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Scientists Develop 10-Minute Universal Cancer Test (theguardian.com)
An anonymous reader quotes a report from The Guardian: Scientists have developed a universal cancer test that can detect traces of the disease in a patient's bloodstream. The cheap and simple test uses a color-changing fluid to reveal the presence of malignant cells anywhere in the body and provides results in less than 10 minutes. The test has a sensitivity of about 90%, meaning it would detect about 90 in 100 cases of cancer. It would serve as an initial check for cancer, with doctors following up positive results with more focused investigations. The test was made possible by the Queensland team's discovery that cancer DNA and normal DNA stick to metal surfaces in markedly different ways. This allowed them to develop a test that distinguishes between healthy cells and cancerous ones, even from the tiny traces of DNA that find their way into the bloodstream.
Healthy cells ensure they function properly by patterning their DNA with molecules called methyl groups. These work like volume controls, silencing genes that are not needed and turning up others that are. In cancer cells, this patterning is hijacked so that only genes that help the cancer grow are switched on. While the DNA inside normal cells has methyl groups dotted all over it, the DNA inside cancer cells is largely bare, with methyl groups found only in small clusters at specific locations. Writing in the journal Nature Communications, the Queensland team described a series of tests that confirmed the telltale pattern of methyl groups in breast, prostate and colorectal cancer as well as lymphoma. They then showed that the patterns had a dramatic impact on the DNA's chemistry, making normal and cancer DNA behave very differently in water. The suspect DNA is added to water containing tiny gold nanoparticles, which turn the water pink. "If DNA from cancer cells is then added, it sticks to the nanoparticles in such a way that the water retains its original color," The Guardian reports. "But if DNA from healthy cells is added, the DNA binds to the particles differently, and turns the water blue."
Healthy cells ensure they function properly by patterning their DNA with molecules called methyl groups. These work like volume controls, silencing genes that are not needed and turning up others that are. In cancer cells, this patterning is hijacked so that only genes that help the cancer grow are switched on. While the DNA inside normal cells has methyl groups dotted all over it, the DNA inside cancer cells is largely bare, with methyl groups found only in small clusters at specific locations. Writing in the journal Nature Communications, the Queensland team described a series of tests that confirmed the telltale pattern of methyl groups in breast, prostate and colorectal cancer as well as lymphoma. They then showed that the patterns had a dramatic impact on the DNA's chemistry, making normal and cancer DNA behave very differently in water. The suspect DNA is added to water containing tiny gold nanoparticles, which turn the water pink. "If DNA from cancer cells is then added, it sticks to the nanoparticles in such a way that the water retains its original color," The Guardian reports. "But if DNA from healthy cells is added, the DNA binds to the particles differently, and turns the water blue."
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If you actually read the article, you will notice that assay results of cancerous and non-cancerous samples have a pretty big overlap. This means that there would be many incorrect test results. Also, they mention that not all cancers have the methylation changes necessary that make the assay possible. So, this is another instance of over-broad claims (by the media) as to the research implications.
It looks like the false negative rate is 10%. any number on false positives?
sed -e 's/Chuck Norris/Rajnikant/g' joke > fact
DNA in solid tumors may not migrate into the bloodstream (you actually don't want this as this is how cancer spreads).
I'm highly skeptical. While cancer does produce hypo-methylated DNA, by the time you can measure it in any significant quantities, the cancer will have already progressed to a very late stage. There are other conditions - including simply aging that can also produce hypo-methylated DNA so that will affect their false positive rate. This seems like the kind of experiment that will not hold up under replication.
It may well be possible to detect certain cancers by clever analysis of DNA in the blood. But the changes in DNA are subtle and variable. Just being able to mix it with gold particles and it turn blue sounds like nonsense.
I have no doubt that some thing was discovered, and it may even relate to cancer, but this summary sound like it has been totally mushed by journalists.
Disclosure: I'm a cancer biomarker researcher, and these types of studies are my bread & butter. I don't know this group, and they chose to look at tumour types that I'm largely not working on.
So this study is pretty uninteresting, and is getting a lot of unhelpful media attention. The core observation is that there are differences in methylation in tumour and normal, and that these can be detected in a pretty simple assay (10 min, blah blah). That's all either known, or pretty simple extensions of existing work. Nothing wrong with it, just not hype-worthy.
Media is then claiming an AUC of ~0.90 (and an operating point with an accuracy of ~85%). The problem is, their test situation is entirely irrelevant. Most of these analyses were based on a comparison of blood from:
1) healthy age- and sex-matched controls
2) patients with metastatic disease (cancer that has spread throughout the body)
This has a litany of problems:
1) almost all patients are symptomatic pre-metastasis, and thus only a small fraction (~5-25%) of cancers are diagnosed at this stage
2) patients diagnosed with metastatic disease have often elected to avoid testing (cost, access, personal decision, etc.)
