DNA Cancer Codes Cracked By International Effort

Enigma23 writes "As reported on news.com.au, scientists from the International Cancer Genome Consortium of 12 institutes around the world will today release the first DNA profiles of some of the most prevalent types of tumors. While the story asserts that 'A new era of cancer treatment has dawned,' I'm a bit more skeptical, given that gene therapy and immunotherapy are still very much in their infancy at the current time."

Comments

So...

[pushing-robot]

Any word on a patch?

Re:So...

[erroneus]

No but God will be suing under the DCMA.

Dude...

[Cryacin]

Be careful what you wish for. If you live in Paris, then yeah, having X-Ray vision is a great thing. However, if you live in Kentucky and happen to work for a purveyor of Fried Chicken, let's just say that ignorance is not only bliss, but a requirement.

I'll take whatever advancement we've got.

[purduephotog]

I was diagnosed with stage 5 cancer at age 17. I'm still alive at age 33.

There's not a day that goes by when I don't look at my disfigured face and wonder what thing would have been like if I'd caught it sooner- according to one doc, I'd have been dead because my body wouldn't have fought it off. Who knows.

But anything that gets a genetic component and allows them to focus better on killing off the cells that have tormented me for over a dozen years I'll be more than grateful. There isn't a trip to the doctor that doesn't send shiver of fear down my spine, whether or not I'll be able to continue to provide for my family- whether or not that cough that started was due to pollen or something else... whether or not that pain in the side is a kidney stone or something more sinister.

Cancer is a killer. Even the survivors die a little every day.

Re:I'll take whatever advancement we've got.

[Wyatt Earp]

I was diagnosed with Acute Lymphocytic Leukemia (ALL) in the fall of 1980, it doesn't have stages like tumor cancers, but at the time I had a 5% chance to make it 3 years. I was clean after 3 months, it relapsed in the fall of 1982, 5% chance to make it 5 years.

Spring of 1991 I was diagnosed early with Stage 0 (Carcinoma in Situ) Testicular Cancer on both sides, surgery and some chemo.

Fall of 2006 I was diagnosed with a non-cancerous tumor in my neck, that left a nice scar.

I'm the only one in my NIH tracking group of ALL from back then to be alive.

Doctors freak me out, IVs of anytime scare the hell out of me, my fear are lumps from a lymph node.

Re:I'll take whatever advancement we've got.

[Calibax]

Staging systems are specific for each type of cancer but I don't think there are any stage 5 cancers. Overall cancer staging goes from stage 0 to stage IV - some cancers go from stage I to stage IV. In all cancers, stage IV means it has metastasized to distant locations in the body, which generally has a very poor prognosis.

In any case, for the majority of tumors, staging has been replaced by the TNM system (tumor, nodes, metastasis). For example, my colon cancer is staged T3N0M0, meaning a stage 3 tumor that has not spread to lymph nodes and has not spread to other organs.

If you have had no re-occurrence of your cancer after 16 then you are almost certainly free of the disease. Most cancers show up before within 5 years if they are going to reappear. That's why people are classified as cancer survivors if they are disease free after 5 years. There are some exceptions (such as breast cancer) that do have a tendency to reoccur in later life, but even then it's not common.

I suggest that after 12+ years you just accept that you are alive and stop living as if there's a Sword of Damocles hanging over your head.

Personally, this cancer survivor does not die a little each day as you suggest - quite the opposite. I try to live life to the full, enjoying my wife and family.

Re:I'll take whatever advancement we've got.

[John Hasler]

> Even the survivors die a little every day.

Everybody dies a little every day. Life is fatal.

Re:I'll take whatever advancement we've got.

[Anonymous Coward]

The great thing about this is that ICGC is releasing all their data under what they call a confederated database DCC. If you browse to their samples they have T4N2M1's and more. I think it's great that the data is getting out there!
However they do seem to be lacking the actual science/criteria behind the submission.

Re:I'll take whatever advancement we've got.

[seven of five]

You can take some solace in that electronics has helped speed medical research in many, many ways.

Re:I'll take whatever advancement we've got.

[DigiShaman]

When available, I try and donate through Folding@Home. It will cost you in an increased power bill (try running it 24/7 for a month, made a huge dent). Not that I mind. But if and when people decide to donate to this project, CPU cycles are not free.

To donate by CPU, go http://folding.stanford.edu/

To donate by direct funding, go http://pgnet.stanford.edu/goto/foldinggift

A slightly more informative webpage

[parallel_prankster]

http://www.qcmg.org/cancer.html It gives a background of what they are trying to do, seems interesting.

Re:A slightly more informative webpage

[Anonymous Coward]

Or go to the source ICGC.

Re:More than gene therapy and immunotherapy

[graft]

> I'm a bit more skeptical, given that gene therapy and immunotherapy are > still very much in their infancy at the current time

Those are not the only applications for this knowledge.

