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First Whole Cancer Genome Sequenced 115

Posted by timothy
from the gee-gnome-sounds-like-a-good-open-source-project dept.
dooling writes "A paper detailing the sequencing of the first human cancer genome will be published in the 6 November 2008 issue of Nature. This is not only the first cancer genome published, it is the first female genome as well. You can read the paper's abstract, DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome, or the story in Science News. This issue of Nature also has articles on the sequencing of the first African and Asian genomes. The sequencing in all three articles was done using the Illumina Genome Analyzer, one of the massively parallel, next-generation genome sequencing platforms."
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First Whole Cancer Genome Sequenced

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  • by Anonymous Coward

    Remember northern blots? Remember how real time PCR and microarrays blew them out of the water? Next gen sequencers take those, divide them by zero in a black hole and kick Chuck Norris' ass 9 ways from Sunday.

  • by syousef (465911)

    This pains me to say - a couple of friends of the family have been diagnosed with cancer- one very dear to me and with limited time to live, the other a very decent man and doesn't know his chances yet.

    I can't help but think that cancer is acting as a brake on the population explosion. If we cured cancer tomorrow these people who are dear to me wouldn't suffer, but we'd be even less sustainable and eventually we'd see wide spread poverty and famine. So the question becomes: If we do gather the knowledge we

    • by CrimsonAvenger (580665) on Wednesday November 05, 2008 @07:51PM (#25653375)

      I can't help but think that cancer is acting as a brake on the population explosion.

      Umm, no.

      Cancer, in general, happens to people well past the age of reproduction. Which means it has little, if any, effect on population growth rates.

      If there are diseases you'd like to keep around to prevent overpopulation, may I suggest lobbying to return Smallpox to the wild instead? Or just become a pro-AIDS activist, since the latter seems to be doing a good job of cutting into African population growth.

      Seriously, some of you people scare me....

      • by CriX (628429) on Wednesday November 05, 2008 @08:01PM (#25653513)

        Seriously?

        People that are no longer able to reproduce still consume resources and are definitely still considered part of the population. The point is that if you curb dieoff you are contributing to population growth.

        • by MadAhab (40080) <slasher@@@ahab...com> on Wednesday November 05, 2008 @08:14PM (#25653717) Homepage Journal

          But at most linearly, and not much - because of increase survival times, as opposed to the geometric effect of birth rates.

          On that note, countries with long lives tend to need to support a fair amount of old people, which makes kids expensive, and keeps birth rates down.

          Countries where birth rates are high and where life spans are short have a strong correlation. And they keep growing.

          Compare, say, any European country or Japan or coastal US vs any sub-Saharan African country.

          And as someone with a spouse with cancer, I have to say go fuck yourself.

        • by geekoid (135745)

          So? what does that ahve to do with anything? That would mean that nature is 'aware' and the evolution can judge when that happens.
          Add to that there is no real pressure in a lot of the world where people live long enough to get cancer for resources.

          Traditionally, the lowering of the resource is balanced by a dying off of the elderly. Usually for the same reason there are fewer resources. Floods, droughts, etc..

        • by MrMista_B (891430) on Wednesday November 05, 2008 @08:40PM (#25654073)

          Okay, so... are you volunteering yourself as the first to be killed in the name of population control?

          How about a random lottery? Every couple years, we chose one in a hundred thousand people, and kill them.

          Or what about shutting down hospitals? If we get rid of all the doctors, I'm sure the reduction in population growth will make you very happy.

          While we're at it, instead of incarcerating murderers, how about we reward them? After all, they're helping curb population growth.

          Or you know what? Fuck you.

          • I'm not sure shutting down Hospitals would even put a dent into the population growth, areas with the worst health care systems seemed to have run-away birthrates.

          • Sweet Logan's Run reference.
        • Think of the cancer cells, they have a right to live too!

