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DNA Cancer Codes Cracked By International Effort

samzenpus posted more than 4 years ago | from the world-wide-tumor dept.

Australia 106

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."

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106 comments

So... (4, Funny)

pushing-robot (1037830) | more than 4 years ago | (#31851540)

Any word on a patch?

Re:So... (0)

Anonymous Coward | more than 4 years ago | (#31851568)

I just hope x-ray vision and cancer security patch aren't exclusive.

Dude... (3, Funny)

Cryacin (657549) | more than 4 years ago | (#31851594)

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.

Re:Dude... (0)

Anonymous Coward | more than 4 years ago | (#31853102)

No problem. I have here the perfect set of goggles. Just put them on and ta dah! . . . Aaarrgh! The goggles do nothing!

Beauty is skin deep (0)

Anonymous Coward | more than 4 years ago | (#31853104)

Why would you want to see women's bones? Me, I'd rather see the outer layer.

Re:So... (1, Insightful)

Anonymous Coward | more than 4 years ago | (#31851598)

Unfortunately, the patch is encumbered by patents.

Re:So... (1)

codepunk (167897) | more than 4 years ago | (#31851626)

yum clean all
yum update

Re:So... (3, Funny)

erroneus (253617) | more than 4 years ago | (#31851898)

No but God will be suing under the DCMA.

Re:So... (1)

gmp (155289) | more than 4 years ago | (#31852816)

Any word on a patch?

We've already tried it - ethyl, methane, sulfinate as an alkylating agent and potent mutagen; it created a virus so lethal the subject was dead before it even left the table.

Re:So... (1)

neonmonk (467567) | more than 4 years ago | (#31854036)

It's too bad she won't live! But then again, who does?

Re:So... (1)

tsm_sf (545316) | more than 4 years ago | (#31854206)

Pfft, I've seen things you people wouldn't belive.

Re:So... (1)

youn (1516637) | more than 4 years ago | (#31854268)

I believe they already a patch out... unfortunately it will only work on the proprietary smoker platform ;)... and is only a temporary patch that does not give results every time, I believe

FAH FTW! (0)

Anonymous Coward | more than 4 years ago | (#31851542)

Oh wait. FAH didn't contribute? Nevermind. ):

More than gene therapy and immunotherapy (1)

John Hasler (414242) | more than 4 years ago | (#31851628)

> 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.

Re:More than gene therapy and immunotherapy (4, Insightful)

graft (556969) | more than 4 years ago | (#31851742)

> 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.

Re:More than gene therapy and immunotherapy (0)

Will.Woodhull (1038600) | more than 4 years ago | (#31852340)

I don't know about the rest of the world, but in America this will certainly be a boon to the health care industry. While it would have been better for the industry before the recent legislation that prevents denial of insurance for pre-existing conditions, 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. It will all be honest and above board and based on industry standard actuarial statistics....

While I am pleased to see this scientific progress, I have serious concerns about how it will play out in the politics of the American health care industry. I'm thinking that capitalism has no place at the sick bed; the profit motive has to be removed from American health care before we can begin to see the true benefits of technology.

Re:More than gene therapy and immunotherapy (1)

wealthychef (584778) | more than 4 years ago | (#31852778)

If capitalism has no place at the sick bed, then you must be advocating the government pays all doctors and funds all research etc. I personally am not in favor of that.

Re:More than gene therapy and immunotherapy (0)

Anonymous Coward | more than 4 years ago | (#31853110)

Unfortunately, risk is a common good, whether you are "in favor" of it or not. Risk is cheaper for everybody if everybody pays for it. This is the number one reason why health care is mandatory.

Re:More than gene therapy and immunotherapy (1)

Rudd-O (20139) | more than 4 years ago | (#31854484)

Unfortunately, whether risk is a common or an individual good (two hypotheses for which you have not presented any evidence, and no, "cheaper if everybody pays for it" is not evidence of risk being a common good), is not the reason why health care is mandatory.

Re:More than gene therapy and immunotherapy (4, Insightful)

silentcoder (1241496) | more than 4 years ago | (#31855158)

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.

