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How To Check Yourself For Abnormal Genes
AnneWoahHickey writes "While the State of California was harassing personalized genomics companies, and hindering the development of personalized medicine, Wired was preparing a guide to genetic testing. It explains how to make sense of the massive sets of raw data offered by 23andMe or deCODEme, and a way to check yourself for genetic abnormalities that are not covered by microarray tests. Facing a medical community that is fiercely resistant to change, the fate of personalized medicine is truly in the hands of consumers."
You up reading Slashdot at this hour. Don't worry about checking. You got 'em.
All you need :
A bucket
A sharp knife
A stapler
if you're reading this, you're unlikely to have offspring.
Do you even lift?
These aren't the 'roids you're looking for.
How To Check Yourself For Abnormal Genes
I am gonna recommend it to my boss.
hilarious
OK - so first of all 23andme et al do not search for "abnormal genes" - they look for common polymorphisms present in human DNA sequences. These are not abnormal, simply different. Secondly, rs numbers found in association with disease are practically valueless without the underlying functional data, plus replication of the association in different populations. For Zeus' sake, bear this in mind if you ever get one of these tests!
No way in hell anyone who hasn't had massive experience with PCR is going to get results from a DIY PCR. Extracting DNA from a sample is dead easy with the latest generation of kits, and DNA Is fairly stable stuff, but PCR protocols, although simple, are incredibly touchy and take a lot of time to get consistent results from.
The rough equivalent of having a page that says to Joe Public that he can either pay some professional to build a custom database for his companies needs, or he can download OpenOffice and do it himself. It's only cheaper if you don't put a value on time, quality or results.
Yes, I know, I must be new here...
I shop at the Levi Irregular Outlet. Good prices!
"Design and Order PCR primers and controls"
"You'll need a cloning kit"
"Copy the DNA with the PCR reaction"
"Sequence the amplified genetic material."
While going to specialists sounds reasonable, we've only just reached the stage where testing large numbers of people is feasible, and only really through DNA microarrays.
The idea that you could do it yourself using methods invented in the mid-90's methods is just silly.
I welcome some oversight since I lack the knowledge in the area to tell the difference between a quack giving me bullshit "test results" and someone who actually knows what they're doing giving me useful information.
No I am not willing to learn enough genetics to spot a quack.
Reading assembler code without a reference manual for the masses.
The simple truth is that interstellar distances will not fit into the human imagination
- Douglas Adams
Online genetic testing exposed as a scam
"I love my job, but I hate talking to people like you" (Freddie Mercury)
Use a mirror. Pointy head? alarmingly low/thick/broad brow? Lantern jaw? Narrow eyes remarkably close together? Then you probably won't easily get medical insurance, what with all the hooch and the home grown tobaccy. But never mind, you still got your banjo, your smooth bore and your free AOL CD.
Now I can find out before the fact whether blasting myself with radiation will kill me or awaken my superhero abilities.
specialized companies test genes. brac gene (breast cancer), apoe (alzheimer's), fragile x, etc. you can do this by mail even
just make sure to use a name like donald duck or dick johnson. you don't want this info getting to insurance companies
might as well test that little 1 year old (not any older, consider the trauma for the kid) for parentage too. it has been speculated that something like 10% of babies born before the age of genetic testing were raised by fathers oblivious to the fact they were not the real genetic father of the kid
intellectual property law is philosophically incoherent. it is your moral duty to ignore it or sabotage it
Yeah, this is never going to cause huge panics amongst the dumb/easily influenced when they mess their test up and get dodgy results.
Yet another way to part the gullible from his money, I guess.
Finally! A way to find out why I get green and big when I get angry!
And remember, if you see something you don't like you've got the source code...