          • by CriX (628429)
            hah. I purposefully left out any opinion on the matter. I was just trying to point out that what OP said was correct, not that it was right or good.
      • by syousef (465911)

        If there are diseases you'd like to keep around to prevent overpopulation, may I suggest lobbying to return Smallpox to the wild instead?

        Wooooaahhhh there buddy. I didn't say I wanted to keep any disease around. Just that we should have a plan that means our population (and consumption) are sustainable so we don't have wide spread famine.

        Cancer, in general, happens to people well past the age of reproduction.

        What are you talking about? There are whole classes of cancers commonly referred to as "childhood c

        • To Quote your original:

          BLOCKQUOTE>This pains me to say - a couple of friends of the family have been diagnosed with cancer- one very dear to me and with limited time to live, the other a very decent man and doesn't know his chances yet.

          I can't help but think that cancer is acting as a brake on the population explosion. If we cured cancer tomorrow these people who are dear to me wouldn't suffer, but we'd be even less sustainable and eventually we'd see wide spread poverty and famine. So the question bec

          • by syousef (465911)

            The notion that you question the notion that a cure for cancer would be an unalloyed good sounds like you consider the possibility that keeping it around might be a good thing. Which is a despicable attitude.

            How the fuck do you get that from "I don't have easy answers. I certainly don't like watching friends and family die, and would like to see a proper cure instead of various poisons in the form of radiation and drugs that take their toll on the person as much as the disease."???

            You're just being an assho

      • by theJML (911853)

        I've known a few people that died because of cancer well before they were "outside the age of procreation". The youngest of which was 2.5 years old.

        I'm not saying all of them that die are young, but certainly not all that die are old. If we say that 25% of people over 60 die because of cancer, we are to say that 25% of people over 60 will now live much longer due to a lack of it.

        I'd also have to say that you may be correct for a single generation, but let's say your example of old people with cancer is true

      • Last time I looked, population growth was the net effect of births and deaths.

        1) income = births
        2) expenditure = deaths
        3) ...
        4) profit!!!

        • by ginbot462 (626023)

          That's why I use double-entry bookkeeping to stay alive. I only allow my life to be paid to UNALLOCATED. Still, death my hack my books. That bitch.

    • by Corpuscavernosa (996139) on Wednesday November 05, 2008 @07:52PM (#25653383)
      It seems to me that any number of debilitating and lethal diseases can be seen this way and that population control should be proactive. If we can cure cancer, it would seem that population control through education would be a far better way to ensure population control without the horrible pain and suffering that the afflicted and their loved ones endure.

      I realize that birth control education/legislation/etc. brings up an entirely new conversation (one I'm not trying to start here) but I'd pretty much support anything that would have kept friends and family from dying a slow, painful death.

      • by syousef (465911)

        It seems to me that any number of debilitating and lethal diseases can be seen this way and that population control should be proactive

        Agreed.

        I'd pretty much support anything that would have kept friends and family from dying a slow, painful death.

        I too would like to prevent this. However note that older people dying of cancer are more likely to suffer a slow, painful death anyway if we prolong their life - other parts of the body give out. (No I'm not saying that means we shouldn't try to cure diseases) Al

    • If they manage to cure cancer, it will likely be too expensive for the average person, and any insurance you can afford won't cover it. Don't think of it a capitalism gone wrong, think of it as medical extortion. That way, we won't have to worry about keeping the elite alive, and the poor can die of "natural causes" just like they always have.

      Sorry, that was a poor attempt at humor. Serously, despite wide and inexpensive availability of contraception, individual humans have very little control or foresight

      • by geekoid (135745)

        "If they manage to cure cancer, it will likely be too expensive for the average person, and any insurance you can afford won't cover it"

        Complete paranoia BS that flys in the face of history.

        If they cure cancer, it is far more likely to get cheaper, cheaper then treatment and benefits.
        It would be in the insurance companies best interest to use it, even if it cost a million dollars.