Re:More than gene therapy and immunotherapy (1)

ebuck (585470) | more than 4 years ago | (#31858290)

<scarcasam>Don't ruin his day, he can't wait to pay the police to follow up on his burglary. The burglars are also banking on stealing items of small enough worth that the cost of police followup makes investigating the crime too expensive. Arguing that some services are social will mess up the whole scheme to have every item under $20 robbed from his house on a daily basis.</scarcasam>

Re:More than gene therapy and immunotherapy (1)

silentcoder (1241496) | more than 4 years ago | (#31859610)

Lol, well put :D

Re:More than gene therapy and immunotherapy (3, Informative)

Abcd1234 (188840) | more than 4 years ago | (#31853516)

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:More than gene therapy and immunotherapy (1)

Will.Woodhull (1038600) | more than 4 years ago | (#31858170)

They sequenced the genes of the tumours themselves.

Good point. I was making an assumption that knowing the sequence of the tumor genes would lead to easy identification of the at risk populations. Technically I should not have done that; while it seems likely that this will be shown, it is not yet proven.

But if I had not done that stretch of logic, we would not have been entertained by the kneejerk reaction to any criticism of the USA insurance dominated Health Care Profit Machine*. Which while tangential to the science being reported, is more central to the livelihood of all USA slashdot readers.

Despite their entertainment value, the apologists for the current way of funding everything having to do with health care through privatized third party payment schemes need to be taken seriously. There is way too much concern about protecting dividends, extending return on investments, and earning the individual bonuses used as carrots in such schemes. These motivations should have very little if any influence on health care research or health care delivery, but in the USA these are motivations are the dominant factors in determining what research is done and how care delivery is shaped.

[HCPM: this millenium's replacement for the now outmoded Military Industrial Complex. This is where all the MIC moneys have gone since the ways of the Cold War are no longer so profitable.]

</rant>

Re:More than gene therapy and immunotherapy (1)

Enigma23 (460910) | more than 4 years ago | (#31859316)

Just because a specific genetic mutation is consistently (but not necessarily always) found in, for example, patients with pancreatic cancer, does not mean that if you have that specific mutation you are in any way guarranteed to get pancreatic cancer, merely that you may have a higher-the-average propensity to contract such a malignancy.

Re:More than gene therapy and immunotherapy (0)

Anonymous Coward | more than 4 years ago | (#31853610)

Correct! As one who is very much involved, the replacement of chemotherapy with immunotherapy/ biotherapy and other more specific methods will give us some hope to treat or cure these diseases.

It's really too bad. (1)

Quantos (1327889) | more than 4 years ago | (#31851638)

There isn't really a whole lot in the article about this. It would be nice if they told us how this could help, or how they hope it might help.

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

Re:It's really too bad. (2, Insightful)

CorporateSuit (1319461) | more than 4 years ago | (#31852270)

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!

Re:It's really too bad. (4, Funny)

wealthychef (584778) | more than 4 years ago | (#31852786)

Everyone always forgets about the deep anal probe!

That's because the aliens make them forget.

Re:It's really too bad. (0)

Anonymous Coward | more than 4 years ago | (#31856534)

No they are too busy playing video games :/

Re:It's really too bad. (1)

hallucinogen (1263152) | more than 4 years ago | (#31852334)

Well I didn't RTFA (this is Slashdot) but I guess they just might provide targets (like for example what proteins ought to be inhibited) for drug development.

Re:It's really too bad. (1)

jbengt (874751) | more than 4 years ago | (#31853182)

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

They need to do an invasive biopsy to evaluate how the cells look and whether the cancer is spreading beyond the margins of the tumor. By the time the genes are found in the blood, it probably has already spread.

cracked? hardly. (0)

Anonymous Coward | more than 4 years ago | (#31851644)

They sequenced the tumor genomes. The hard work of "cracking the code" e.g. associating DNA mutations with cancer phenotypes is just beginning. But congrats to Sean Grimmond and his team on the press release and publicity. Any publicity for science like this is good.

I'll take whatever advancement we've got. (4, Informative)

purduephotog (218304) | more than 4 years ago | (#31851654)

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. (5, Interesting)

Wyatt Earp (1029) | more than 4 years ago | (#31851734)

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. (0)

Anonymous Coward | more than 4 years ago | (#31851904)

People like you are why I regret going into electronics. All I do with my time is help design next year's landfill. I wish I could be working in something more biological so I could prevent posts like yours.

Re:I'll take whatever advancement we've got. (1)

FrozenFOXX (1048276) | more than 4 years ago | (#31852580)

People like you are why I regret going into electronics. All I do with my time is help design next year's landfill. I wish I could be working in something more biological so I could prevent posts like yours.

