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Scientists Crack 'Entire Genetic Code' of Cancer 235

Posted by samzenpus
from the whole-tumor dept.
Entropy98 writes "Scientists have unlocked the entire genetic code of skin and lung cancer. From the article: 'Not only will the cancer maps pave the way for blood tests to spot tumors far earlier, they will also yield new drug targets, say the Wellcome Trust team. The scientists found the DNA code for a skin cancer called melanoma contained more than 30,000 errors almost entirely caused by too much sun exposure. The lung cancer DNA code had more than 23,000 errors largely triggered by cigarette smoke exposure. From this, the experts estimate a typical smoker acquires one new mutation for every 15 cigarettes they smoke. Although many of these mutations will be harmless, some will trigger cancer.' Yet another step towards curing cancer. Though it will probably take many years to study so many mutations."
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Scientists Crack 'Entire Genetic Code' of Cancer

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  • Benign (Score:4, Funny)

    by Smivs (1197859) <smivs@smivsonline.co.uk> on Wednesday December 16, 2009 @07:19PM (#30466960) Homepage Journal

    I didn't use to like skin cancer, but it grows on you

  • Powers (Score:5, Funny)

    by sakdoctor (1087155) on Wednesday December 16, 2009 @07:20PM (#30466980) Homepage

    Although many of these mutations will be harmless, some will trigger cancer

    And some will give you super powers.

    • Re: (Score:3, Funny)

      Good luck with that. I smoked 45 cigarettes yesterday and all I got was fast metabolism 1, deformed body 1, and teleportitis without TC.
      • by nmb3000 (741169)

        and teleportitis without TC.

        Oooh, I remember when Lieutenant Barclay got that. Pretty nasty stuff.

        Just have them coalesce your pattern through the transient bypass buffer a few times. That should sort you out.

  • by Thagg (9904) <thadbeier@gmail.com> on Wednesday December 16, 2009 @07:21PM (#30466992) Journal

    What does it mean that melanoma has 30,000 errors in the DNA? Is it that the one melanoma they looked at had 30,000 differences from the other cells in the patient's body? It appears that, far from finding the needle in the haystack, they've found 30,000 haystacks.

    • Re: (Score:3, Interesting)

      by Anonymous Coward

      The breakthrough isn't in the results, it's in the technique. They're developing new methods and software to perform this sort of analysis faster and faster. That's what's big about this work. They can now do a very difficult task much more rapidly than before.

    • Re: (Score:3, Interesting)

      by johncadengo (940343)

      I have very little background in this area. But I'm curious. If skin cancer is caused by exposure to the sun, then it must be different for each patient? Because it's cause isn't inherited it seems to me that each patient with skin cancer has a unique and individual genetic cause to their skin cancer. Something akin to snow flakes. Perhaps once they find the absolute minimum change within the genes of an otherwise healthy human to having skin cancer, headlines can claim that scientists "crack entire genetic

      • by izomiac (815208) on Wednesday December 16, 2009 @08:28PM (#30467634) Homepage
        That's pretty much on target. UV light is absorbed by DNA, and it causes changes like Thymine-Thymine dimers (ATCG are DNA bases, a T-T dimer is when two adjacent T's on the same strand bind to each other). Cells have DNA repair mechanisms, some of which are accurate, others of which are not. If the repair is inaccurate you have a mutation in a semi-random location (needs something like two adjacent thymines, and it probably needs to not be in it's condensed storage form). A mutation in each of about 8 genes that control the cell cycle will lead to uncontrolled replication and further mutation. Certain types of cells are vulnerable to different things, and require certain genes to be knocked out (or overexpressed) to form certain types of cancer. It's all very random, but there are trends within each type of cancer (hence its behavior).
      • by PRMan (959735)
        Ah, but it is somewhat inherited, because pasty white boy is far more likely to get cancer than ultra-dark black man, because his melanin doesn't block the sun and lets more mutations happen.
        • by RDW (41497) on Wednesday December 16, 2009 @09:07PM (#30468008)

          In these particular studies, they're only looking at 'somatic mutations' (mutations confined to the tumour, and not found in the patient's normal cells). Anything they inherited that might have made them susceptible to cancer in the first place gets 'cancelled out' by comparing the tumour DNA to normal DNA (e.g. from blood). You have to do a different type of study to find susceptibility genes, e.g. by using a large collection of 'normal' DNA samples from a population and collecting their medical data. Right now, this is being done at a relatively low resolution using 'SNP arrays' that usually only look at a few hundred thousand DNA bases (a few million max). But because of genetic linkage, this can still give you very useful information about where the important genes are. When the genome sequencing technology gets _really_ cheap, we can except this sort of study to be done by sequencing too.