        "despite wide and inexpensive availability of contraception, individual humans have very little control or foresight when it come

        • On the contrary, it's not overcrowding (though that is the case in some areas), it's over use. I'm no tree-hugging hippie, but it seems that we are utilizing resources at a pretty unsustainable rate, and our population is mostly unchecked so it's just going to get worse. Some governments (Germany and Russia come to mind) are actively encouraging an expanding birth rate to support their social programs which are essentially pyramid schemes. That's counterproductive in the long run.

          Most of our "modern" societ

      • Re: (Score:3, Informative)

        Serously, despite wide and inexpensive availability of contraception, individual humans have very little control or foresight when it comes to controlling the number of offspring they have.

        To the contrary. As people get wealthier, birth rate drops significantly. This is known as the "demographic transition [wikipedia.org]". Birth rate also decreases directly with education level, and with access to birth control techniques. (That latter would be, you'd think, duh no surprise, but nevertheless it was a surprise to sociologists).

        So if you want to control population, make everybody rich, educated, and have access to birth control.

    • Re: (Score:2, Informative)

      Worldwide, cancer barely makes in to the to 10 causes of death. And the one type of cancer that does make it is caused primarily by smoking.

    • Eh? Cancer is a disease of the elderly who are about 10 times more likely to get cancer [usc.edu] than younger people. Cancer has very little impact on rates of reproduction and so it's obvious that it's not any kind of serious brake on population growth. Finding more successful treatments for cancer will have almost no impact on population growth.
      • Cultures with run-away population growth tend to be poverty-stricken and under-educated cultures where people begin families in the earlier teenage years. In these cultures the Grandparents tend to have a very active role in rearing the grand-children and ruling the extended households. Losing the Grandparents would seriously undermine any stability these cultures have.

    • by Klootzak (824076)

      If we do gather the knowledge we need to cure various forms of cancer so that those dear to us don't suffer, what are we going to do to balance things out and prevent the population from skyrocketing?

      You're making two (possibly incorrect) assumptions here - That someone hasn't already got the knowledge, and that people haven't already posed the very question you ask and come to the conclusion that there should be no 100% effective cancer cure developed... at least until the species is sufficiently sustainable within its immediately available ecosystem to grow the population even faster than it currently does.

      Plus, Pharmacutical companies don't actually like CURING things, there's no profit in a take-one

    • I would be more worried about "overpopulation" if the entire world was full of greedy bastards. But fortunately, the "savages" figure out ways to live on 1% of the oil while we "civilized" Americans continue to plunder and use 25% of the worlds oil.

      Capitalism and exponential market growth are 100x as big of a cancer on this planet as over-population will ever be. The sad thing is, those who consume the least, and contribute the most, are the least likely to get this treatment (at least at first), while so

      • Re: (Score:3, Insightful)

        by m0rph3us0 (549631)
        I'm interested in your market with exponential growth. I'd like to invest as it seems to give much higher returns than the NYSE, NASDAQ, FTSE, DAX, etc.
        • Consider that GDP is 1.04% brwoth, that means the economy will need to be 50x as large in 100 years to sustain growth. That far outpaces population growth which also follows an exponential growth curve. One example of even greater exponential growth (which isn't relatively stable like GDP) is our recent housing bubble.

          Or, you can go to finance.google.com and plot out the market growth over the past 30 years. In a micro economic sense, markets grow exponentially, then crash, rebuild, find new areas of exp

    • by geekoid (135745)

      "I can't help but think that cancer is acting as a brake on the population explosion."

      Your grasping for a patterns and reason where ther is none.

      There are many rason why thi si not true, but I'll just point out 1:
      It usually happens to people who ahve had a chance to reporduce.

      k, on more:
      Evolution isn't a goal, nor does it have a mind or agenda. It isn'a a ladder or a path.
      There is no Goal, no forward or backward as people tend to think of them.

      Yes, it is terribly sad, I wish you and your friends the best, b

    • by rdnetto (955205)

      Then we get a new disease to replace it. e.g. bird flu or something like that. I'm hoping that by the time we start having real trouble with the population explosion, we'll have terraformed Mars (and maybe a few of the less inhabitable deserts).