3) sadly almost all metastatic disease is lethal -- we routinely cure patients with localized disease with surgery or radiotherapy
4) genomic and epigenomic changes accumulate over time, and metastatic tumours on average have significantly more
5) there is no health-care economics argument for screening for metastatic disease
So essentially, the paper says "we can distinguish black from white with 90% accuracy". That's fine, but the media reports are missing the fact that ~95% of real-life cases are gray, and the accuracy of this test will probably be lower in these white vs. gray comparisons. The likelihood is that this "90% accurate test" is actually going to be ~70-80% accurate in real-world settings. Which is fine, but, you know, matches existing cheap diagnostics in most tumour types anyways!
So in short, this study is over-hyped and goes far to creating a bad culture where people think we are closer to a "cure" than we really are. It's solid science, but in no way worthy of a slashdot article!
Too bad all of the best responses to this story are all AC, they should all be ranked higher.
"There is more worth loving than we have strength to love." - Brian Jay Stanley
hey investors wanna loose another billion? Go for it.
Because he used a neural network
Just another day in Paradise
Elizabeth Holmes.
That may account for the 10% false reading.
Although the obvious solution - pun possibly intended - would involve the peptides used to duplicate dna in dna testing.
The ratios aught to remain the same.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Which is way better than getting a false negative,
Damn. I learn so much on slashdot. Water really ISN'T blue? I just drank a glass of blue water this morning. I wonder what was in it?
In case of cancer, that's wrong. Many cancers are fairly harmless, while procedures to find them and put them into remission are extremely damaging, far more so than cancer itself.
A good example is the modern findings on prostate cancer, which in many cases is much less harmful than measures that clinicians used to put it into remission. Nowadays, certain prostate cancers aren't treated at all and instead merely monitored for example, and patients are likely to live with minimal to no symptoms for decades. Whereas treatment would cause severe symptoms immediately and to an extent permanently.
So in many cases, as shocking as it may sound, it's actually better in terms of health outcome to the patient to get a false negative on cancer test than an accurate positive one. Especially true if it's a generic case like this, where someone may go look for cancer that ends up as a small benign tumour with a series of exceedingly invasive biopsies that may cause severe damage to patient's health.
Oncology is really, REALLY difficult field of medicine, because not only is the illness effectively incurable in most cases, but oncologist must always contrast the harm caused by his actions vs harm caused by the problem he's looking for or trying to address.
Is this going to be another Theranos?
Is there an IPO associated with this? Cause it sounds like there's an IPO associated with this...
They need to talk about the specificity, not the AUC for a sample that has more instances of cancer than not-cancer. If you use this to screen the general population, the vast majority of whom do not have cancer, the false positives will overwhelm the true positives unless the specificity is very high.
Biopsy will always be the definitive test. You can see the cancer cells right there in front of you in the microscope. You can determine exactly which type and which stage, as well as appropriate treatments. However a cheap and effective screening test is more than welcome before you start taking a knife/needle to everyone. That way you can divide people into a group that needs further study and a group that doesn't need to be studied for almost no cost. You don't waste time and resources studying false positives (by other means) and hopefully no false negative slips through the cracks and gets sent home.
Seven puppies were harmed during the making of this post.
I don't think you understand what positive and negative mean. You are testing for cancer. If the color remains pink, the test is positive for cancer. If the color turns blue, the test is negative for cancer. You are assigning emotional values to a test result, because for you cancer is "negative" so it would be a "negative" result. Fortunately science doesn't work that way.
As for false positives: you REQUIRE cancer for the color to remain the same. Why would there be false positives? If there is cancer, the color remains the same. A false positive would be a test where a color change happened on the presence of disease, only it also happens sometimes when you shake the test tube. So look, the color changed, it must be positive! No, Sally just shook the tube again, it's a false positive. Get it?
Seven puppies were harmed during the making of this post.
Presumably there will always be healthy cells and therefore always some amount of bluing. If possible would you have wanted to leave the water clear for healthy cells and turn blue for malignant ones?
And I shall name you Yang.
"There is more worth loving than we have strength to love." - Brian Jay Stanley
But I'm literally taking the talking lines from relevant lectures and studies done by people who are cutting edge specialists in the field. This isn't hidden, a few google searches on things like example I provided will give you the same information from people who unlike myself have the relevant credentials.
Note how I never appealed to my authority. That was your invention, start to finish.
For most people this would be the dumbest thing they ever said, but for SuperKendall it's a daily occurrence.
What is color but a characteristic of appearance? What other means is there to influence color for anything that transparent to light? If blue is the resultant color of light passing through water, then what other color can water possibly be?
It takes a special intellect to be wrong about so much while saying so little, and by special I mean short bus special.
Hey I always appreciate corrections but you missed the larger meta-context around the post, as such you are not responding to the message I actually wrote.
I mean even if you had just read the responses you would have seen my Scientific American link on why water appears blue and then you would have probably saved yourself a lot of bother by having an inkling my post was not as it seemed... You did at least save yourself from a witty riposte similar to my response to 10101010 (who similarly misunderstood), so thumbs up there for at least starting your misunderstanding from a better point.
Thanks again though, I appreciate the support! All responses propel me onwards and upwards to ever greater Slashdot posting frequency!
"There is more worth loving than we have strength to love." - Brian Jay Stanley
I guess we found Neil deGrasse Tyson's alt account...
Ezekiel 23:20