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Hunting Disease Origins By Whole-Genome Sequencing
ChocSnorfler writes "James Lupski, a physician-scientist who suffers from a neurological disorder called Charcot-Marie-Tooth, has been searching for the genetic cause of his disease for more than 25 years. Late last year, he finally found it — by sequencing his entire genome. While a number of human genome sequences have been published to date, Lupski's research is the first to show how whole-genome sequencing can be used to identify the genetic cause of an individual's disease."
With every advancement in figuring out genetic diseases, I can't help but think that the combination of this plus drug testing will lead to genetic discrimination, or at least defamation.
Plus, even then is there much we -can- do if we figure out something is genetic?
Taxation is legalized theft, no more, no less.
How long before sequencing becomes part of a routine physical exam, and having the disease-prone genes becomes a pre-existing condition for health insurance purposes?
Your genome has a lot of differences from the reference genome. They narrowed down the differences based on a lot of previous work discovering genes linked to the disorder.
Only then were they able to zero in on precisely what gene in his specific genome caused the problem, and confirm it by testing other family members.
This brings the phrase "do it yourself" to a whole new level.
To do list for Windows
What's this Hunting disease they talk about?
To do list for Windows
Interestingly, this is a very similar article published by the NYT the day before - http://www.nytimes.com/2010/03/11/health/research/11gene.html?ref=health
ogglelog
They've sequenced a lot of diseases but they're keeping them secret because of HIPPA
Perhaps it's time to open source genomes so that many eyes can find the interesting stuff.
You may have a polymorphism that causes disease and you may not get insurance because of it but you and your children might benefit by a cure found by examining the data.
Which is better?
...will be those they expect to find in the genes, but won’t. Like many of those so-called “age-related” diseases. Because then they have to admit it’s caused by the environment. Like the actually food-related group.
Any sufficiently advanced intelligence is indistinguishable from stupidity.
he uses Gentoo or LFS.
Don't we share 99% of our DNA with monkeys? People share 70% DNA with bananas. I guess all that sharing makes us compatible.
we'll have great hair!
every day http://en.wikipedia.org/wiki/Special:Random
My local paper had this story in today's edition. Are they getting better or is Slashdot getting, um, sluggish?
"I believe in Karma. That means I can do bad things to people all day long and I assume they deserve it." : Dogbert
I have two distinctly different mental illnesses, a neurological condition that affects my brain, and a circadian rhythm disorder that more or less makes it impossible for me to hold any kind of nine-to-five job.
I have Bipolar-Type Schizoaffective Disorder, which is just like being Schizophrenic and Manic Depressive at the same time. That was diagnosed in 1985. I also have Obsessive-Compulsive Personality Disorder. That's quite a different thing than the more well-known Obsessive Compulsive Disorder (OCPD vs OCD). I was told of the diagnosis in 1994 but I have reason to believe the diagnosis was made long before, but my therapist chose to wait many years to give me the bad news.
The neurological condition is Attention Deficit Hyperactivity Disorder. I got that diagnosis in 2008. ADHD isn't taken very seriously by a lot of people, with some believing that it's not a real illness. It's no joking matter: I got the diagnosis in a psychiatric hospital where I committed myself rather than go off the Golden Gate Bridge as a result of my profound inability to focus on my work. I had been begging all manner of medical and mental health practitioners for help with it for ten years, but none of them had the first clue as to how to help me. It was only the shrink in 2008 who was able to make a real difference.
My circadian rhythm disorder is Delayed Sleep Phase Syndrome. It is the main reason I am a software engineer - my degree is in Physics, and not Computer Science. When I noticed that many of my programmer friends worked at night, I figured that being a coder would be the only way I would ever be able to hold a real job. All of my life I have slept during the day and stayed up all night. My mother said I was this way even when I was a newborn in the hospital.