If it makes you feel better remember that not everyone can be a cancer researcher. That's okay though, they couldn't really do their jobs very well without a place to put the junk they discard in their search. :)

But I find stories like the grandparent are the reason why this research is freakin IMPORTANT. Nobody should have to go through that, and I wish there was more I could do to help. At the same time, you folks that keep surviving against all odds give me hope, not just for myself (had a few cancer scares myself, but nothing malignant), but that LIFE continues even in the face of oblivion. Not giving up, not giving in...well, it gives me hope somehow, hope that it's not all just pointless, that life is too damned important to give up on.

Ah well, sorry for not contributing much. Had to say something. Thanks you folks that keep fighting, me and my wife are rooting for you.

Re:I'll take whatever advancement we've got. (2, Informative)

DigiShaman (671371) | more than 4 years ago | (#31853804)

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/ [stanford.edu]

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

Re:I'll take whatever advancement we've got. (2, Insightful)

seven of five (578993) | more than 4 years ago | (#31853448)

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. (1)

Wyatt Earp (1029) | more than 4 years ago | (#31853924)

Kinda related to cancer, I had a small bleeding in my brain in the spring of '05. While I recovered the only communication I had with the outside world was WoW and my computer, so keep making the electronics.

Oh and from my neck tumor I had to get a Medtronic nerve stimulator, so more electronics. They all help.

Re:I'll take whatever advancement we've got. (1)

shadowbearer (554144) | more than 4 years ago | (#31852854)

  I had a friend who went thru something similar (don't remember details anymore, he never talked much about it) back in college in Minnesota (this was in the mid 80s.) He got thru school, and although we lost touch a long time ago, I still admire his attitude towards it - never ever give up.

  I'm remembering that nowadays in my early forties; my family doesn't have much of a history of cancer, but we do of early heart disease, and every little blip I have scares me.

  Good luck to you...

SB

Re:I'll take whatever advancement we've got. (4, Informative)

Calibax (151875) | more than 4 years ago | (#31851992)

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. (2, Interesting)

Anonymous Coward | more than 4 years ago | (#31853198)

The great thing about this is that ICGC [icgc.org] is releasing all their data under what they call a confederated database DCC [icgc.org] . 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. (2, Insightful)

John Hasler (414242) | more than 4 years ago | (#31852196)

> 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. (0)

Anonymous Coward | more than 4 years ago | (#31852336)

Life is a fatal gift, indeed.

Re:I'll take whatever advancement we've got. (1)

FrozenFOXX (1048276) | more than 4 years ago | (#31852588)

> Even the survivors die a little every day.

Everybody dies a little every day. Life is fatal.

Aw I dunno about that. But then again it's important to remember that nobody gets out of this alive. ;)

Re:I'll take whatever advancement we've got. (-1, Troll)

Anonymous Coward | more than 4 years ago | (#31852362)

I call shenanigans on this post, No such thing as a stage 5 cancer. It reads like a bunch of BS. Or the guy's a hypochondriac.

Re:I'll take whatever advancement we've got. (0, Interesting)

Anonymous Coward | more than 4 years ago | (#31854188)

die a little every day.

Hurry the fuck up before you bankrupt the rest of us.

Lest that stand completely heartless, look here. I feel for you. Really. Cancer must suck, and I've seen people melt from it too.

If there was a $1,000,000 permanent fix, I for one would be among the taxpayers happy to pay for it.

But, if you cost $1,000,000 per year to keep alive for the rest of your life, the rest of us would be far better served to look after your family on your behalf. Where do you think the $1,000,000 per year comes from? Do you seriously think your+employer's $800/month plus $20-$75 copays actually cover the checks going out? Is there some reason to expect your costs to drop?

Health insurance is nothing else but the most colossal Ponzi scheme of all time. The very notion of insurance is to spread risk, where rising health costs aren't a risk, but a certainty. Everyone is going to die, and most of us are not going to enjoy feeling it come.

Previous poster was right. Top end health care cannot be provided to all while the profit motive remains; rephrase, while the system has a vested interest in -not- scaling well.

Re:I'll take whatever advancement we've got. (1)

andot (714926) | more than 4 years ago | (#31854360)

I was diagnosed with stage 4 lymphoma 4 years ago. Very agressive form, nerve damage, multiple organ damage, awful pains. Got MUCH chemotheraphy and stem chell transplant. Chemotherpahy nearly killed me. Anything making chemotheraphy easier to live with is blessing. P.S I thought before cancer, that american medical system is good. Now i have changed my views. Fortunately I live in europan country where health insurance is for everyone.

Re:I'll take whatever advancement we've got. (1)

Nyder (754090) | more than 4 years ago | (#31854974)

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

Weird, so is Life, 'cause we all die a little day by day.

