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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."
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.
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".
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.)
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.
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.
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.
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"