This article was clearly written by someone who has no clues to this kind of work. It covers the basic steps although the draft described would not even work (designing primers just by picking 20 bp sequences without checking if you design them into some repeat, or other non unique sequence, without checking that there is no hairpin formation, no primer dimers etc, also he just says 40 cycles in PCR machine without saying that for each prime pairs you need a specific annealing step and describing what other heating steps are required in the PCR machine). Other thing is that he forgot to mention costs and time to do this. Lets say a primer pair is just $1 (it is more even if you order the smallest amount) and one PCR run is roughly 2 hours (with 40 samples) also preparing 40 different samples takes like at least 1 hour of work. Plus you need the materials for PCR (PCR grade water, MgCl2, buffer, the polymerase ensyme, for like 100 reactions at cheapest you can buy them for like $50-100). The PCR machine cost will be almost negligible with its $1000. Now calculate the costs and time needed for like 1 million SNPS. And you realize that home made traditional PCR techniques won't work. Lastly what if you find some SNPs different than others. You need to know the different databases, you need to be able to filter the 99% junk from somethign valid since most of the SNPs are just variations without any change of the functionality. At best they are linked to some disease at a given population and could have no meaning at an other population.
but i am already envisioning the late night infomercials
a little bit of knowledge + a lot of fear = $$$
intellectual property law is philosophically incoherent. it is your moral duty to ignore it or sabotage it
"Facing a medical community that is fiercely resistant to change..." really? Thats a bold claim to make especially considering the amount of medical research that happens in this country.
The next step will be the ability to get an assay done on a potential mate, or even random partner (as in Gattaca). While that might be a good thing for he human race in general I'm sure there will be a lot of hate and discontent over it - oh wait, there already is...
Why you'd want this: Hypochondriasis
If a train station is a place where a train stops, what's a workstation?
Services like those mentioned in TFA may be able to provide information on which genetic variants a person carries, but will not interpret those results. Non-scientists, and even scientists seem to over estimate the ability of modern genetics to assign meaning to common genetic variation. Your average M.D. when confronted with a print out of a patients 'mutations' would be completely unable to make heads or tails of them. There are few instances such as cystic fibrosis, where the etiology is well known, and known mutations WILL cause disease. In other cases such as BRCA in breast cancer, 'mutations' are risk factors for disease. In the vast majority of cases, modern genetics has no idea what a 'mutation' at rs39842093 might actually do. These services are expensive, ambiguous, and require a certain measure of vanity on the part of the consumer. If you have a family history of disease X, there may be a small number of 'mutations' for which you might be tested that could actually impact your future health, and those services are provided by someone other than 23andMe. Biology is a bit different than technology in that observing that biology works does not imply that someone knows how it works. (Creationists can bite me.)
about said genetic abnormalities? I have one that caused me(and my brother) to be born with 6 fingers and toes, we had surgery as infants to correct the abnormality, but obviously the code is still in my genes. How would one go about telling someone that they wanted to have kids with about a genetic abnormality? Or should you wait until after the bun is in the oven so to speak....
Monstar L
Can anyone tell me if this is complete hyperbole, or if it's the real deal? For that matter, why does the CA legislature even care about this?
There's an easy test-- if your hand is bigger than your face you have abnormal genes...
Step 1: Hold your leftmost tentacle approximately 4-6 inches from your middle eye.
Speaking as someone who has done a PhD on genome-wide microarray SNP analysis, I can tell you that we are not yet at a point of maturity where you can simply put a drop of blood in a machine and get reliable prognostic information or lifestyle and treatment recommendations.
The technology is actively researched, i.e. most often we're not looking at the results from a clinical standpoint but as an indicator of the performance of a certain method. Practically speaking, only research centers are interested at the stuff and you would be extremely hard pressed to convince practicing doctors to incorporate current results in their everyday work, even though some studies have appeared in famous medical journals (New England Journal of Medicine, Nature etc). Using software notation, the results are "alpha" grade at the moment.
That being said, there is no harm in knowing that you have an Adenine in position XXXX. Harm comes from acting upon that knowledge without sufficient clinical evidence.
P.
From my future hiring boss:
We're sorry, but we cannot entertain the possibility of hiring you on the grounds that your genes are far too normal. We have a very strict policy of only hiring miscreants and dead-weight with abnormal genes. This may seem... odd at first glance, however, hiring individuals with clear sense and an overall good mental and physical disposition are counter-intuitive to our mission statements goal of creating an immoral, crooked and inefficient operation. You see, the more problems YOU have, the less you will attempt to undermine OUR low standards by introducing your "perfect 23" culture. Maybe check back with us after some reverse gene therapy.
Sincerely, Mr. Asshat HR Dude
If you have a huge proboscis and you're wearing Jordache, you're screwed on both counts.