Not to make it seem like your cancer doesn't suck or anything, but it's part of life. You are one of the unlucky ones, yes, but that is life.
Some peeps have other problems, some don't have any problems, just part of life.

But just so you know, we are all dying a little, day by day, you got nothing special on that.

Emma Thompson (1)

abbynormal brain (1637419) | more than 4 years ago | (#31851702)

Just make sure she's not involved and one of us won't have to become a Legend.

A slightly more informative webpage (5, Informative)

parallel_prankster (1455313) | more than 4 years ago | (#31851726)

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

Re:A slightly more informative webpage (5, Informative)

Anonymous Coward | more than 4 years ago | (#31852056)

Or go to the source ICGC [icgc.org] .

No USA sites in the international list? (0, Troll)

Calibax (151875) | more than 4 years ago | (#31851736)

From TFA: "Scientists from research institutes in Australia, Canada, Japan, China and the UK will today release the first DNA profiles of some of the most prevalent types of tumours."

Note that the USA isn't in the list. Are the US folks are too busy patenting their discoveries so they can monetize them?

Or is the USA falling behind because of the asinine science related policies of previous administration?

Or is there another reason?

Re:No USA sites in the international list? (-1, Flamebait)

Anonymous Coward | more than 4 years ago | (#31851752)

If you think that the decline of science is just because of the previous administration then you've got a shitload to learn, boy.

You're either an idiot, a lemming or a troll.

Re:No USA sites in the international list? (-1, Flamebait)

Anonymous Coward | more than 4 years ago | (#31852028)

"You're either an idiot, a lemming or a troll."

At least the previous poster isn't a rude arrogant prick who makes claims
without providing any facts in support of those claims.

As for the previous administration, science aside, if you think they
did anything good then YOU are a dumb shit. The previous administration
took numerous steps to ruin the country, period.

Re:No USA sites in the international list? (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#31852038)

Written by a true (anonymous) Republican.

huh? (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#31852052)

Written by a true (anonymous) Democrat

Re:No USA sites in the international list? (2, Informative)

Calibax (151875) | more than 4 years ago | (#31852118)

Oops, sorry a typo on my part

s/administration/administrations/

Somebody seems to be a little defensive there :)

Re:No USA sites in the international list? (2, Informative)

Anonymous Coward | more than 4 years ago | (#31851850)

The US of A is involved. Check out ICGC [icgc.org] for the public release of the data. The original news source was published in Nature [nature.com] today.

Re:No USA sites in the international list? (3, Informative)

kharchenko (303729) | more than 4 years ago | (#31852026)

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

Re:No USA sites in the international list? (2, Informative)

Anonymous Coward | more than 4 years ago | (#31851924)

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? (3, Informative)

reverseengineer (580922) | more than 4 years ago | (#31852074)

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? (0)

Anonymous Coward | more than 4 years ago | (#31852244)

Actually, the NIH is doing what it thinks are the best cancers to study and there is a lot of overlap.

As A Cancer Researcher... (4, Interesting)

00Sovereign (106393) | more than 4 years ago | (#31851794)

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... (2, Interesting)

graft (556969) | more than 4 years ago | (#31852266)

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... (0)

Anonymous Coward | more than 4 years ago | (#31852496)

Be like mathematicians and drink more coffee!

Re:As A Cancer Researcher... (2, Interesting)

morty_vikka (1112597) | more than 4 years ago | (#31854108)

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!

ICGC.org data browsing and access (0)

Anonymous Coward | more than 4 years ago | (#31851952)

ICGC [icgc.org] is the main public access point to this data.

Yeah me too (-1, Offtopic)

ivan_w (1115485) | more than 4 years ago | (#31852000)

When I was 12, my buddy swashed me with a flashlight, which resulted me in being abducted by aliens.

I therefore sue the company that extracted the minerals necessary to build the metals that subsequently were turned into the casing of the very flashlight that caused me to be abducted.

--Ivan

Re:Yeah me too (1)

nextekcarl (1402899) | more than 4 years ago | (#31852072)

Am I the only one to read this post and go WTF? I had to check your other posts to see if you're just some random bot, but it appears your other posts make sense, so I'm back to WTF?

Re:Yeah me too (0)

Anonymous Coward | more than 4 years ago | (#31852148)

I think he meant to post in this thread:
http://science.slashdot.org/article.pl?sid=10/04/14/188253 [slashdot.org]

Re:Yeah me too (1)

ivan_w (1115485) | more than 4 years ago | (#31852636)

Yup.. Apparently I commented on the wrong thread indeed.. (blast ye Ajax - or my recklessness)..

