Even with a cheap sequencer like this, doctors wouldn't be able to give results to patients. That is because many of the genes that cause disease are patented, and the holders of those patents will sue the crap out of any doctor that tries.

Mentat: Hooray. Yet another sequencer that will pump out gigabases of data that no one will have the time or resources to fully analyze.

As the article points out, a number of common errors and disease traits are already fairly well understood. Once you know the faulty sequence and where it is, checking to see if the patient has x genotype is just a matter of a GOTO line whatever followed by a boolean operation (actual sequence == x).

I mean, it's slightly more complicated than that, but the barrier to diagnosis once the disease is understood is, at present, mostly the need to send the sample off to an off-site lab with all the issues that implies.

Xythero: Even with a cheap sequencer like this, doctors wouldn't be able to give results to patients. That is because many of the genes that cause disease are patented, and the holders of those patents will sue the crap out of any doctor that tries.

It's about time those patents were challenged, and this technology will bring that battle into the public eye. I don't see how any sane person can agree that genes that occurred naturally are patent-able.

vpb: Good. All these in-valids are starting to get on my nerves.

I just want Uma Thurman in a tight pants suit.

Jessss... jesss...

Eugenics : The Nazis :: The : The Nazis

Jim_Callahan: but the barrier to diagnosis once the disease is understood is, at present, mostly the need to send the sample off to an off-site lab with all the issues that implies

Sure, once the disease is understood, which is still a few decades out.

We've got an IonTorrent at the lab, and yeah it makes tons of data for relatively low cost, but that has nothing to do with understanding the data or the biomolecular systems impacted by a mutation, even if you could find it.

I'm working on a family with some disease, we have had all of their genome sequences for a few months now and there's a hundred thousand mutations per person on average, so which one is the trouble? We need to find out which protein is malfunctioning and then what the impacts of that would be, but a biological system has tons of redundancy, everyone has got dozens of malfunctioning genes and lives just fine.

Its nice to have cheap sequence, and we've got the CPU power to do whatever, but the problems dont solve themselves..

/i should probably get off fark and back to work

Fisher Price's My First Genocide

Zel: Its nice to have cheap sequence, and we've got the CPU power to do whatever, but the problems dont solve themselves..

so hire me as a biochemist/bioinformatician, already.

utah dude: so hire me

Call your congressman.

NIH funding rates drop to record lows
http://blogs.nature.com/spoonful/2011/05/nih_funding_rates_drop_to_re c o.html

I'm actually here because the lab could only afford a part-time bioinformatician.

I heard that getting your kids genome sequenced can cause autism. Is that true?

Realize that eugenics is all about correcting things a large enough chunk of society regards as "faulty" or mutated. As we start trying to "fix" ADD and autism, and otherwise homogenize our offspring, who knows what value we lose. Before too long we'll have a society of soulless conformists.

rdyb: Realize that eugenics is all about correcting things a large enough chunk of society regards as "faulty" or mutated. As we start trying to "fix" ADD and autism, and otherwise homogenize our offspring, who knows what value we lose. Before too long we'll have a society of soulless conformists.

Except for the reserves where the feral humans live.

And we won't have homogenous offspring. There will be five classes. Maybe we can name them after Greek letters.

Thinks there might be a downside to this.

/hot....like the future

Mentat: Hooray. Yet another sequencer that will pump out gigabases of data that no one will have the time or resources to fully analyze.

It keeps me employable for the forseeable future. We've actually been approaching the $1000 genome pretty steadily for the last few years, for the HUMAN genome that is. Where for MOST purposes doing a short-read mapping assembly to the current reference build from NCBI is good enough. If you want to do a de novo assembly though you run in to problems, especially with most of these 3rd gen sequencing technologies and the short reads they produce.

There's also the fact that Ion Torrent has some known quality issues compared to the latest 454 variants. But it does produce a hell of a lot more data in a single run so it has that going for it.

Now if PacBio's SMRT is as good as advertised, and ever becomes widely available that will be awesome. Or some of the other promised 4th gene technologies that are rapid and produce lots of long-reads.

Zel: We've got an IonTorrent at the lab, and yeah it makes tons of data for relatively low cost, but that has nothing to do with understanding the data or the biomolecular systems impacted by a mutation, even if you could find it.

I'm working on a family with some disease, we have had all of their genome sequences for a few months now and there's a hundred thousand mutations per person on average, so which one is the trouble? We need to find out which protein is malfunctioning and then what the impacts of that would be, but a biological system has tons of redundancy, everyone has got dozens of malfunctioning genes and lives just fine.

Its nice to have cheap sequence, and we've got the CPU power to do whatever, but the problems dont solve themselves..

No, but it does make the type of experiments and data crunching you can do to look for the problem that much broader. I've been doing some part-time work on a large disease genomics project while I finish my PhD (defend in a month then move on to this project full-time as a Post-Doctoral Fellow) and it's pretty amazing what sort of experiments we will do because the cost has come down so much. Hell even doing SNP genotyping at 2.5Million SNP resolution is only a couple of hundred bucks per sample now, and you can use that data to narrow down the search a hell of a lot most of the time. Couple it with exome sequencing and traditional sanger of probable targets and you can get decent answers for lots of diseases relatively quickly.

Of course then you hit the wall with some projects where it takes a lot more sequencing and a lot of different techniques to even identify the candidate gene(s) let alone characterize them.

But all of that analysis is good for me as a bioinformatician since my background is also in biochemistry.

Jim_Callahan: As the article points out, a number of common errors and disease traits are already fairly well understood. Once you know the faulty sequence and where it is, checking to see if the patient has x genotype is just a matter of a GOTO line whatever followed by a boolean operation (actual sequence == x).