      • by RDW (41497) on Wednesday December 16, 2009 @08:52PM (#30467862)

        It's true that each patient is extremely likely to have a unique 'cancer genome', a specific combination of mutations found only in their tumour. But the vast majority of these will be 'passenger' mutations that aren't relevant to the progress of the tumour. The trick, as you suggest, is to home in on the 'driver' mutations that are really causing the disease. One way to get at these is to look first at the mutations in the coding sequences of known genes (and because of the human genome project and all the work that's followed it, we pretty much know where all the protein-coding genes are located).

        I just had a quick look at both papers, and it turns out that in the lung cancer case, fewer than 100 of the tens of thousands of mutations actually cause an amino acid change in a protein sequence (for the melanoma, the figure is less than 200). This doesn't mean that there aren't other interesting needles to find in the haystack of mutations (e.g. changes in regulatory sequences), but they might as well go after the 'low hanging fruit' first. With current technology, it's very easy to sequence 100-200 genes in a pretty large set of samples from different patients. Any of these genes that turn out to be mutated in multiple tumours immediately become subjects for further study.

        As the technology starts to ramp up and gets cheaper every year, we can begin to go after the less obvious changes. Each of these studies is in effect an entire human genome project (they haven't just done a low resolution map, they've completely sequenced the genomes). Pretty soon we're going to have a large collection of sequenced tumour samples to compare and use to find common alterations.

      • Common damage (Score:5, Interesting)

        by AlpineR (32307) <wagnerr@umich.edu> on Thursday December 17, 2009 @07:27AM (#30472124) Homepage

        If you fire a rifle at a running car, it might survive several shots and still keep running. Some of the shots go through the windows, some through the doors, and some just bounce off the pillars. But some shots could poke holes in the body and leave underlying parts exposed. Then further shots might puncture the gas tank or the radiator. A little less likely, shots might break the fuel pump or electric distributor. And just maybe a shot will interrupt the ignition circuit.

        Even though any particular car's damage will be unique, the damage that made cars stop running will be common. Most will involve the gas tank or radiator. And a few will involve smaller parts.

        A study like this is looking for those major parts which are likely to be damaged in cancer cells. It might also reveal common patterns of damage which disabled protective mechanisms and left those key part vulnerable. Then you might have an idea of how to detect critical damage, how to repair subcritical damage, how to armor critical areas, and how to completely disable malfunctioning cells.

    • by ceoyoyo (59147) on Wednesday December 16, 2009 @07:35PM (#30467116)

      I suspect they looked at tissue from a bunch of melanomas and have generated data showing where they differ from normal samples.

      But 30,000 errors in the DNA doesn't mean those cells were exposed to 30,000 mutating events (the 1 for every 15 cigarettes or whatever). Generally what happens is that a cell gets mutations in a few critical locations and then subsequent issues during cell division do dramatic damage to the genome.

      • by nacturation (646836) * <nacturation AT gmail DOT com> on Wednesday December 16, 2009 @08:49PM (#30467820) Journal

        But 30,000 errors in the DNA doesn't mean those cells were exposed to 30,000 mutating events (the 1 for every 15 cigarettes or whatever).

        Enough of your logic. You're upsetting the smokers who want to believe that as long as they smoke less than 450,000 cigarettes they won't get cancer.

    • by ColdWetDog (752185) on Wednesday December 16, 2009 @07:36PM (#30467118) Homepage

      Is it that the one melanoma they looked at had 30,000 differences from the other cells in the patient's body? It appears that, far from finding the needle in the haystack, they've found 30,000 haystacks.

      Not quite. It's more like they ** think ** they've found a map to the 30,000 needles in a single haystack and they hope that the haystacks (individual humans) are similar enough that they can generalize a bit on how to find the other needles in other haystacks.

      FTFAbstract:

      All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.

      The researchers state (and I haven't really had time to look at the article) that they have identified all, or at least the vast majority, of mutations from a single cancer and furthermore have managed to characterize (see above) the mutations. Other researchers have done similar research for other cancers. The idea is that, after all of this information is digested, somebody can use this knowledge to figure out better treatments for cancers. Of course, this remains to be seen. It's reasonable but by no means certain. The babble at the end of the BBC article is typical hyperbole.