If you do what you always did, you get what you always got.
Whoever wrote this article shows a gross misunderstanding about how genetics actually works. The central dogma of genetics applies here: DNA is transcribed into mRNA, and translated into proteins, which can then be post-translationally modified.,
First - a single nucleotide change may or may not cause a "genetic defect." Translation involves taking three nucleotides (aka bases) and getting the appropriate amino acid from that. There are 20 common amino acids, and 64 combinations - so there is some overlap. If the changes nucleotide doesn't change the corresponding amino acid, it doesn't matter.
Second - not all mutations are harmful. If a mutation happens in an exon (a piece that is cut out), there may well be no difference if there is a mutation there or not. Even if it' is in a part that is kept, it may not be in a part of the protein that dictates structure or function.
Third - most organisms, including humans, have built in redundancies and backups. Losing a gene doesn't usually mean losing the protein, because often something else will make the product another way, or compensate. In diploid organisms often this can be duplicated genes or the other allele.
In short, in order to truly make sense of the data given by these companies you really need to know at least the basics of genetics and have an understanding of how the gene and protein work. These are no small tasks and, surprise, generally results in getting a degree in some branch of biology.
Now I just to go thru 10 years of medical training and we'll be good to go!
oogly boogly!
Requiring the test results not be released to anyone but the PATIENT would strike me as a benefit to privacy. No releasing to anyone but the doctor is a whole different issue, having nothing to do with privacy and everything to do with an (justified or not) lack of faith in the general public's ability to have access to their own data without turning into raging hypochondriacs.
I would approach such genetic testing with caution if the health care provider (or service) isn't going to provide a lot of education about your risk factors and how to interpret your results.
Last year, I participated in a medical study to find out what patients' reactions would be to genetic testing http://www.nih.gov/news/pr/may2007/nhgri-03.htm . Education was a key part to interpreting the results. It helped you understand your risk factors.
The genes the NIH tested were largely offset by lifestyle choices--exercise, diet, etc.
Trust me, I went through a whole range of emotions--intrigue, anxiety, curiousity. Hey, it even got our family to talk about our medical histories. By the time I got my results, there were no surprises.
The average person, no. The obsessed amature with training in a closely related enough field to be able to follow protocols precisely (any branch of biology and a lot of chemistry), with enough money to afford these supplies (probably dozens of times over given how finicky PCR can be even under controlled laboratory conditions) would probably genotype themselves for 5-10 alleles. But I think a lot of people are missing the point of this article. It's not that everyone could do it, or even anyone really SHOULD do it. It's that these techniques have become simple enough and cheap enough that people who are sufficiently interested can do this at home. It's the same reason people install Linux on their toasters, or mod a 360 into a laptop, not because the end result is that useful, but because it's so cool that they CAN.
Most abnormal genes arent expressed for unclear reasons. You just spend money on useless information and mental energy worrying about the results.
> a (justified or not) lack of faith in the general public's ability to have access to their own data without turning into raging hypochondriacs.
Maybe it would be good for people to know more about their risks of having certain diseases. It puts other things in perspective. Why worry about terrorists when you are 10.000 times more likely to die in some other way? Why be a hypochondriac when it is X times more likely that you'll die in a car-crash?
Hey is that a mutation in your genes or are you just happy to see me?
Deserves 5: Insightful
by filing a Freedom of Information Act request against the FBI, which has undoubtedly already taken my DNA from some place or another under a secret government civilian spy program...
If you're reading slashdot, you can already check off one of the abnormalities...
(grin)
I might know what I'm talkin' about, but then again, this is Slashdot...
That's extremely difficult especially for multifactorial maladies which environment plays a major role. If you want serious answers get a professional explain and investigate, don't simply rely on DNA companies.
In other words, it's not that the medical community that is "fiercely resistant", but because the questions that need to be answered are much more than percentages.
"Sum Ergo Cogito"
1. sits in basement all day
2. eats nothing but junk food
3. consumes "energy drinks"
4. is an expert in Perl and hates Python
5. belongs to many mailing lists
6. has an excellent Slashdot Karma
7. Runs Slashdot
One of the main problems is the education they give you is usually along the lines of 'Well it seems your genes say you and your children will die unless you buy our patented combination of nutritional supplements'.
