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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.
if you're reading this, you're unlikely to have offspring.
Do you even lift?
These aren't the 'roids you're looking for.
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.
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)
Bucket? Stapler?
I think you're talking about the more advanced operation "How to remove your liver and live just long enough to put it in a bucket.
People should start with "Remove your liver" that just requires the knife, and then grow up to more complex things.
If you enjoyed this comment you may also like:
"Replacing your blood with pink lemonade and how to stop the brutal pain".
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.
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
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.
"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.
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.)
If you're at the point where you're discussing the strong possibility of starting a family, you owe it to your partner and yourself to be completely open about your medical history and that of your ancestors. Waiting until after what many people consider to be the point of no return is grossly unfair to your partner and the potential child.
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.
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.
about said genetic abnormalities? I have one that caused me(and my brother) to be born with 6 fingers....
I know someone who is looking for you...
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.
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?
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...
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"
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
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 ]
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.