So my -1 off topic is commended for my comment.

Oh well, I'll survive ;)

Re:Yeah me too (2, Funny)

ivan_w (1115485) | more than 4 years ago | (#31852662)

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

Singularity (1)

Databass (254179) | more than 4 years ago | (#31852314)

This kind of thing of thing gives me a little hope that if I can just hold on 40 more years or so, they'll keep inventing better and better stuff that could keep me alive for several more (former) lifetimes.

Honestly, dying right before that stuff really gets going would be quite a shame.

war on cancer, war on drugs (2, Insightful)

bcrowell (177657) | more than 4 years ago | (#31852388)

The war on cancer [wikipedia.org] and the war on drugs [wikipedia.org] 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 (1)

FrozenFOXX (1048276) | more than 4 years ago | (#31852632)

Oh I dunno, I thought it was pretty obvious what caused cancer. Just make sure you're not born at the end of June.

Checks birthday

Oh shit.

Re:war on cancer, war on drugs (1)

shadowbearer (554144) | more than 4 years ago | (#31852914)

  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.

  Or viral causes, for that matter.

  While we're waiting for the fundamental biology knowledge to get figured out, we could concentrate on convincing people not to smoke tobacco.

  We're already doing that, but I think that legislation and sin taxes aren't the right way to do it. Stopping people from smoking is going to be a very long term effort. Education - along with elimination of tobacco subsidies - seems much more effective in my opinion.

  (I am a former/ongoing/quitting again smoker, so I have a vested interest in the problem :) )

SB

Re:war on cancer, war on drugs (2, Insightful)

Daniel Dvorkin (106857) | more than 4 years ago | (#31853834)

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 (1)

bcrowell (177657) | more than 4 years ago | (#31858638)

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.

Two problems with your argument:

  1. You seem to be assuming that cancer treatment has made great strides since 1970. Actually it hasn't. I can understand how you'd get the impression that it has, because that's the relentless PR drumbeat of the medical establishment. E.g., in my newspaper I see ads with healthy young people holding up notes on pieces of paper with messages like "Dear Cancer -- We are so over. -- Colleen." The message is that if you go to that particular hospital, they'll cure your cancer. Actually most cancers have pretty much the same prognosis today they did in 1970. The list of cancers that was incurable in 1970 and is curable today is extremely short. In many cases, all the new treatments do is give you an extra month of living in excruciating pain. Many people dying of cancer get treatment #1, which fails, then treatment #2, which also fails, and so on. By the time you get to treatment #3 or #4, essentially you're just a sacrificial animal being used to churn money through the healthcare industry.
  2. I never advocated ceasing research on cancer. I advocated changing the focus: more basic research and less rush-job attempts to find new treatments. If research had had the focus I'm advocating for the last 40 years, I claim that the state of the art in cancer treatment today would be *better* than it is, not worse.

The fundamental problem is that the practice of medicine is usually not sufficiently based on evidence. This is why we need terms like "evidence-based medicine." If you think about it, what would be the alternative? "Voodoo-based medicine?" "Prayer-based medicine?" "Wishful-thinking-based medicine?" The examples I quoted in the GP post (PSA, mammograms for young women, increased fiber) are all scientific hypotheses that were acted on first, and only later tested (and found to be false). But the power of wishful thinking is enormous, hence the effectiveness of the PR campaigns in convincing people that cancer has become a treatable disease since 1970.

Re:war on cancer, war on drugs (2, Informative)

Daniel Dvorkin (106857) | more than 4 years ago | (#31859788)

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 [cancer.org] (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:war on cancer, war on drugs (0)

Anonymous Coward | more than 4 years ago | (#31859592)

Both have taken much, much longer and accomplished much, much less than Nixon and his contemporaries anticipated.

I'm not sure you understand the motivation behind the war on drugs. It's about putting people you don't like in jail. For the most part back then it was hippies and blacks. It's also about protecting caffeine and alcohol providers. They did very well and it's still a success by those measures. Don't believe me? They why was the penalties for crack cocaine so much higher then regular cocaine? Best I can tell, it was always because rich white people didn't take crack.

It is not a code! There is no crack! (1)

RoadNotTaken (1702106) | more than 4 years ago | (#31852484)

World: please stop calling DNA sequences "codes" that can be "cracked". There is no encryption going on here and, if you really want to use that metaphor than what they're doing is not cracking (decrypting) the code, but determining its sequence. Sequencing 4 cancer genomes is an enormous achievement that will provide countless biological insights, but nothing was "cracked". I'm a biologist, but aren't there cryptographers out there that are annoyed by this terminology???

