short lived responses we have seen with single agent therapy, the median duration of response for the BRAF naive patients with the combination was 11.3 months. Treatment given for a median of 10.7 months and just over a third (38%) were still ongoing. With regards to efficacy, PFS was 7.4 months across all dose cohorts, which is slightly above what one might expect for single agent therapy at full dose. 
 ...
He highlighted several key mutations that are druggable – aside from BRAFV600E and K, there is also c-KIT, Q61NRAS, NRAS wt and BRAF wt, where wt stands for wild type. Inevitably, the survival rates for these subsets varies, with NRAS mutants having the worse prognosis.

Friday, July 13, 2012

Complete Genomics: Full Tumor Sequencing for $4000



http://www.completegenomics.com/public-data/cancer-data/
http://www.completegenomics.com/services/cancer/
Quote:  
"The Nature paper by Peters et al. describes how our LFR technology uses ‘barcoded' DNA to generate whole genome sequencing with approximately one error in 10 million base pairs, or just 600 errors in an entire human genome," said Dr. Rade Drmanac, the company's chief scientific officer and inventor of the LFR technology. "This represents a 10-fold increase in accuracy for Complete and is unmatched by any high-sensitivity method currently available."
In addition, Complete's LFR technology provides, for the first time, accurate whole-genome sequencing from as few as 10 to 20 cells (only 100 picograms of DNA), making it an ideal choice for small sample clinical sequencing applications including circulating tumor cells, fine needle aspirations, and pre-implantation genetic diagnostics 
More quotes:Gene sequencing companies, which also include bigger names Illumina Inc and Life Technologies Corp, cater to a client base that mostly comprise educational and research institutions and compete on price.
The sector has recently come under pressure from a cut in the funding provided by the National Institutes of Health (NIH) for basic science research.
As the technology is yet to see widespread commercial adoption, the funding cut is one of the biggest issues faced by the sector that is on a persistent drive to bring down the price of gene sequencing to about $1,000.
Currently, the average price is $4,000-$5,000.



My take:  This price is affordable for some patients.  Comparible to the $2000 charged by Oncotype DX, and BRCA testing and others, generate a lot more information.  Its accuracy and how little sample it takes (CTC) is a big sell for me. 
Some types of BC has tumor mutations that are not standard BC, more like standard other cancer, which may have well targetted drugs for them.       It could perhaps help your onco find a better targetted 2nd/3rd/4th line chemo/biological and gave the patient valuable time with better tolerance.   It could give researchers more insight on why you are or are not responding to certain treatment or become resistant.   It could in future change the way clinical trials are run and lead to the cure.   Faster, more accurate, cheaper.  
So my Cato bit:  support research, support clinical trials to find the MBC cure.   Note the NIH funding cut, the public needs to invest more money into basic science, better technologies and finding the cure, and spend less money on expensive tests/procedures/drugs/charities that really don't deliver the bang for the buck.



Except they are having trouble convincing doctors to use them.   Here is where patients could come in.   Patients have the right and the duty to demand the newest and best and cheapest technologies, to encourage innovation and save money for themselves and for the health care system.   Illumina's 90% market share is not healthy for the development of this nascent market and notice how Illumina had to drop their price from $20000 to $4000 due to the new entrants into this market.    


Quote from wikipedia:
In June 2009, Illumina announced the launch of their own Personal Full Genome Sequencing Service at a depth of 30X for $48,000 per genome,[1] and a year later dropped the price to $19,500.[2] This is still too expensive for true commercialization but the price will most likely decrease substantially over the next few years as they realize economies of scale and given the competition with other companies such as Complete Genomics and Knome.[3][4] As of May 2011, Illumina reduced the price to $4,000.[5][6]

Saturday, July 7, 2012

Not enough Patients in Clinical Trials, much less Combination Drug Trials


It's a great talk by Prof Thomas Tursz from EU.   I agree that the status quo in BC clinical trial is not acceptable.   Each semi-successful drug takes 15 years from bench to approval, 100s million dollars, not to mention the 9/10 failed drugs.    Combination drugs may well help, (Herceptin, Everolimus, Pertuzumab all succeed in combination treatment) but there is a big problem with mathematics.