      • by uncqual (836337)
        The cost in Earth based resources to ship the excess population to Mars will likely exceed the resources required to simply keep those people on Earth for the rest of their lives.

        Shipping people off won't impact the ability of the remaining people to spawn - and if any net resources are freed up by shipping people to Mars, those remaining on Earth will simply increase their spawning rate until, again, Earth suffers from overpopulation. If this wasn't the case, the Earth's population would have frozen bef
    • Re: (Score:3, Insightful)

      by Rakishi (759894)

      The exact opposite holds true and I really wish people would first look at the data before spouting out something. Developed nations with long life expectancies have a lower population growth rate than other nations. In fact the world's population growth rate is going down as more nations become developed. It's expected that the world's population will reach an equilibrium of 12 billion or so in under 40 years.

    • I believe cancer may be the only 'natural' way to die. If we are lucky and healthy and live to be very old, the amount of times our cells divide goes up accordingly. Every time they do divide, there is a small chance for mutation, and a small chance of that mutation to be deleterious to our health. Apparently, genetics and lifestyle effect how often and to what extent these mutations occur. This is why I don't think cancer will ever be 'cured'; it's a disease we can only delay.
      • by mattack2 (1165421)

        What about telomere shortening? http://en.wikipedia.org/wiki/Telomere [wikipedia.org]

        Basically (my total layman interpretation, go read the wikipedia article and others) the cell division is limited by the shortening telomere. Usually that causes cell death, but sometimes cancer. So even after the cancer has been cured, there's still the cell division limitation, until we can get past that.

    • what are we going to do to balance things out and prevent the population from skyrocketing?

      I'd imagine as that concern becomes closer to reality, government(s) would have have to start imposing limits on the number of offspring a person is allowed to have (much like how China does in an attempt to prevent overpopulation). I realize this imposes on our freedom to reproduce, but given the alternative I'd say it's by far the lesser of two evils.

      • by geekoid (135745)

        the government would not have to forcibly do that.
        Just educate kids about birth control, and how having kids impacts there lives.
        Add to that the risk of catching a disease that can kill you.

        Let them learn about condoms, and get condoms.

        All evidence shows that an informed educated society has less children, no forcing reproductive laws required.

        of curse this will curb naturally when food becomes scarce.

    • by NonSequor (230139)

      I don't think that sustainability is the problem that it's made out to be. We'll work out the details over time. We always have.

      It's a disservice to the world if a truly good person does not reproduce.

    • Re: (Score:3, Interesting)

      by MikShapi (681808)

      Have a read through the mprize and SENS pages [mfoundation.org], projects geared at tackling not only cancer but ageing in general.

      Aubrey De Grey addressed this question a while back - what if people stopped dying from aging altogether? Will population explode? Will we immediately cause a bigger problem than we've solved?

      Following his reasoning (plus real-world numbers) the answer is no. Personally, I agree with him.

      Even in the most extreme of cases, were everyone to just stop dying of age-related causes altogether (includin

    • by Vellmont (569020)


      I can't help but think that cancer is acting as a brake on the population explosion.

      Not in a significant way. The truth is that the birth rate for most (all?) industrial nations is near or under replacement. The U.S. is only growing because of immigration. Curing cancer would have an almost nill effect on the population.

      and eventually we'd see wide spread poverty and famine.

      Thomas Malthus [wikipedia.org] had a similar fear. His theory was essentially that as resources expanded, the population also grew to consume all t

      • by Alsn (911813)
        Most people who die from cancer are well past their retirement age. Just saying...
    • Overpopulation is a myth. The problem is with resource allocation. Don't take my word for it, do your own research before you go about propagating such a dangerous myth. This has been discussed on slashdot [slashdot.org] before.
    • If nothing else, we can make a rule that if you want to live forever, then you can't have children.