Err, to fill in that empty shell of a comment, specifically, this will hopefully generate at least a few new genes that are useful as drug targets. Anything that can make chemotherapy a bit more specific instead of just a general metabolic poison is a bonus.

As A Cancer Researcher...

[00Sovereign]

I've been following this for awhile. Looks like I get to update my "hit list" of gene targets to investigate. And that's what this will ultimately be...a list of interesting genes to look at for further investigation. No cures right away, it will take time to absorb this data into the collective intelligence of the medical research community and years to turn it into new treatments.

Re:As A Cancer Researcher...

[graft]

It also occurs to me that you can use this to identify specific alleles associated with increased risk of cancer. Not that genetic screening is generally very useful yet, but more maps like this will give a better idea of an individual's chance of developing specific types of cancer, maybe even associated with specific activities. E.g., "if you have these particular variants, you're much more likely to develop lung cancer, so you should smoke even less than a normal person." (I hope to GOD we (in the US) have public health insurance before this becomes widespread.)

Re:As A Cancer Researcher...

[morty_vikka]

I hear ya, it's exciting stuff... Just to add a twist, it should be noted that the vast majority of mutations found in tumours that have been fully sequenced so far occur outside protein coding regions. Not to say protein coding genes are not important, but it's likely that mutations in intergenic regions, promoters, noncoding RNA 'genes' and introns are also likely to play a major role in transformation to a cancerous phenotype in many cases.

The issue is going to be getting enough data for statistical robustness, even before any candidate mutations are investigated in the wet lab. I wonder how many thousands of each type of tumour should be sequenced? In any case, there will be buckets of data getting pumped out of the next generation of next-gen sequencers pretty soon, so plenty of work for bioinformatics nerds in the near future!

Re:No USA sites in the international list?

[Anonymous Coward]

The US of A is involved. Check out ICGC for the public release of the data. The original news source was published in Nature today.

Re:No USA sites in the international list?

[Anonymous Coward]

Google "The Cancer Genome Atlas" and you will be answered. TCGA (wry joke for you molecular biologists out there) has a massive amount of NIH funding dwarfing the international effort. Publication came out a while back for glioblastoma multiforme and a different tumor publication is being prepared now. A few terabytes of publicly available data there for you to download .

Re:No USA sites in the international list?

[kharchenko]

Indeed, the US is sequencing more genomes than any other participating country.

Re:No USA sites in the international list?

[reverseengineer]

The US participates via a parallel project in The Cancer Genome Atlas administered by the National Institutes of Health, which while remaining independent of the international project, shares data and tailors it's foci to not overlap with those of the ICGC.

Re:No USA sites in the international list?

[Calibax]

Oops, sorry a typo on my part

s/administration/administrations/

Somebody seems to be a little defensive there :)

Re:It's really too bad.

[CorporateSuit]

Can they identify these tumors with a simple blood test now or do they still have to do an invasive biopsy?

Don't forget -- you might be able to get it done with a deep anal probe too! Everyone always forgets about the deep anal probe!

war on cancer, war on drugs

[bcrowell]

The war on cancer and the war on drugs are pretty similar in certain ways. Both date back to Richard Nixon, ca. 1970. Both are vast, expensive projects of the federal government. Both have entrenched political/financial constituencies that want the federal money to keep flowing. Both have taken much, much longer and accomplished much, much less than Nixon and his contemporaries anticipated.

When it comes to cancer, the hype about prevention, early detection, and treatment has vastly overrun the actual medical gains. We were told for decades that eating lots of fiber would prevent colon cancer, but the first carefully designed study on this topic shows that it doesn't. We were told that PSA tests would save lives by allowing early treatment of prostate cancer; actually, the first good double-blind study showed that it saved no lives at all (while making many men incontinent and/or impotent). We were told that extending screening for breast cancer to younger women would produce better outcomes, but actually it turns out that it doesn't. In general, modern imaging techniques pick out tons of abnormalities than patients then demand to have treated, whether or not they would ever have caused a problem. People thought that personal genomics would allow individuals to get better prevention and treatment, but it turns out that there really don't seem to be any common mutations that predispose large numbers of people to a high risk of a particular cancer.

What we really need is more fundamental research on the biology of cancer. These half-assed attempts to find a quick answer have turned out to be mostly fruitless. It's like trying to send men to the moon without knowing Newton's laws of motion. We don't understand basic things like whether many cancers are caused by chromosomal abnormalities or whether the chromosomal abnormalities are caused by the cancers. While we're waiting for the fundamental biology knowledge to get figured out, we could concentrate on convincing people not to smoke tobacco.