      • Re: (Score:3, Interesting)

        More importantly, since they've shown that they can apply this technique (it's not really specified, but I'm assuming it's whole genome sequencing) and applied it to one patient, there's nothing stopping them (except money) from applying this to other patients with the same condition. Maybe a different patient has 25,000 mutations, maybe another has 27,000, etc. Chances are these mutations are not all going to be affecting the same sequence positions in all the different patients. If they can find mutations

    • by moogied (1175879)
      Cancer is basically when your cells are broken and are spawning hellish death cells to kill you. These cells 'break' when they mutate. Errors in the DNA has long been assumed as the cause of the cells turning to cancer, so if they found 30k errors in the DNA of melanoma VS standard issue skin cells.. and that one of those 30k errors may be causing cancer. Yes, it is like finding 30k haystacks... however its better then the infinite # of haystacks we had before.
      • by sevennus (1702060) on Wednesday December 16, 2009 @07:45PM (#30467214)
        Remember, it takes three events for a cell to become cancerous. 1. It must mutate to be able to express appreciable amounts of telomerase. 2. It must mutate in such a way that it circumvents its apoptosis (self-destruction) checkpoints. 3. It must mutate in such a way to allow constitutive, amplified replication. True, there are probably a gazillion different combinations of different mutations that can cause allow all of these things to happen, but I'm pretty sure it can't be caused by ONE mutation. But it's just my first post, so don't take my word for it.
    • Re: (Score:3, Interesting)

      by AdmiralXyz (1378985)
      Not necessarily. If they can find a protein corresponding to one of these mutations that is not produced in a healthy cell: presto, instant cancer test.
    • by DebateG (1001165) on Wednesday December 16, 2009 @10:26PM (#30468572)

      So I work in biological sciences, and I have the special privilege of having the guy who sequenced the first cancer genome working down the hall from me (he's also my thesis committee).

      There is now technology to sequence entire genomes very quickly using massive parallel sequencing. Ideally, if you were sequencing a tumor from a single person, you would get tissue from the tumor and also from the non-tumor (usually skin) and sequence them at the same time. Then you compare the two to distinguish what is simply variation in each person's genetics and what is acquired by the tumor. In my opinion, that's the best way to do things and probably the most informative because you're looking a tumor in a real person that is subject to all the selective evolutionary pressures that occur in people.

      These groups didn't take that approach for reasons unclear to me. Instead, they sequenced cancer cell lines. If you cut out a person's tumor and stick it in a test tube with various growth factors, it will almost certainly die within a week or so. However, you occasionally get some cells that can grow in this situation because they've acquired some mutation that lets them grow in tissue culture. You then expand and passage these cells until they grow rapidly in culture. The problem here is that you're no longer dealing with a normal human tumor; you're selecting for tumor cells that grow in the artificial tissue culture environment. The second problem is that you're not sure what to compare the tumor sequence with. Due to privacy concerns, you almost never know who actually gave the tumor that was made into a cell line (as an aside, look up the HeLa cell line and its sordid history) so you have to compare to the human genome project. The problem here is that there are differences between people and you can't tell whether the "mutation" you see is just a normal variation or actually something in the tumor.

      These are the important limitations you have to consider when evaluating these papers.

      Now, on to your question. They have 30,000 changes in the DNA compared to their reference "normal" genome. Nearly all of those are in "junk" DNA: as far as we know, they don't code any genes or anything else that regulates genes. Of the ones that are in interesting regions, the vast majority of them are called synonymous mutations which means the DNA is changed but due to the way it is interpreted, the protein that it makes is identical (to use a computer analogy, imagine that an the opcode for JMP was changed from 01 to 02 but both 01 and 02 are translated by the computer as JMP).

      Now, a certain number of mutations aren't like that. They either lead to truncated proteins, alter the amino acid sequence of proteins, alter mRNA splicing, etc. There are also other genetic changes such as duplications where the gene sequence is unchanged but may be copied several times to increase the gene dose. These are really the interesting things because they alter protein function or gene dose. From a brief reading, it looks like there are around 100 of these.

      Now, it's really difficult to tell whether these mutations are really relevant to cancer progression. Some of them might just happen due to tumors just mutating really fast and not really affect the cancer progression one way or another; they are so called "passenger" mutations that just come along for the ride. You can introduce these mutations into cells in lab to see if they do anything, but the real test is to sequence a bunch of human cancers and see if certain mutations are recurrent. This work is currently underway and will prove very informative about how genetically heterogeneous tumors really are.