      Of course, in the future we will live in virtual worlds, where space is unlimited.

      • by uncqual (836337)

        Of course, in the future we will live in virtual worlds, where space is unlimited.

        But, imagine how quickly virtual people can spawn new virtual people - Moore's law would be very scary here as the rate of spawning would double every 18 months or so. Where will we put all the bits needed to uniquely define each virtual human - there are only a finite number of atoms conveniently close to us!

    • If we do gather the knowledge we need to cure various forms of cancer so that those dear to us don't suffer, what are we going to do to balance things out and prevent the population from skyrocketing?

      Well, problem is, we probably will have a skyrocketing population. What you'd have to do in order to counterbalance things is:

      (A) Replace the free market economy system with something workable. Say, you get decent food, decent clothing, and decent shelter as a basic human right. You want more, you work for it, and upgrade. That's how I see the Star Trek universe working, which evolved beyond the need for money. (TNG: The Neutral Zone)

      (B) Offworld colonies. You'd have to find a way to get people offworld, at least in space stations or something.

      (C) Synthetic food. We'd have to find a way to make fake food with all the nutrients. What would be cool (though I have no idea how sound this is) is to reassemble the atoms and molecules in things like garbage into something consumable and nutritious.

      Tech's come a long way, but it needs to go further before we start removing the population caps.

    • Did anyone else see Logan's Run?
    • Cancers usually horrible - painful, disfiguring, debilitating. There are more peaceful ways to die in old age. besides eliminating cancer does not add too many years to the average lifespan - about six. Antibiotics and hygene nearly doubled lifespan.
    • That's a rational but twisted point of view. We should cure cancer. It's widely shown modern civilizations (e.g. many of today's EU) stable out on their own and the key is easy access to contraception in all its forms. If becoming a parent is always a rational choice, populations tend to stagnate or even shrink a little. Solve it on the supply side.

  • That's nice but... (Score:5, Insightful)

    by the_humeister (922869) on Wednesday November 05, 2008 @07:47PM (#25653291)

    There's always a "but." They sequenced an FAB classification M1 AML. That's nice, but these things tend to have a heterogenous genetic makeup. It'd be nice if they sequenced more of those things and compared them as well.

    • by samgeribo (1309565) on Thursday November 06, 2008 @08:03AM (#25659265)
      I'm also concerned that these might be mutations in the hematopoietic stem cell that don't "drive" the disease. The lengthy points at the end debunking this possibility aren't convincing to me. Here are the 1st two (FTA):

      1) "genetic instability does not seem to be a general feature of AML genomes."

      Are they on crack? Perhaps I don't fully understand the context of this statement; genetic instability and evolution are seen in most cases of AML.

      2) "Alternatively, all may have occurred simultaneously in the same leukaemia-initiating cell, but only a subset of the mutations (or an as-yet undetected mutation) is truly important for pathogenesis (that is, disease 'drivers' versus passengers). Although we suggest that the latter hypothesis is very unlikely on the basis of our current understanding of tumour progression"

      Simultaneously occurring? Again, this flies in the face of common knowledge. The theory is the hematopoietic stem cell is extremely long lived and only divides once a year and so has plenty of time to accumulate genetic mutations. This explains both the average relapse time of one year and also the genetic homogeneity of the leukemic clone. Thus many of their new found eight mutations may be accidental and not disease causing.

      Does anyone have any new light to shed on this? I am not a doctor and would benefit from some guidance on this issue.

      • Re: (Score:2, Informative)

        by Scubaraf (1146565)
        Mod this up - this is the *KEY* argument that needs to be made in light of this work. First - 8 of the unexpected mutations could not be found in leukemia cells from 187 other patients with AML. http://news.bbc.co.uk/2/hi/health/7706487.stm [bbc.co.uk]

        This strongly suggests that these are "passenger" mutations that were acquired during the life of the hematopoietic stem cell that later underwent clonal expansion.