On a personal note, I'm interested to know if knowing your genotype has changed your life or lifestyle in any way?
Check out snpedia.com and look up the rs number. http://snpedia.com/index.php?title=SNPedia
You can figure out what disease you're susceptible to based on the rs number.
The "rs number" is the ID number for the "SNP" : the single nucleotide polymorphism.
There are a lot of people bashing this and I agree, something like what deCODEme and 23andMe provide is probably not for most people.
On the other hand, I could actually use something like this. I have some unusual issues that are very probably genetic in origin. In fact, I have a good idea of one possible genetic cause to 3 major symptoms that I have. I've spent years with various diagnoses and none of them have panned out.
There are no other tests for the particular genetic defect I suspect I have. For $985, I can find out (I checked, and the SNPs for the gene I'm looking for are covered). Given that it's took 7 years to find a medication that worked for one of my issues, nailing down the cause could end up saving me money in the long run (and if this had been available 7 years ago, might have saved me a lot of grief).
So, I'll grant, this isn't for everyone. The results are very hard for a lay person to interpret. But for some people, they could be quite handy.
On a similar note, New York's government has recently tried to pass a law requiring licensing for the people operating air-quality monitoring devices:
See? It is all for our own good. Don't you worry your pretty little head and let the (licensed) professionals do their jobs. And when/if the Executive government decides to withdraw a license of some of the operators, it can do that — without the hurdles of going through the Judiciary — just as it can already do with the drivers' licenses. (What an invention that was!)
In Soviet Washington the swamp drains you.
Give me a break - the medical community is enthusiastic to the point being mesmerized by personalized medicine. Consumers need to worry about the "self fulfilling monopoly" aspects of personalized therapy. Once you have spent a lot of time and money diagnosing your unique disorder, the drug company offering you a customized treatment effectively has no competition. There is a good chance that they will charge painfully exorbitant prices. Look at recently released cancer drugs like Avastin, treatment costs $90k per patient per year!
The real issue is demonstrating that these strategies are effective when the specific treatments are only being given to a single patient. Hard to design an objective clinical trial validating efficacy under those conditions. The fate of personalized medicine is truly in the hands of the FDA.
P.S. Agree completely with the comments that this "how to" article is infeasible and written by someone with serious misunderstandings of the technology and underlying science.
Statesman
This is egregiously incorrect and demonstrates a fundamental lack of understanding of the situation. If you think it's as easy as: "I have mutation A, so I need to do B, and then I will be cured of C" then you're sadly ignorant of the reality, unfortunately. (I wish it were that easy. I am an oncologist who works some with targeted therapies, which is what we are striving to achieve. But it is very complicated due to the reasons listed below, which in themselves are a gross simplification of the reality.)
in my jeans.
Why such a weird question? Just look at parents, or gather the hearsay if you can't look. I am a splitting image of a dead grandfather. My parents from another universe. You could even study botany. A pink and blue flower made a red one... the red one two generations previoused, thought to be disappeared. So very simple.Anything is possible. Environment makes changes, the mysteries never seen. Bullcrap question done.
Why don't you tell me why I need someone with an MD behind their name to tell me what a standard output from a machine which takes a centrifuge of my spit, processes it through a standard chip and pulls out my dna composed against probable issues I could have, which THEN I can do a high-end explicit test from an MD afterwards?
You don't need the MD for the actual processing of the sample. As you put it, a monkey could do it.
You need the MD for the counselling that goes together with the result giving. To avoid people misinterpreting the results, putting wild theories because one test came back as positive, or to notice that the patient is too much distressed after some news and might be at risk of doing something crazy.
You also need an MD to discuss before hand of the utility of the test, their significance, what they are *actually* going to bring, dispel false beliefs or flase hopes the patient may have, etc.
In short, the MD is not here for the test, but for everything that comes around it.
People keep on forgetting that these test are never set as a be-all, end-all for probable medical conditions and therefore you use this as a stepping stone to check out things further.
The problem is, if you don't regulate thing a tad, there are bound to be companies that will try to profit by selling their results *AS the ultimate end-all* and who are going to profit from all the gullible idiots who'll believe them. /.er. You're a geek able to understand what such tests might mean. Believe me : 90% of the patient stepping inside a doctor's office aren't.