      So, in short, there are about 100 haystacks. Further sequencing of other tumors will show if these are relevant to cancer in general. In my personal opinion, I think that further sequencing will identify very few common mutations and everyone's cancer will be essentially unique in the mutations it acquires. That will force us to completely rethink how we view cancer on a broader scale as not a single disease but a collection of highly related diseases that need to be treated individually.

      • There is now technology to sequence entire genomes very quickly using massive parallel sequencing.

        How's that on the cheap/fast/good criteria? Is it feasible to sequence individual, non-millionaire, patients yet?

        • Re: (Score:3, Informative)

          It costs on the order of $10k to sequence a single genome. But you wouldn't do it for every cancer patient. Instead, you'd do it for a couple hundred cancer patients, and study the results. You'd hope to find a few dozen common mutations which indicate which treatment to use. Checking a cancer for a few dozen known marker genes is considerably easier than sequencing an entire genome.

  • Patent? (Score:4, Insightful)

    by innocent_white_lamb (151825) on Wednesday December 16, 2009 @07:23PM (#30467008)

    I wonder if they will patent this so everyone who develops a treatment using techniques discovered here must cough up a royalty?
     
    Why are patents allowed on naturally occurring phenomena like genes anyway?

    • Re: (Score:2, Funny)

      by speedingant (1121329)
      If it's lung cancer, they'll be coughing up more than just a royalty. Badom-pish!
    • by langelgjm (860756)

      Why are patents allowed on naturally occurring phenomena like genes anyway?

      That's just it, though - the patent is granted for the isolation, refinement, or modification of the gene. The issue is what is considered 'naturally occurring.' Chemical composition patents are granted based on the assumption that the composition isn't just sitting around and easy to get at.

      The policy question is whether just protecting the process used to isolate something is enough, rather than protecting the actual thing itself.

    • Re:Patent? (Score:5, Interesting)

      by AdmiralXyz (1378985) on Wednesday December 16, 2009 @07:59PM (#30467358)

      Why are patents allowed on naturally occurring phenomena like genes anyway?

      I've read interviews with multiple government and legal officials, whose basic point seems to be that patents on genes are a "necessary evil", because research into genomics is really, really, really expensive, and without patents + licensing fees giving biotech firms some way to recover some of their investment now (as opposed to ten years down, when drugs based on their discoveries could conceivably come to market), no businessperson would even think of throwing his money at that kind of research. According to them, without patents, there would be no research and progress in this field whatsoever.

      I'm not saying whether or not I agree with that, but that's the way it is.

      • Re:Patent? (Score:5, Insightful)

        by BiggerIsBetter (682164) on Wednesday December 16, 2009 @08:57PM (#30467906)

        This sort of thing should probably be done by academia or government then. Progress for the greater good doesn't have to be commercially driven.

        • Or, you could leave it up to the private sector with a few caveats. For one, once a patent holding corporation recoups the investment costs (plus a profit margin), the patent is rendered null and void.

          Basically, give the private sector enough incentives to allow capitalism to fulfill its primary role while at the same time not hinder the common good of everyone else.

          • Seriously, what you are suggesting is ether unreasonable; recoup direct investment costs only, or; basically, the regulated utility model, where you could turn a profit by redecorating the presidents office and old investments where never called failures or obsolete, just run forever (and ever and ever) with guaranteed ROI.

            You've heard of the floating break-even? (Hollywood accounting) Do you really want to inflict that on R&D? That's the first obvious unintended consequence.

            As long as patents don'

        • by khallow (566160)
          I don't buy the claim that gene patents are necessary, especially since they won't be honored by a number of competitors. There's a lot of money here for private firms to get interested. That seems good enough to me.
        • The problem is that a lot of the research within academia and government is being done for corporations or by corporations.
          Did you see that little commercial with the man with the funny ? suit saying there's free government money.
          Well I can tell you most of it goes to corporations or companies where they do the research.
          The thing about the research is that the company doesn't have to divulge everything they found to receive the money.
          All they have to do is show that they tried. In the mean time they ma
        • by westlake (615356)

          This sort of thing should probably be done by academia or government then. Progress for the greater good doesn't have to be commercially driven.

          But it does have to be adequately funded.

          Here is an example of a small scale project that has the potential to reap significant benefits. But it still costs $5 million - and there are hundreds - and more likely thousands - of projects no less deserving.

          The Bill and Melinda Gates Foundation has awarded a $5 million research grant to a Hebrew University of Jerusalem

      • Re: (Score:3, Interesting)

        by tg123 (1409503)

        Why are patents allowed on naturally occurring phenomena like genes anyway?