My reason for wanting my genome sequenced is not at all to help myself, but to help others with my conditions. Besides understanding my various illnesses, I also want the medical community to figure out why I have done so well despite what would normally be a profound disability:
It is very, very rare for someone with Schizoaffective Disorder to live independently, let alone hold any kind of real job. I have a degree in Physics and have been a coder for twenty-two years. But most who share my diagnosis have to live off the disability check, be cared for by their families, spend their lives in institutions, or survive somehow on the streets, tormented by despair and madness.
There was a time when I was so hopelessly in the grip of my delusions that when God Almighty Himself sent me visions in the sky, I would photograph them. But when the pictures came back from the developer without my visions in them, I figured it was due to my inexperience as a photographer and not because those hallucinations were the products of my own demented imagination.
My hope is that by having my genome sequenced, I might not only ease the sufferring of others, but prevent a lot of otherwise needless suicides.
I am absolutely serious: mdcrawford at gmail dot com
Request your free CD of my piano music.
I have been through some profoundly awful times. During my early twenties I spent five years almost continuously suicidal. Yet somehow I made it through all that.
I have met many other schizoaffectives, but so far I have not met even one who is had been able to hold a job for any length of time.
Request your free CD of my piano music.
First rule of medicine (well no, not really, it's probably down there around number 87) is "Thou shalt not brute force medicine".
Of course looking at medical shows, no wonder the public believes that the medical art consists of rattling off possible diagnoses at random and running tests until a magical positive result is found. And good for Dr. Lupski if he found a genetic cause for his disease. However after what was probably not a trivial expense, at the end of the day he went home knowing that, well, he had Charcot-Marie-Tooth disease. Er yeah, but he already knew that.
Above putative rule #87 is another rule: If a particular test will not change your diagnosis if it gives a positive (or negative) result, don't do the test. Because tests use up limited resources like paper, reagents, labs, money and time. And especially the patient (or his insurer) usually doesn't have an unlimited supply of these things. While as a doctor I could theoretically order every test in the world to rule out that the stuff oozing out of your nose is not caused by anything other than the common cold (cerebro-spinal fluid leaks, anyone?), the ART of being a doctor is making the RIGHT diagnosis and ordering the minimum RIGHT tests to confirm that diagnosis.
This is something that the medical community has forgotten, somewhere along the way through technological progress (read - lots of neat toys to play with) and defensive medicine (I did the tests so if I get sued I can prove that I thought of this). Of course going out and getting your whole genome sequenced will make lots of biotech companies very very happy. Of course once in a while someone somewhere will discover some condition they never knew they had. However firstly if it's in your genes there's not much you can do about it anyway except in very rare cases, and secondly exactly how much will this cost again? Maybe when the $5 genome sequencing is available this could be an option for mass screening, but for now - please, let's use some common sense. Especially when the costs of doing something like this are born by OTHER people - like in insurance or state run health care scenarios.
Just because you CAN do something doesn't necessarily mean you SHOULD do something. But hey, I'm just an aging family doctor, what do I know.
Seven puppies were harmed during the making of this post.
I'm getting my PhD in a statistical genetics program.
The quality of "newly discovered genes" in the literature is very, very poor. Any scientific "discovery" should be replicated by other researchers, but that is not being done. Negative results rarely get published. Since we have tens of thousands of genes, one can find any number of genes that have a "significant association" with a given condition.
In reality, many diseases are known to have multiple origins. The same disease could be caused by entirely different genes in different people. And that's assuming it is a genetic condition, as opposed to other causes. Researchers have spent decades looking for genes that cause diabetes, but there is increasing evidence that diabetes is really caused by viral infections. In particular, type I diabetes was assumed to be genetic, but there is a fairly large amount of evidence that it is caused by viruses such as Coxsackie B4. The incidence of type 1 diabetes is increasing throughout the world, which cannot be explained by genetics.
To dispel a couple of other myths, genetic diseases are not always recessive. Many of them are dominant. Also, "bad" genes do not always get selected out of the gene pool; diseases that cause problems later in life, such as Alzheimer's, heart disease, Huntington's, happen after reproductive age and so there is no selection pressure.
Humans use their minds to recognize traps. There aren't a lot of us who know how to avoid the 'genetics' hook, but it is possible...