I mean, it's slightly more complicated than that, but the barrier to diagnosis once the disease is understood is, at present, mostly the need to send the sample off to an off-site lab with all the issues that implies.

The stupid thing is that even when you have a causative gene or set of genes identified for a particular disease, the companies doing diagnostic genomic tests are charging ridiculous amounts of money for their tests. I've seen some where it is actually cheaper to do a patients entire exome with next-gen sequencing and look for it that way. Its ridiculous.

Mentat: Hooray. Yet another sequencer that will pump out gigabases of data that no one will have the time or resources to fully analyze.

All your gigabases are belong to us.

rdyb: Realize that eugenics is all about correcting things a large enough chunk of society regards as "faulty" or mutated. As we start trying to "fix" ADD and autism, and otherwise homogenize our offspring, who knows what value we lose. Before too long we'll have a society of soulless conformists.

It's true. We should just let whatever ridiculous form of suffering nature throws at us run amok because somewhere in all the suffering and death might be some good. Indeed, why we we bother to air condition and heat our homes? Why do we even have homes? Certainly the temperature isn't faulty, and who knows what value we've lost now that we're not toughing it outside when the weather sucks.

For science smrt people: How accurate could something so cheap be?

My thoughts are you get what you pay for and $1000 for gene sequences seems shady.

/ not science smrt
// did not rtfa

You can't trust those things. I know someone who had their genome sequenced once, and his balls fell off. Literally dropped the whole sack. It's dangerous, and I'd advise you to stay away. Unless you're scheduling surgery to head that direction already. Another guy I know, his head turned inside out. That was a mess.

The quest I have is... so what?

What does having my genome mapped out do for me, now?

/serious

The_Time_Master: The quest I have is... so what?

What does having my genome mapped out do for me, now?

/serious

Personalized medicine mostly, but knowledge of predispositions and better screening for drug effects to start.

Link (new window)
Later on it could be useful for other modifications, but that's sometime off.

bdub77: shiat is about to get real.

I feel bad for my daughter, who is less than 2. Probably within 20 years we will have full-scale Gattaca clinics. By the time these super-kids graduate college at age 14, she'll be so hosed in the job market.



Good book. It talks about a "triage system" for medical care in which insurance companies will be able to legally let you die, because you have bad genes. Oh, and that's already happening in in some devloped countries.

Mentat: I hate most of the current technologies because of the gigabases of short read crap you get out. I have hopes for PacBio, but I've heard the error rate is pretty bad. The long read lengths might make up for that though.

It really all depends on what you are doing. My PhD lab does evolutionary biology and phylogenetics on really diverse protists. The short read lengths can make things difficult but we restrict it to mostly doing Transcriptomics instead of full genomes and it works well. The lab I will be doing my post-doc in is doing human medical genomics and once you have a reference genome to use as a scaffold the short read length isn't a problem.

The way I look at it there is no silver bullet technology, you have to carefully construct your investigations to use the best combination of sequencing technologies available, at the price you can afford.

I'm hoping my post-doc lab decides to just go ahead and get a Mi-Seq.

MBA Whore: For science smrt people: How accurate could something so cheap be?

My thoughts are you get what you pay for and $1000 for gene sequences seems shady.

It's actually a highly competitive market with several major players in the field. So prices have been dropping like a rock across the board in terms of sequencing. So in this case cheap doesn't mean inferior, it means that is what the market price is. And that is only the sequencing cost.

The_Time_Master: What does having my genome mapped out do for me, now?

For you specifically as an end-user with no knowledge of genomics? Not much. For people like me working on the science end of it? It means a hell of a lot. Right now you can get about the same amount of information out of a SNP scan like 23andMe which looks for known variants with some connection to various human diseases. So you can get a fairly accurate picture (albeit incomplete) of your relative genetic risk for say Alzheimer's, certain cancers, etc.

But medical genomics is advancing very rapidly right now. In the next few decades patient genome sequencing is very likely to become a fairly routine part of medicine.

Summer Glau's Love Slave: Good book. It talks about a "triage system" for medical care in which insurance companies will be able to legally let you die, because you have bad genes. Oh, and that's already happening in in some devloped countries.

Which countries? I know here in Canada having a genetic variant identified actually gets you access to care you might not otherwise routinely get. If you have a known BRCA1 or BRCA2 variant for instance you may be covered for mammograms more frequently. You'll also have other options such as preventative mastectomy and reconstructive surgery all covered.

And for some conditions there really isn't anything you can do other than palliative care.

GlassWalker: rdyb: Realize that eugenics is all about correcting things a large enough chunk of society regards as "faulty" or mutated. As we start trying to "fix" ADD and autism, and otherwise homogenize our offspring, who knows what value we lose. Before too long we'll have a society of soulless conformists.

It's true. We should just let whatever ridiculous form of suffering nature throws at us run amok because somewhere in all the suffering and death might be some good. Indeed, why we we bother to air condition and heat our homes? Why do we even have homes? Certainly the temperature isn't faulty, and who knows what value we've lost now that we're not toughing it outside when the weather sucks.

I know it's passé but EABOD.

ASD isn't all about suffering, it's a fundamental way of experiencing reality and it's a part of humanity.

Just because some authority decrees a phenotype to be abnormal don't make it right to wipe it out. The less power authoritarian assholes have to act on the basis of ill-informed views, the better. (and we won't be well-informed until we have a philosophy everyone can agree on, at which point we'll likely all be part of a homogenous and meaningless society anyway)

I want another pair of arms and innate night vision just as much as the next person, but I don't wish that the bigoted halfwits that dominate society had had their parents sterilized. À la carte genetic selection, picking and choosing which gene lines survive, is basically the same thing. Well, shoot, maybe you're right... maybe that is what I want. At least we'd better be saving backups of the genes we're tossing out....