        .......no businessperson would even think of throwing his money at that kind of research. According to them, without patents, there would be no research and progress in this field whatsoever.
        I'm not saying whether or not I agree with that, but that's the way it is.

        The reality is business people / drug companies do not invest in drug research period.

        Business investment tends to goes into marketing the drug its the university's and research institutes that do the drug research.

        http://www.uab.edu/reynolds/MajMedFigs/Index.htm [uab.edu]

      • I'm not saying whether or not I agree with that, but that's the way it is.

        No, it is not. Research is expensive, but a lot of that is already paid for by taxes. Furthermore, the resulting medicines are themselves very profitable and expensive, and a lot of that profit is, again, derived from the government.

        Additionally, market forces aren't working: profitable drugs (the ones drug companies have an incentive to develop) are not the drugs that people actually need. Drug companies love to develop drugs that

    • I wonder if they will patent this so everyone who develops a treatment using techniques discovered here must cough up a royalty?

      Why are patents allowed on naturally occurring phenomena like genes anyway?

      The genes aren't patentable. The methods they developed probably are. Patents are there to provide incentive for the research to take place at all. There may be some problems on how long patents last and process issues, but fundamentally they are supposed to provide incentive to invest in research and science.

      • by Telephone Sanitizer (989116) on Wednesday December 16, 2009 @08:49PM (#30467818)

        > The genes aren't patentable.

        Tell that to Monsanto. If the genes from their GE plants turn up in a farmer's soy crop, he's in for hell even if they just drifted over as pollen from neighboring fields.

        In the United States, patents protect not just the device or technique, but also the product of it. Thus, those who patent techniques for isolating genes also have patent-protection for the genes, themselves. Patents do not ordinarily cover "products of nature," but when something exists in a lab in "purified" form, it's exempted from this limitation. http://www.ornl.gov/sci/techresources/Human_Genome/elsi/patents.shtml [ornl.gov]

        Here's what Monsanto does with their patents:
        http://www.commondreams.org/headlines05/0115-04.htm [commondreams.org]

        Under U.S. patent law, a farmer commits an offense even if they unknowingly plant Monsanto's seeds without purchasing them from the company. Other countries have similar laws.

        In the well-known case of Canadian farmer Percy Schmeiser, pollen from a neighbor's GE canola fields and seeds that blew off trucks on their way to a processing plant ended up contaminating his fields with Monsanto's genetics.

        The trial court ruled that no matter how the GE plants got there, Schmeiser had infringed on Monsanto's legal rights when he harvested and sold his crop. After a six-year legal battle, Canada's Supreme Court ruled that while Schmeiser had technically infringed on Monsanto's patent, he did not have to pay any penalties.

        Schmeiser, who spoke at last year's World Social Forum in India, says it cost 400,000 dollars to defend himself.

        "Monsanto should held legally responsible for the contamination," he said.

        Another North Dakota farmer, Tom Wiley, explains the situation this way: "Farmers are being sued for having GMOs on their property that they did not buy, do not want, will not use and cannot sell."

        • by hedwards (940851)
          That's not entirely true. Chemical patents are process or molecule, not both. And in this case you couldn't patent the gene sequence to begin with since it's a matter of discovery rather than creation.
        • > The genes aren't patentable.

          Tell that to Monsanto. If the genes from their GE plants turn up in a farmer's soy crop, he's in for hell even if they just drifted over as pollen from neighboring fields.

          In the United States, patents protect not just the device or technique, but also the product of it. Thus, those who patent techniques for isolating genes also have patent-protection for the genes, themselves. Patents do not ordinarily cover "products of nature," but when something exists in a lab in "purified" form, it's exempted from this limitation. http://www.ornl.gov/sci/techresources/Human_Genome/elsi/patents.shtml [ornl.gov]

          I think you're deliberately misunderstanding a patented product produced by genetic manipulation so that you can introduce a completely unrelated topic.

          Genes are not patentable. Products created through genetic manipulation are. Processes by which damaged genes can be identified are. Genes themselves are not.

          • Re: (Score:3, Informative)

            I think you're deliberately misunderstanding a patented product produced by genetic manipulation so that you can introduce a completely unrelated topic.

            Genes are not patentable.

            Sequences of genes are patentable.
            http://en.wikipedia.org/wiki/Gene_patent [wikipedia.org]

            Many of the farmers sued by Monsanto have never used Monsanto seed and never had Monsanto seeds end up in their fields.