Usually a good treatment (not a specutacularly good 70-100% response treatment, maybe a 30-50% response treatment) takes 500 patients in a randomized blinded controlled trial to get statistically significant proof that it actually is good, not just a statistical fluke, a placebo.   I explained this in another thread:  A clinical trial on 23 patients is like 23 coin tosses. After 23 coin tosses, say I get 15 heads vs 8 tails. I could say that this coin is weighted heads/tails ratio almost 2, that's very different from 1. But I am not very confident of this conclusion because the sample size is too small. Now if I toss 500 times, and still gets heads/tail ratio of 2, then I become very confident of this ratio.
That's why randomized double blinded clinical trial with 500+ patients is still the gold standard in clinical trial. That's expensive and requires lengthy recruiting. When you consider that different subtypes of BC (TNBC, claudin-low, normal-like, basal) may have only 2%-10% patient population, you realize how tough it would be to find 500 patients with this small subtype to test a drug specifically targeting this type. Add to that cancers evolve to become drug resistant, it become even tougher. 
Now, let's move on to the even more difficult tasks of testing combination treatment.  Suppose we have 3 drugs (A,B,C) that has cleared phase II trial with good results, each requires 500 patients to go through phase III trial for approval, that's 1500 patients required total.   Now if we want to explore combination treatment, then there are at least 4 combos, AB, AC, BC, ABC.   That would require 7*500=3500 patients for a full test.
Suppose we have 4 drugs (A, B, C, D), there will be 15 combos+singles to fully test, requiring 15*500=7500 patients.   Suppose we have 5 drugs, we will need 31*500 patients.   So on and on.

It's exponential, doubling with every new promising drug to test and we do not have this many patients.     But "In clinical trials, 97% of patients in Europe are not in a trial", I think numbers are similar in US.   That is a HUGE problem.

Traditional clinical trials especially on early stagers require long time commitment (like 5 years) from patients. So traditionally late stagers are the main force of clinical trials.  Late stagers are fewer in numbers (50000/year), the ones with the right subtype of BC rarer (say 5000/year for TNBC, which has more subtypes), the ones with good performance statuses are fewer still (say 2000/year), the ones with good performance statuses living near a research facility are rarer yet (say 1000/year), the ones with good performance status who are willing to serve in clinical trials are still fewer(I don't know how many, but certainly less than 50% from my observation), and so it's hard to recruit enough of them to test new drugs, much less combinations. End result is: traditional clinical trial process takes 15 years and 1 billion dollars for any good drug to make through.

This is why I'm so excited by ispy-2.org. Newly dxed early stagers needs to commit only months to either control or experimental arm. Basically a couple of dose to see if it (standard chemo or standard+new drugs) works, if not, they change chemo or go ahead to surgery. The new drugs are generally the most promising drug that has already been tested for safety. 200k/year newly dxed patients with good performance status could potentially be recruited which means quick recruitment. A new drug if demonstrating efficacy, could go from bench to approval in as little as 5 years. Even FDA is excited.

If Henry Ford is on Titanic, he would not say: let's do a handmade lifeboat for everyone. He'd make an assembly line that churns out lifeboats. Ispy2 is the kind of assembly line for new cancer drugs that he'd be proud of.

ispy-2 has potential to increase patient participation dramatically by reducing patient commitment.   That said it only could test certain type of drugs.   In general, we need much greater patient participation across the board, and we need a different clinical trial model with different end-point (phase I, II, III may need to be changed),  we need to invest in better animal model/preclinical model, better blood/imaging tests for progression, different end-point.   We will get the MBC cure, but the PROCESS for developing cure urgently needs to be improved. 

