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First Whole Cancer Genome Sequenced
Posted by
timothy
on Wed Nov 05, 2008 06:18 PM
from the gee-gnome-sounds-like-a-good-open-source-project dept.
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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That's nice but... (Score:5, Insightful)
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.
Re:That's nice but... (Score:4, Interesting)
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.
Parent
First Female Genome Sequenced (Score:3, Interesting)
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)
Two genomes from the same person (Score:5, Interesting)
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.
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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.
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Maybe they could do the same thing that EA suggests - just keep trying random data at the end until it all works.
This is perfect! (Score:4, Funny)
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!
Well now (Score:2)
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?
Cancer Gnome (Score:2, Funny)
I'm pretty sleepy but at first glance I thought the first whole Cancer Gnome sounded pretty scary!
Re:Next gen sequencers are fucking awesome (Score:5, Interesting)
Parent
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Nanopore...hmmm... Sounds to me thats one step closer to those DNA readers in Gattaca.
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Re:Next gen sequencers are fucking awesome (Score:4, Funny)
Remember northern blots?
Honestly? No, I've BLOTTED it out.
It's so rare you get to make a molecular-biology related pun, you have to take every opportunity you get, even if they are that bad. I'm sorry.
Parent
Re:Next gen sequencers are fucking awesome (Score:4, Funny)
It's not that rare - heck the Northen blot itself is a pun:
Southern Blot - developed by Ed Southern
Northern Blot - see what they did there...
Western Blot - yes, yes - very funny. Now get back to work.
Parent
Re:Population and cancer (Score:5, Insightful)
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....
Parent
Re:Population and cancer (Score:4, Insightful)
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.
Parent
Re:Population and cancer (Score:5, Insightful)
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.
Parent
Re: (Score:2)
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..
Re:Population and cancer (Score:5, Funny)
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.
Parent
Re: (Score:2)
I mainly replied in response to the comment "Seriously, some of you people scare me..." which was annoying and unnecessary.
As opposed to your comment of "It is a cold hard fact that when people do not die they are called 'alive' and therefore are contributing to the number of people considered to be the 'population.'"? Did you take "Malthus' theory misinterpreted 101" last quarter or something?
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Glad to hear you won't be procreating.
Somehow, I doubt it. The best way that most of us can be meaningful to the next generation is to pass on our good genes, assuming we have any. If you decide to forego that part, you may as well never have lived.
Or do you expect
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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
Re: (Score:2)
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
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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
Re:Population and cancer (Score:4, Insightful)
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.
Parent
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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
Don't worry (Score:2)
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
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"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
Re: (Score:2)
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.
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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
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"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
Re: (Score:3, Insightful)
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.
Re: (Score:2)
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.
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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.
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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)
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
Re: (Score:2)
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
Re:Population and cancer (Score:5, Insightful)
or just raise education levels. Japan has negative population growth, and it's not due to government intervention.
Parent
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as i understand it, they didn't want to invade the U.S., they didn't even really want to go to war with the U.S.
what they wanted was to be like the U.S., and all the other major western powers, and become an industrialized society. but Japan has no domestic oil supply, and since all the European powers were colonizing other lands and spreading their empires at the time, the Japanese wanted to do the same with Southeast Asia.
but the Western nations, particularly the U.S., didn't want Japan to become too powe
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Yes but then you end up with a very rapidly aging population (like China does) which means a shrinking working base supporting a growing elderly base. Probably the most effective solution would be a yearly "birth" license, get one and you get to have a child don't get one and no kid for you. Perhaps cold and uncaring but also effective and allows you to carefully control your population growth.
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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.
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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
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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!
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Know eye deed knot.
Know eye deed knot.. (Score:2)
Ice wear.