Re:It is not a code! There is no crack! (2, Informative)

RoadNotTaken (1702106) | more than 4 years ago | (#31852570)

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 [wikipedia.org] for amino acids and that was cracked by Khorana, Holley and Nirenberg in the '60s.

Re:It is not a code! There is no crack! (3, Interesting)

Anonymous Coward | more than 4 years ago | (#31853296)

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:It is not a code! There is no crack! (1)

MachDelta (704883) | more than 4 years ago | (#31853382)

Blame whoever came up with the term "codon" :)

Re:It is not a code! There is no crack! (2, Interesting)

RoadNotTaken (1702106) | more than 4 years ago | (#31853552)

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:It is not a code! There is no crack! (0)

Anonymous Coward | more than 4 years ago | (#31853192)

If you keep on cracking enough DNA codes, eventually you'll run into one that decrypts to "Bruce Schneier".

Re:It is not a code! There is no crack! (0)

Anonymous Coward | more than 4 years ago | (#31855162)

The word encoded does not mean it is "encrypted." Just as software is "coded", "DNA" is coded too. So the process of determining what gene is encoded how and has what meaning for an organism is really "cracking the code".

Re:It is not a code! There is no crack! (0)

Anonymous Coward | more than 4 years ago | (#31855938)

"and has what meaning for an organism..."

right. This is the part they're not doing.

Dawn (2, Insightful)

Monkey-Man2000 (603495) | more than 4 years ago | (#31852822)

"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. (2, Insightful)

geekmux (1040042) | more than 4 years ago | (#31852930)

"...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:Corruption will keep this at bay. (1)

Elyas (59360) | more than 4 years ago | (#31856156)

The rest of the world's government run health care programs are welcome to do something too....

I don't like this (0, Offtopic)

Profane MuthaFucka (574406) | more than 4 years ago | (#31854446)

My cock was so tiny before the tumor started growing down there. Now just as my dick was finally getting larger, they tell me they're going to cure me? Life is just not fair.

Exciting (1)

whong09 (1307849) | more than 4 years ago | (#31855010)

Even if this doesn't lead to any sort of treatment(which seems highly doubtful), it still has applications to cancer treatment and prevention. One thing that comes to mind might be to collect cells from a patient's body in various places and do a genome sequencing of these cells. Take that information and compare it to common cancer mutations and you've got a way to assess the risk of how likely someone is to develop cancer. Genetics is epic.

Stop mundane comments (0)

Anonymous Coward | more than 4 years ago | (#31855026)

Reverse engineering of DNA is one of the biggest challenges of humanity. That may open far more possibilities than just a few illness cures. For the moment, this reverse engineering is very coarse grain and focus mainly to identify most visible bugs like tumors.

Fundamental research like that will probably also produce unexpected discoveries and a better understanding of medicine. I hope a complete revolution of allopathic medicine.

What about a DNA simulator that would allow to test and debug DNA changes. That would be cool.

Hurrah for the rich (0)

Snaller (147050) | more than 4 years ago | (#31855554)

Who can now be cured - whilst the poor and stuff it.

WTF (0)

hesaigo999ca (786966) | more than 4 years ago | (#31856094)

So you think you get some applause because you found out the mapping to the tumors and how to grow, ....here you go /claps...
no stop trying to stall and make all the pharmaceuticals more money and give us the cure already.....I bet if we had a higher rate of cancer, they would go just a little faster....yet when there is enough of us to go around, they take their time and think they can make some extra money on the side while making us wait.

Anyone trying to mod me down, will get cancer....and make the pharmaceutical companies more money.

Meanwhile in prevention world... (1)

Hurricane78 (562437) | more than 4 years ago | (#31858614)

...nobody cares for it to not happen in the first place. At all.
While we still live in toxic shit, wear toxic shit, breathe toxic shit, eat toxic shit, and put toxic shit on our skins, as if that were the most normal thing in the world to do.
And big pharma plus all the doctors make a nice profit off of it.

Sorry, but we as a species, deserver cancer for that extreme horrible ignorance of ours.

I'm skeptical of reiteration. (1)

StikyPad (445176) | more than 4 years ago | (#31860418)

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.

I'm pretty sure that 'infancy' and 'dawn' are analogies for the same concept... Now if they had said "cancer is history," you might have a point.

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