            Often, GE pollen crosses a few fields and contaminates neighboring farms. Monsanto's agents do (sometimes illegal) spot-checks and discover that a farmer's crop contains genes from the Monsanto seeds and then they sue to confiscate the entire crop or to force the farmer to incinerate his fields as an infringer.

            It is n

    • Re: (Score:3, Insightful)

      by joocemann (1273720)

      I wonder if they will patent this so everyone who develops a treatment using techniques discovered here must cough up a royalty?

      Why are patents allowed on naturally occurring phenomena like genes anyway?

      Both are good questions. And to the latter, I would say it is likely because most of our peers, politicians, and people involved in everything we do in life, do not understand these specific things to any degree to which they can make better INFORMED decisions about them. Most people don't understand what is going on in most sciences, but develop opinions on it anyway; in turn, we shape our cultures and politics in a somewhat similar form (yes, the corps will influence politics heavily with their lobbying

    • Re: (Score:2, Insightful)

      The ICGC's policies and guidelines are very specific, http://icgc.org/icgc_document/policies_and_guidelines/ [icgc.org] "The objective of ICGC policy regarding intellectual property (IP) policy is to maximize public benefit from data produced by the Consortium. It is the view of the ICGC members that this goal is achieved if the data remain publicly accessible without any restrictions."
  • Better yet (Score:4, Interesting)

    by MrEricSir (398214) on Wednesday December 16, 2009 @07:23PM (#30467018) Homepage

    Maybe we can make cigarettes that don't cause cancer.

    • by FooAtWFU (699187)
      Like this?* [google.com]

      * (possibly perhaps maybe)

    • Re: (Score:3, Insightful)

      Pretty much anything that involves inhaling delicious incomplete-combustion products is bound to be a bad plan(it doesn't get the anti-drug crusaders upset, so nobody really cares; but chronic inhalation of the smoke from nasty little heating/cooking fires in the unventilated shacks of the developing world causes enormous morbidity and mortality [who.int]). Outside the chem101 and/or very carefully tweaked laboratory world of perfect hydrocarbon combustion into carbon dioxide and water vapor, breathing combustion pro
      • On the plus side, if you just want to deliver nicotine, we have plenty of ways to do that, in pretty much any quantity and release curve you fancy, with health risks no greater than those imposed by the nicotine directly.

        Nicotine is only a small part of the addiction, though. The crinkle of the wrapper, the smell of the pack, the logo on the carton, the mouth feel of the cigarette, the paling around with smoke buddies, and, of course, smoking, are all significant. Straight nicotine probably isn't enjoyabl

  • I for one welcome our cure for cancer finding overlords.

    Both my parents died from it and I suspect I probably will too. Or maybe not if they can find a cure.

  • by Meshach (578918) on Wednesday December 16, 2009 @07:26PM (#30467040)
    Interestingly the article seems to only reference "preventable" cancers:

    The scientists found the DNA code for a skin cancer called melanoma contained more than 30,000 errors almost entirely caused by too much sun exposure. The lung cancer DNA code had more than 23,000 errors largely triggered by cigarette smoke exposure.

    Hopefully this will lead to treatments for other cancers as well.

    • Re: (Score:3, Informative)

      by RDW (41497)

      They started off with a couple of common cancers, but the plan is to do many more:

      http://www.sanger.ac.uk/about/press/2008/080429.html [sanger.ac.uk]

      'The ICGC will identify a list of approximately 50 cancer types and subtypes that are of clinical significance around the globe, aiming to study cancers of all major organs, including breast, ovary, prostate, lung and blood cancers...All the data generated will be made rapidly and freely available to the global research community. '

      • by sznupi (719324)

        Though it would seem more tactful to go first with cancers that are also common, but as far as we can tell essentially "random", with no good working tips @prevention.

  • Comparison (Score:3, Insightful)

    by Jkasd (1663231) on Wednesday December 16, 2009 @07:30PM (#30467084)
    It seems that they should do this with cancer cells from several different patients and compare them to find out which mutations actually trigger the cancer.
    • by RDW (41497)

      'It seems that they should do this with cancer cells from several different patients and compare them to find out which mutations actually trigger the cancer.'

      Believe it or not, they have thought of this! An international consortium has been set up to use exactly this technology on a really large scale. See e.g.:

      http://www.sanger.ac.uk/about/press/2008/080429.html [sanger.ac.uk]

      'Each ICGC member will conduct a comprehensive, high-resolution analysis of the full range of genomic changes in at least one specific type or sub

  • Hacking would be to add or change something on that code on a original but cheap way to produce a practical result. Chop chop.. hack hack.

