Scientists Crack 'Entire Genetic Code' of Cancer 235
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."
Re:Sadly, the article makes no sense (Score:5, Informative)
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:
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.
Misleading... (Score:1, Informative)
This is a terrible summary. There is no *single* cancer genome. They sequenced the genome of one cancer biopsy. There are probably as many different cancer "codes" (also a horribly misleading term) as there are tumors in the world.
Cancer is not a single disease, it is a phenomenon, like evolution. This would be like sequencing the genome of two organisms and claiming to've "cracked the evolution code".
The extrapolation for lung cancer is badly flawed (Score:5, Informative)
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.
drivers vs passengers (Score:4, Informative)
we have a long way to go before we defeat cancer, and sequencing can only take us so far.
Re:Sadly, the article makes no sense (Score:5, Informative)
Tell That to Monsanto (Score:5, Informative)
> 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."
Re:Sadly, the article makes no sense (Score:5, Informative)
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.
Re:Sadly, the article makes no sense (Score:4, Informative)
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.
Re:How real is this? (Score:2, Informative)
Try to mod good posts up, rather than look for ones you disagree with and mod down. If you must, then a -1 Flamebait or Overrated would be more appropriate here.
Re:Two preventable cancers (Score:3, Informative)
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. '
Re:"Entirely Caused By Sun" - Show Me The Evidence (Score:3, Informative)
'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 of C>T substitutions...[Lots of technical stuff about the sequence context of the mutations with some impressive looking p-values] ...Therefore, the mutation spectrum and sequence context indicate that most C>T/G>A somatic substitutions in COLO-829 are attributable to ultraviolet-light-induced DNA damage.'
Re:Might be okay, might not. (Score:3, Informative)
This is why car drivers that complain about cigarette smokers annoy me. The will spew all sorts of particulate matter and chemicals into the air and then whine when a cigarette smokers do it. Yes, I drive, and no I don't smoke, but I'm not going to be a hypocrite and claim that my air pollution is better than their air pollution.
It wouldn't necessarily be hypocrisy to claim that.
1) Cigarette smoke contains 10x more particulate matter [medicalnewstoday.com] than engine exhaust. There's a reason we have catalytic converters.
2) Cars don't typically blow smoke at face level or hang around doors (or indoors in more permissive places).
Re:Might be okay, might not. (Score:3, Informative)
I read a few years ago that people who drink hot coffee have a higher incidence of throat cancer. Heat is a big factor here, and certain oxidized compounds are likely involved too, but it's not entirely obvious which ones.
Re:Tell That to Monsanto (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 not the presence of the original product (the Monsanto seeds) that they sue over. It is the presence of sequences of genes that they own the rights to. If the only thing that they had rights to were the original seeds then they would have no standing to sue over hybrids from pollen from their seeds.
The situation is getting worse as time goes on and courts get involved more often. When they sue, they try to cover as many broad arguments as they can. Companies patenting sequences of RNA are now even claiming rights over the proteins and DNA that the RNA codes for. As they usually sue poor agrarians who can't afford to put up a good defense, bad judgments are becoming strong precedents.
Look up "product by process" for more info.
Here's a start for you:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2220018/ [nih.gov]
Re:Population and cancer (Score:1, Informative)
Nope. There's been a large reduction in cancer deaths due to research and treatment advances
Unfortunately, that's not really true - the overall mortality rate [nytimes.com] for cancers is roughly the same as it was in 1950, as aresurvival rates for people diagnosed with cancer. [lww.com]
I would suggest that spending more money on cancer research is unlikely to have a significant impact on survival rates. From the proteins on his surface to the sequence of his DNA, we know the enemy. What we lack is the bullet that can reach him and kill him - essentially the same problem that prevents us from curing AIDS, antibiotic-resistant bacteria, and many genetic diseases. Now that gene therapy has proven to be a dud, there's no incremental advancement on the horizon that could lead to a large increase in cancer survival rates. Funding is unlikely to help because the advisory boards making the money decisions prioritize incremental research [nytimes.com] deemed most likely to succeed over more ambitious experiments. The few major breakthroughs in treating specialized forms of cancer have mostly come from lone wolves [wikipedia.org] who secured funding from private benefactors.
No one can argue against funding cancer research while so much of our economic output is earmarked for empire building or making really great sitcoms. But I do not believe that additional funding for cancer research is likely to produce a large increase survival rates.
Re:Sadly, the article makes no sense (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.
A slightly more technical summary (Score:3, Informative)