Re:war on cancer, war on drugs

[Daniel Dvorkin]

If you're diagnosed with cancer, feel free to restrict yourself to the level of treatment that was available in 1970. Be sure to let us know how it works out for you. But you'd better do it quickly, because odds are you won't have very long.

Re:war on cancer, war on drugs

[Daniel Dvorkin]

You seem to be assuming that cancer treatment has made great strides since 1970. Actually it hasn't.

It has, whether you want to admit it or not. Are you going to dismiss the ACS as a shill for the health care industry? Here (PDF file) is a pretty comprehensive overview; I direct your attention particularly to the "Trends in 5-year relative survival rates" table on page 18.

And yes, of course cancer treatment centers oversell their treatments. But your claim that:

Actually most cancers have pretty much the same prognosis today they did in 1970.

is absolutely false. You do a nice bait-and-switch there, noting correctly that:

The list of cancers that was incurable in 1970 and is curable today is extremely short.

and then pretending that it supports your earlier claim. But in fact the two claims are completely different. We may not be able to cure most cancers, but we can greatly extend both the quantity and quality of life available to patients who are diagnosed with cancer relative to what we could do 40 years ago. While it is quite true that treatment for almost any kind of cancer is a miserable experience, if you think the level of misery is anywhere near what it was in 1970, then you simply haven't been paying attention.

I'm not going to argue against the idea that more basic research is needed -- hell, I work in basic biomedical research, so it would be absurd for me to make that argument. But I came here from patient care, and I can tell you that we need more research at all levels, "from bench to bedside" as the cliche goes. You can't tell a patient who's been diagnosed with a painful and probably fatal disease, "Well, we might have something that can help you fifteen years from now, but you're SOL since you'll be dead for twelve of those years."

Also, I detected a whiff of anti-government, anti-"Big Science" in your original post. Where exactly do you think the money for basic biological research comes from? Hint: it ain't Merck and Pfizer.

Re:It is not a code! There is no crack!

[RoadNotTaken]

Let me follow-up with a car analogy: Imagine you found the blueprints for a car that had a slight problem (say occasional aberrant acceleration, for example). Sequencing cancer genomes is akin to *finding* these blueprints. But it gets worse, the blueprints are in a different language and have no idea what 70% of the parts in the plans actually DO. Yes - the blueprint is helpful. Very helpful. In fact there's not much you can do without it. But it doesn't immediately help you FIX the problem. The only feature of DNA that is truly a *code* that was had to be *cracked* was the triplet code for amino acids and that was cracked by Khorana, Holley and Nirenberg in the '60s.

Re:Yeah me too

[ivan_w]

Don't you think a 'random bot' would post AC ?

I'm going for the browser - or more likely - an issue with the entity between the chair and keyboard.. (never happened to you eh ?)

--Ivan

Re:It's really too bad.

[wealthychef]

Everyone always forgets about the deep anal probe!

That's because the aliens make them forget.

Dawn

[Monkey-Man2000]

"I'm a bit more skeptical, given that gene therapy and immunotherapy are still very much in their infancy at the current time."
Hence the phrase "era of cancer treatment has dawned" instead of "era of cancer treatment has nooned [or twilighted]". Putting the cart in front of the horse perhaps?

Corruption will keep this at bay.

[geekmux]

"...I'm a bit more skeptical, given that gene therapy and immunotherapy are still very much in their infancy at the current time."

Yup, and it'll likely stay that way if big pharma has their way with things. Why ruin a multi-billion dollar drug and treatment industry just to save a few thousand lives, right?

Greedy fucking bastards.

Re:It is not a code! There is no crack!

[Anonymous Coward]

Well, that's not entirely true. There's also some weird stuff going on with methylation that still needs to be cracked. That's a part of the "code" if there were to be one. Also, you could say there's a histone code, with it's own methylation. I'm sure there's other mysteries in there as well.

But, as the parent says, sequencing is sequencing --- not code cracking.

Also, can I make a plea to the world that we stop saying scientists "map" a genome when they really sequenced it. Mapping is a completely different thing. They may have done some mapping when they sequenced it, but likely you really mean "sequenced" when you say "mapped". You can't throw these jargon terms around like they're synonyms, because they aren't.

And I'm not nit-picking here (nor is the parent poster). To put it in terms here that everybody can understand, it's like when my wife refers to the tower case of my PC as the "hard drive" of the computer.

Also on the issue of sequencing cancer "genomes" I think we'll find it to be a big a waste of money, as the HapMap project was, in a couple years. Maybe they'll find a few drug targets, but I predict the more cancer "genomes" that are sequenced, the more we'll find that anything is possible in cancers. What we really need to find is the driver genes that start the cellular changes leading to cancer, and lead to progression of the cancer. I'm not sure sequencing a genome that's a total mess because it's *already* a cancer cell is going to make it immediately apparent what those driver changes were. Not doubting it can be done, but it is a big effort, and I'm not sure it's the best way to do it. I think more likely you will end up with a lot of sequence data that's really difficult for most people to interpret, and contributes not that much to cancer biology. Good to know what the deal is with the cell lines they've been using all these years as models, but beyond that, who knows. (Heck, maybe I'm wrong and we'll find a bunch of previously unknown viral sequence integrated in the genomes.)