    The article sounds more like deassembling the code. but IANGE.

  • by WhiskerBiscuit (811421) on Wednesday December 16, 2009 @07:45PM (#30467216) Homepage
    Cancer cells start accumulating mutations as a consequence of rapid cell division and poor quality control on DNA replication; they also have problems keeping their chromosomes intact. This is called "genomic instability" and it is a hallmark of cancer.

    The critical point here is that most of these mutations are acquired *after* the cancer gets going, regardless of whether the mutagen in question is still being administered.

    Therefore, it's not proper to infer a linear relationship between the dose of mutagen and the number of mutations.

    Beyond that, the numbers involved in that extrapolation seem to have been pulled out of thin air, and I question whether they knew the smoking history of the individual who donated the material that created that cell line. (The lung cancer in question had 30,000 mutations, so by their logic the smoker must have smoked 345,000 cigarettes, or 17,250 packs of 20. That's a pack a day for 47 years, which is admittedly within the bounds of possibility, but still an awful lot of smoking.)

    Whatever. Smoking is still awful for you, but this kind of nonsensical extrapolation without regard to detail is terribly annoying.

    • I agree. Most confusing summary.

      Are they saying that all 30,000 mutations are the DIRECT result of exposure to sunlight, or are they saying an initial mutation caused by sunlight exposure was then multiplied by cell division/replication?

      If it was the first case, how did they determine the cause of each mutation? If it was the second case, the question still remains--How did they determine the cause of ANY of these mutations?

      "Whatever. Smoking is still awful for you, but this kind of nonsensical extrapolatio

  • It's exhilarating to see such visceral confirmation of the superior efficiencies of free market capitalism. If the scientists working for this cancer research corporation didn't have the profit motive behind them, who knows how long it would have taken for them to reach this point in their research, that is, if the project had even gotten off the ground at all!
    • Is this poster savagely mocking the Randroids and Glibertarians that infest /., or is he one of the Randroids and Glibertarians that infest /.?

      "It's exhilarating to see such visceral confirmation of the superior efficiencies of free market capitalism. If the scientists working for this cancer research corporation didn't have the profit motive behind them, who knows how long it would have taken for them to reach this point in their research, that is, if the project had even gotten off the ground at all!"

  • by thetoadwarrior (1268702) on Wednesday December 16, 2009 @08:02PM (#30467380) Homepage
    Cancer will be issuing a DMCA take-down notice and sue the pants off the scientists for cracking its code.
    • Under the new ACTA agreement, this is considered to be an international act of mass genocide. But before they get tried for that, they'll be sued one million dollars per Human Genome End-User License violation (you'll learn more about that when the time comes) - somewhere around 6.8 quadrillion dollars - by the Pharmaceutical Industry Association of Earth (again...you'll find out about that later).

      Remember, the PIAE only wishes to protect your rights as a Human Genome licensee from those who wish to unde
  • you can smoke 344,999 cigarettes and not get cancer but if you smoke just one more BAM! CANCER!
    I know it doesn't but the article kinda hints at that.
    Wouldn't it be great though if it was that precise.
    15 cigs = 1 DNA error
    23,000 errrors = CANCER
    15 Cigs X 23,000 = 345,000 cigs
    345,000 Cigs = Cancer
    Average life span ~67 years
    If you start smoking at 18 that's ~17,897 days till your dead anyway
    So you can have 19 Cigarettes a day.
    Hey cigarette companies I think I have a new marketing campaign for you. You
  • by scapermoya (769847) on Wednesday December 16, 2009 @08:18PM (#30467556) Homepage
    I just completed an intensive undergraduate course on cancer with a focus on genetics at UC Berkeley. We spent a significant amount of time on cancer genomes, and I have to say this announcement doesn't mean that much unfortunately. Cancers are genetically very unstable, and any given tumor you sequence will have many mutations that are completely unrelated to the cancer's survival and proliferation. they are known as passenger mutations, and need to be separated from the causative 'driver' mutations. sequencing many tumors of the same type and applying statistical analysis has been useful in this area, but considering that there are potentially millions of different combinations of active and inactive genes that lead to tumor formation, this approach has its limitations. this is especially true given that some genes are both tumor suppressors and tumor activators in different contexts (eg the TGF-b pathway). even if you identify a genetic locus as highly associated with a particular cancer, it is hard to go from there to understanding the molecular biology behind that association.

    we have a long way to go before we defeat cancer, and sequencing can only take us so far.
  • "The scientists found the DNA code for a skin cancer called melanoma contained more than 30,000 errors almost entirely caused by too much sun exposure."
    This is obviously such a ridiculous statement that I'm surprised it made it into the BBC article.
    Show me the evidence that almost 100% of DNA errors in skin cells or skin cancer cells are caused by sun exposure...