        Many of the patients remaining normal stem cells probably carry a few insignificant mutations here or
        • by bishnu b (1401647)
          That these 8 unexpected mutations do not occur in other patients does reinforce the importance of the recurrence of the other two (FLT3 and NPM1). That being said, personally, I am at a loss as to why genome sequencing 1 patient is more desirable than gene expression analysis over a larger sample; but I am not familiar with the state of the art in AML research.
  • by sexconker (1179573) on Wednesday November 05, 2008 @07:55PM (#25653427)

    Really?
    Is that significant?
    If so, why? If not, why hadn't it been done before? (Other than the whole "zomg this job is taking forever" thing)

    • The first genome cost $3 billion. This one did two genomes for $500K apiece. Future costs are expected to drop another thousand in a decade. They may need to do a thousand of these kind of sequencings to capture the range of the major cancers.

      Plus once you know the range of genomic differences for each kind of cancer, you could develop a set of cheaper makers. Each cancer is expected to consist of a couple dozen mutations, maybe ten or so for each specific instance.
  • I call shenanigans, since at least 7% of the genome is repetitive elements, centromeres, cnvs etc. etc. Also, remember that they use a reference genome, which itself is not complete. What happens if the cancer/person has a sequence not found in the reference genome. I know, it is not reported. It is more informative to say 90% of the tumor was sequenced. Probably the last 10% was the important part anyways (cnvs and the number of repeats are very important), so this is just anther "first post" in Scien
    • by guycouch (763243)
      Fine, but you can't do the research if you don't have the genome. The title of the article wasn't "Cancer Genome Sequence, Cure Eminent."
      • Fine, but you can't do the research if you don't have the genome. The title of the article wasn't "Cancer Genome Sequence, Cure Eminent."

        I am saying if you claim to that you have the genome, you should probably have the genome. They don't. I said nothing about cures for cancer. Again my point stands, since they only have the differences between the tumor genome and a "reference genome" (same for the normal genome of that person). They then compare the two to see the differences in the differences. The have a 10% data missing problem.

  • by jfengel (409917) on Wednesday November 05, 2008 @08:14PM (#25653719) Homepage Journal

    The Science News article says that they sequenced both a cancer cell and a non-cancer cell from this woman. So we can specifically say "these are the bases that are different" and from there (with luck) to "this is the mutation that happened".

    That should prove quite illuminating.

    • It should be "It was hard to sequence the whole thing, so we quit after 90%"
      • by karnal (22275)

        Maybe they could do the same thing that EA suggests - just keep trying random data at the end until it all works.

    • It should. The next step, I think, would be to sequence more people with AML M1 because the genetics heterogeneous. Then we can compare genes to normal controls and within the specific types to find the genes in common, if any, and maybe direct treatments against those genes/gene products.

  • by Majik Sheff (930627) on Wednesday November 05, 2008 @08:15PM (#25653731) Journal

    All the lab has to do now is patent the gene sequence and then sue mother nature for everything she's worth every time someone expresses this gene!

    There's your above the fold headline: Lawyers cure cancer!

  • Ok, I'm going to lose major Karma for this.... but what the hell..

    This is not only the first cancer genome published, it is the first female genome as well.

    Wait, wait, wait.... you mean they're different?

    • by Khemisty (1246418)
      I was thinking the exact same thing. I didn't realize that men and women have different genomes. According to this page [wellcome.ac.uk]

      "Surprisingly, a male genome is not the same as a female genome â" and it even appears that genomes may be engaged in a genetic 'tug of war' within a developing embryo."

      It continues saying

      "An example is the insulin-like growth factor system, which has a strong influence on the size of a baby. The logic is that the paternal genome works to maximise the growth of the offspring, to g
  • by Anonymous Coward

    I'm pretty sleepy but at first glance I thought the first whole Cancer Gnome sounded pretty scary!

    • So, is she hot?

      well they published her genome, so you can make your own and find out.
      The source code is a little buggy though.

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