Now, I'm not trashing personalized medicine, where you sequence a patient's tumor line, and then use that to determine a treatment tuned to the cancer cell line they have. I think that's exactly how things need to go. But I am trashing this idea of creating a catalog of *all* cancer "genomes" (for the reason I mentioned above) as the goal of a "genome project". Try sequencing some new and useful genomes instead.

Overall, I don't like "gold-rush" biology, and there seems the be a lot of that going on. Be the first one in, and leave a big mess of data for the next guy to deal with.

Re:More than gene therapy and immunotherapy

[Abcd1234]

it can still be used to set up tiered insurance charges so that people who don't have the genes will only pay a little more for insurance than they do now (doing business as it has always been done), while people who have the genes will be in a different risk group and will be required by law to pay much higher premiums than anyone has ever had to pay before

Buh? They didn't sequence the genes of cancer patients. They sequenced the genes of the tumours themselves.

Re:It is not a code! There is no crack!

[RoadNotTaken]

You're right - that's probably where it started! That said, codon refers to the only (that I can think of) true code in biology. The other potential codes just mentioned (DNA methylation, histone mods, etc) are really more biochemical features that interact with proteins to regulate gene expression. The triplet code (code) is basically universal. TAA means STOP to every organism on the planet from worms to fish to bacteria to man. Histone mods and DNA methylation matter, but they're much more specific to particular cells/organisms.

Re:More than gene therapy and immunotherapy

[silentcoder]

You must favor the complete privatization of police forces, so the protection of lives and property and the arrests of criminals is bought on an open market and only available to those who can afford to buy it.

See what I did there ? Let's analyse your post:

Fallacy 1: Begs the question
Fallacy 2: Does not follow.
Fallacy 3: Strawman attack.

Stating that capitalism has no place at the sickbed does not imply or advocate that the correct method of paying doctors and research is governmental. This is the most common alternate system that has been tried (with huge success in general) but it's by no means the only one. There are quite a few completely different setups out there. Even your own country has thousands of free clinics run by charitable donation - e.g. there is no profit motive and it's not paid by government EITHER.

There are at least four other healthcare systems in the world where the cost of healthcare is shared by various entities - so not all paid by government and that's just what's in active use.
The amount of possible ways to do it that hasn't been tried and perhaps hasn't even been thought of yet is potentially infinite.

The parent pointed out problems with profit-motive in healthcare. You assumed without any evidence that he must therefore be advocating government paid healthcare. He may or may not advocate this, but the point is - you don't know if that is what he advocates because he did NOT suggest any particular alternate system - he merely said that he is not in favor of capitalist medicine. You then took what you perceive as the worst possible alternative, stated that he *must* be advocating it, and attacked that. Three fallacies in one short sentence- impressive.

Or is it just typical American dualist thinking ? Every issue only has two sides and two possible answers right ? That's why you can have a "democracy" where only two parties have any actual power, it works because your your entire 350 million strong population consists of people who have only one of the same two opinions on everything, and conveniently - your opinion one one issue means you must have the exact same opinion on all other issues as all the other people who share your opinion on this one...

Actually... that sounds rather silly when you think about it... it suggests a culture that has utterly and completely marginalized any individual thinking when all the other parties out there (the greens, the libertarians etc.) even in coalition can't get enough votes for a single seat in government. You've had an independent candidate in every single election for at least a hundred years, but I don't believe you've had an independent candidate *win* the presidential election in your entire history...

Well... the real world is not so simple. Most issues don't have just two extremes as answers, and people who actually think about things can adjust their opinion to the specific issue rather than attempting to fit one ideological extreme to all issues.
The best way for society to solve any given problem may be completely different from the best way to solve another.
Very few people would think that police protection should cost you money - because when you need it most, is often when you can least afford it (not to mention - a truly private police force would have zero motivation to pursue a murderer unless the family of the victim is wealthy). You happily accept that law enforcement is best done when provided entirely by the government (there is no logical requirement that the people who make the law should enforce it - we do it that way because historically we've learned it works best) but you cannot contemplate that perhaps the same failures of the market may apply to healthcare ? So maybe the government paying for all would, while not perfect, actually be better than a capitalist system ?
You didn't actually state your reasons for being against that - you merely declared that you are with no justification - when the arguments in favor of it are quite strong, and cleverly avoided having to even consider that there are a multitude of OTHER ways medicine could be funded which may be better than EITHER capitalism OR government paid.

In short... EPIC FAIL.