    • Re: (Score:3, Informative)

      by RDW (41497)

      'Show me the evidence that almost 100% of DNA errors in skin cells or skin cancer cells are caused by sun exposure...'

      Not 100% perhaps, but from the paper:

      'DNA damage due to ultraviolet light leads to the formation of covalent links between two adjacent pyrimidines. Consequently, C>T mutations due to ultraviolet light usually occur at dipyrimidine sequences. Therefore, to evaluate further the role of ultraviolet light in the pathogenesis of somatic mutations in COLO-829, we examined the sequence context

  • by xrayspx (13127) on Wednesday December 16, 2009 @08:40PM (#30467740) Homepage
    One of the things driving me when I began the quitting process was that my back of the napkin math showed I had smoked in the area of 148,000 cigarettes. I had a hard time putting that in terms of anything else. I couldn't compare it to any other non-reflexive thing. I haven't signed my name 148,000 times, or tied my shoes. What have I done 20+ times per day for 20 years?

    Now I learn that that means I have 10,000 cell mutations on top of that. Neato. Of course, 10,000 cells is kind of a drop in the bucket compared to the inner surface of my airway.

    To smokers: Please note his does not mean that I'm not still hopefully addicted to nicotine. Now it just comes in the form of Cherry Commit Lozenges [commitlozenge.com]. They work pretty OK. I've had maybe 1 cigarette per month for the last 5 months.

    On the other hand, I miss that I no longer look cool.
  • If this is true, does that not mean (by cause and affect) that there is a provable direct relation between cigarette smoking and cancer? Would that not indicate that a lawsuit is in order?
  • Misleading title... (Score:5, Interesting)

    by hahn (101816) on Wednesday December 16, 2009 @09:10PM (#30468044) Homepage
    Saying they've "cracked" the code to these two cancers (skin and lung) is not really as big a step as the title implies. They've found the genetic mutations associated with the cancers. That's probably the easy part (and it wasn't so easy). The problem in studying cancer is that the function of genes is often dynamic and interdependent. Think of a room with 30,000 light switches. Sometimes light switch #5 will turn on the light bulb, but sometimes it won't. It depends on whether light switch # 7, 100, and 10542 are all on simultaneously or not. And if switch #2742 is on, the light, if it's on, will be very dim. This why even though we give a cancer a single name - e.g. "melanoma" - there are often very different mutations present, any one or multiple ones which can affect the person's survival, but not necessarily all the time. There are cancers which reliably result from single mutations, but the most common ones are due to mutations in many many different genes. To the point that most cases of cancer can or should be considered unique.

    IMHO, where I think the results of these studies may be most helpful with regards to treating people successfully is figuring out which mutations cause the cancer to spontaneously regress [nih.gov], whether it's by self-destruction or immune mechanisms. Even then, maybe it's not even because of a cancer mutation. Maybe some people possess some genetic trait in their immune system that allows them to destroy cancers. In which case, too many people would be looking in the wrong haystack for a needle.
  • "the experts estimate a typical smoker acquires one new mutation for every 15 cigarettes they smoke."

    I will now become a heavy smoker in hopes of gaining X-Men-like superpowers.

  • by reboot246 (623534) on Wednesday December 16, 2009 @09:26PM (#30468170) Homepage
    After much research and thought, I've come to the conclusion that white mice actually cause cancer.
  • Michael Chin (Score:2, Interesting)

    One of the reasons why slashdot is good is because its readers tend to be aware of the state of the technology. Thanks commenters for precise answers to some very stupid genetic advertising. And yes, skin cancer grows on you....:D
  • by CuteSteveJobs (1343851) on Thursday December 17, 2009 @02:34AM (#30470378)

    Though the story is newsworthy, this has the misleading title of the century. They didn't unlock it. They sequenced it. There's a big, big difference. It's the difference between having a map of South America and doing Sharon Stone on the throne of the Lost City of Gold.

    http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/sequencing.html [umich.edu]

  • by Hrshgn (595514) <rince2001 AT gmx DOT ch> on Thursday December 17, 2009 @05:48AM (#30471564)
    Nature has a nice summary of the original research paper published in the same journal: http://www.nature.com/news/2009/091216/full/news.2009.1143.html [nature.com]

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