You're a
The worse is : by believing that these test are end-all, the clients of unscrupulous test-seller could jump to conclusion and do really, *really* silly stuff.
The world is full of very ill-informed patient who read random junk on the net and distrust all doctors because none of them agrees with what the patient thinks having understood.
This is a paternalistic approach but until you have something better to propose, it's the simplest thing to avoid problems.
But I personally think that this is a little bit too restrictive. The technology should be sold as home-use kits to everyone, as long as the buyer has received proper counselling before hand by the doctor, the licensed reseller or the pharmacist which provided him the test.
I can understand if they were falsely advertising themselves as a substitute to the ultra-stringent high-end tests used for serious conditions, but as long as they aren't, this is anti-american as it gets.
Trust the human greed. If nothing forbids it, someone is bound to try it.
Even if it is not actually written on the box (that would be false advertising), some company will definitely try to make sure that the buyers think it.
It's the SAME DAMN THING!!!
Except nobody has commited suicide over a air pressure level. Yet.
Disclaimer: IA*A*MD, and although I currently work in research, I have met lots of the gullible patients putting more trusts into random pieces of junk they read over the intertube than into people with several years of study and several years of experience who are trying to help them.
"Sufficiently advanced satire is indistinguishable from reality." - [Tips: 1DrYakQDKCQ6y52z6QbnkxHXAocMZJE61o ]
And we'll teach you how to become one of the talking heads!
Its simple, remove your head, and Ta f***in Da! You're a talking head!!
Abnormal Genes?
I thought you said -
Have Normal Jeans!
Instead of those baggy, crotch-at-the-knee, Maytag repair man vista clones.
But I guess 'Abnormal Jeans' works too.
Start reading the title as, "How to check yourself before you wreck yourself"? I did.
That is true but we must acknowledge that many if not most such claims have failed to replicate and they are probably mostly statistical errors -- do enough research and you will eventually "find" something that isn't real. Those of us in the business are highly skeptical of all original claims unless they are overwhelmingly strong. In the absence of consistent replication we tend to withhold judgment on the validity of a result.
The article continued:
If you are checking yourself for a certain genotype, then we could say that you are checking yourself for an inherited trait, but we usually don't refer to genotypes as traits. I think the author of the article is presuming a strong relationship of a genotype with some trait like a form of cancer, asthma, longevity, schizophrenia, myocardial infarction or stroke. He then suggests that readers can study that trait in themselves by looking at their genotypes. Unfortunately, even if the studies that claimed to establish an association of the genotype with the trait were correct, the association might be so weak that it isn't clinically useful. For example, if schizophrenia occurs in 1% of the general population but in 1.2% of people with a certain genotype, that is a 20% increase in risk for that genotype, which might lead to a statistically significant result that is published in a journal, promoted by a university press release and then published in newspapers all over the world. But to any individual, knowing their genotype would change their schizophrenia risk by only 0.2%. Is it worthwhile to know about such a minor risk factor?
It gets worse. The person who tests himself might then decide that he is a high-risk person or a low-risk person based on this one genotype, but that is a very bad way to decide risk. With schizophrenia, for example, a positive family history can increase your risk by a factor of 10 or more (depending on which relative[s] are affected). Also, having pre-schizophrenic symptoms will imply higher risk. Age of onset is usually before age 40, so people older than 40 who are not already schizophrenic have low risk. So a 20-year-old man who is having mild hallucinatory experiences, coming up with really odd ideas and who has two schizophrenic brothers might take the test, find out he doesn't have the 1.2% genotype and conclude that he is at low risk of schizophrenia. He would be mistaken.
With regard to heart disease: Ignore your genotype but watch your blood pressure, eat well and exercise. Same for stroke, diabetes, obesity and many other traits.
Most of the value in new genetics research for so-called "complex diseases" (a.k.a. multifactorial diseases) is in the implications for breakthroughs in understanding pathophysiology. Most findings have little or no implication for individuals.
here in kentucky we've used personalized testing for genetic abnormalities for years. When she takes her shoes off, if she has six toes, genetic abnormality sighted. No need for microarrays, just don't date that chic if you also have six toes. It's the rule of toe in my family.