Wednesday, July 4, 2012

AIDS and breast cancer



Anti-HIV drug may work against TNBC.  Currently it's in mouse only.   But we need to find the bull's eye on triple negative cancer cells, so that new drugs can target these basal (=TN) beasties.

Since these drugs are already available for HIV patients, they may get to human clinical trials  sooner and the whole process can be easier.   

Another interesting article on AIDS and Breast cancer risk
"Neoplastic breast cells commonly express CXCR4 but not CCR5. In vitro, binding HIV envelope protein to CXCR4 has been shown to induce apoptosis of neoplastic breast cells. Based on these observations, we hypothesized that breast cancer risk would be lower among women with CXCR4-tropic HIV infection"
It appears very few patients have both AIDS and breast cancer, yet, for some reason.
The impact of HAART on the HIV epidemic includes greater life expectancy, a decreased risk of AIDS-defining cancers, and an increased risk of some non-AIDS-defining cancers.3,21,22 Breast cancer incidence has not been shown to be higher among HIV-infected individuals.21,22 Among women, a pattern of decreasing risk of breast cancer has been shown with increasing time since AIDS diagnosis.23 Among men and women, a statistically significant decrease in the incidence of breast cancer has been observed following the AIDS epidemic in Tanzania.24 In France, the incidence of breast cancer was significantly lower in HIV-infected women than in the French general population7,8 This apparent deficit in breast cancer cases may be explained by underreporting or competing mortality. In the United States, the deficit of breast cancer cases among women followed in the Women's Interagency HIV Study is explained by an overall lower frequency of established risk factors.25,26 

MMTV virus in breast cancer



 Unfortunately, even if there is a cure based on this interesting findings, it will take 15 years to go through clinical trials and 1 billion dollars.   In the meanwhile, it needs to compete with 100s of promising drugs (which turn out to be duds) for patients, researchers and dollars.   It's possible it may lose in the early competition for lack of tweaking, lack of patients, lack of money and languish forever.
That's why I keep trumpeting the virtues of ispy-2 trial, and other new clinical trial designs.    Cancer evolve drug resistance fast,  cancer drugs development is too slow in the last 30 years.  
Cancer drug development is sadly lagging the AIDS drug development.  AIDS bursted unto the scene in 1980s, killing its patients within 1 year.   The urgency of AIDS epidemic translated to 10% of NIH funding and massive researching effort and within 10 years, science worked out many of the previous unknowns and there were multiple drugs that target HIV.   Now AIDS patients could look forward to a normal life expectancy.   AIDS was the greatest challenge and the greatest triumph of modern medicine.
Metastatic breast cancer or lung cancer is not there yet.
For Independence Day post, this is the lyrics for Neil Diamond's Coming to America.  It could be easily about any form of human affliction, be it poverty, tyranny, AIDS, MBC or Metastatic Cancer for general.   Cancer is smart, so we need to keep trying keep dreaming keep investing:

Far, We've been traveling far, Without a home, But not 
without a star
Free, Only want to be free. We huddle close Hang on to a 
dream
On the boats and on the planes, They're coming to 
America. Never looking back again, They're coming to America.
Home, don't it seem so far away Oh, we're traveling light today In the eye of the storm, In the eye of the storm
Home, to a new and a shiny place. Make our bed, and we'll say our grace, Freedom's light burning warm, Freedom's light burning warm.
Everywhere around the world They're coming to America. Every time that flag's unfurled They're coming to America
[. From: http://www.elyrics.net/read/n/neil-diamond-lyrics/america-lyrics.html .]
Got a dream to take them there; They're coming to 
America. Got a dream they've come to share, They're coming to America
They're coming to America
They're coming to America
They're coming to America
They're coming to America
Today, today, today, today, today
My country 'tis of thee, Today, Sweet land of liberty, Today, Of thee I sing, Today, Of thee I sing -- Today