I think even the most coldhearted persons must admit that your genetic makeup is something you cannot influence
I may be the most coldhearted person you'll never meet (the man who used to train mercenaries said I missed my true calling), and I do a damn good job of influencing my genes.
DNA Is Not Destiny (Discover Magazine)
Why Your DNA Isn't Your Destiny(Time Magazine)
Why do some people with the "bad gene" develop a given disease, while other people do not? Epigenetics FTW! :)
Eat right, productively deal with your stress, balance your nervous system, indulge in creativity, etc, and you won't have to worry about your genes.
Learn the rules so you know how to break them properly.
www.teslabox.com
Evolution has been going 100 times faster in the last 10,000 years than in the long, tedious years before it during which we let our "weak" people die because we hadn't invented medicine more advanced than "lie down and hope you get better soon." http://discovermagazine.com/2009/mar/09-they-dont-make-homo-sapiens-like-they-used-to/article_view?b_start:int=0&-C=
Now, kindly turn in your keys at the door and never come back.
A symptom called "Flat Affect:" makes it nearly impossible to express emotion in any normal kind of way. It's not that I don't experience emotion - I very definitely do - but I am unable to show my feelings outwardly. My expression is always wooden, a poker face. It makes it very, very difficult to connect with other people, especially the opposite sex.
My most prevalent schizoaffective symptom is depression which is often profound and can be suicidal. I also experience a profoundly euphoric state called mania. One might think that it's not so bad because it is actually a very happy, joyful feeling, it is actually the worst of the schizoaffective symptoms because when I am manic, I am utterly and completely out of touch with reality. I am like a bull in a china shop. When I am manic, it is a matter for the police - lots and lots and lots of police.
But all of this pales in comparison with my Obsessive Compulsive Personality Disorder. One reason is that I understood from the very beginning that my schizoaffective disorder was bad and just why it was bad, so I was able to work from the very beginning to overcome it. But I had been in psytherapeutic and psychiatric treatment for twenty-four years before I was finally able to understand just how destructive my OCPD had been, not just to me, but to everyone that I cared about.
Simply being crazy is not so bad. There are many ways to cope, many ways to get by. What really is bad is to be crazy, yet completely unaware of it, Thus it was with me and my Obsessive Compulsive Personality.
I would be very grateful if you would read this short essay, it is just five pages or so:
Kuro5hin's undermyne said of me:
I am grateful for all of your kind understanding.
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Don't worry about natural selection; it's still killing us. While it's true that we're no longer being eaten by giant bears and saber-tooth tigers, we have a bunch of new things that can kill us, like traffic, drug addiction, and modern warfare. Also, the old killers like disease and famine never went away. Modern society probably puts different selective pressures on us, but we still have to adapt to our surroundings.
Stimulant treatment for ADHD gets a bad rap. It's commonly said that we are drugging our children just to get them through school. It's not that way; ADHD is treated with stimulants because they boost certain neurotransmitters in a way that overcomes most of the illness' debilitating effects. People with ADHD don't generally get high when we take stimulants. In my case, taking Amphetamine calms me down and enables me to write code productively. When my medicine is working particularly well, it gives me a rather lethargic, calm and almost sedated experience - during which I am able to write mountains of code.
Request your free CD of my piano music.
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They may not be looking at the exact form of the disorder that is affecting you, but at least it's close. You might want to contact the authors and see what they can do. The posted article points out that researchers are moving into studying more rare and complex disease forms, so your case might interest them.
GWAS = http://en.wikipedia.org/wiki/Genome-wide_association_study/. I have no idea if they are using the same technology as in the posted article, but it's a very recent study (2009) so it's an active research area.
As an aside, I really feel for you, man. My mother used to run a care facility for Schizophrenics, so I grew up seeing some of the effects. They usually did not show symptoms as severe as yours, though now and then there were more complicated clients. Not a pretty sight, even for those with more "manageable" forms of the disorder. I can only imagine a case like yours.
Good luck
It's hard work being a degenerate, you know. It's good to know that my efforts are paying off.
Request your free CD of my piano music.