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March 19, 2014 10:51 AM   Subscribe

You Are Not My Genetic Counselor, But Neither Are Any of these Self-Styled Uncertified Genetic Counselors on the Internet. The latest fad/quackwatch for desperate parents and patients dealing with autism spectrum disorders or chronic illness seems to be running raw data from consumer genetics testing through an app (or paying hundreds of dollars more for a "nutrigenomics" panel) to check for polymorphisms. Consumers get back lists (helpfully color-coded like traffic lights) of normal, heterozygous, and homozygous gene pairs, but how common are these variations to begin with (setting aside how often they are actually expressed as illness)?

Most popular seem to be "methylation pathway analysis" reports, that look like this sample here (provided by the test site).

Another service also provides reports for genes grouped under further categories like "mitochondrial" (ATP5g3, ATP5c1, COX5a, COX6c, NDUFS3, NDUFS7, NDUFS8, UQCRC2), IgE (FCER1a, Il-13 C1112T, DARC, IL13, RAD50, C3, SOCS-1 -820G>T), etc.

How common are polymorphisms for everyone, healthy or sick, neurotypical or ASD? (Setting aside the issue of how often polymorphisms are actually expressed as illness by any given individual, or whether this info is of any use for diagnosis or treatment by physicians--those would be worth their own questions, but I'm specifically just asking about "abnormal" test reports.) There is enough info on out there accessible to a layperson that, for instance, I can determine that a very large part of the population (variable ethnic group) has a +/- mutation on the infamous (and widely studied) MTHFR, but I'm having trouble finding information on whether anyone who gets back these reports should actually alert their physician about the yellows and smatterings of reds you see in the reports people are sharing online.
posted by blue suede stockings to Health & Fitness (3 answers total) 3 users marked this as a favorite
If all you want is how common a polymorphism in a gene is, you can use the NCBI gene lookup tool (example for COX6C). In the "variation" section the "SNP geneotype report" will list known SNPs and the MAF (minor allele frequency = how common is the less common allele, eg .1322 in the first SNP means 13.22% of all copies are the minor allele). There is of course lots of other data on that page including papers focusing on that gene. What you should go to your doctor with is a separate question.
posted by a robot made out of meat at 1:30 PM on March 19 [3 favorites]

As far as how common they are, generally, as much as Wikipedia is not always a great source, if they've got their definitions right, well... "All the common blood types, such as the ABO blood group system, are genetic polymorphisms." So, well, if you have a blood type, you have a polymorphism, as far as I can tell. It isn't a place where your genetic code is somehow malfunctioning, it's just a variation.

There are lots of things where genetic variation clearly does explain all or part of various illnesses, but, well, it's an easy target for the woo-woo practitioners. As far as whether you should talk to a doctor, I think it would depend heavily on what the report shows. Big difference between "surprise, you have an atypical case of cystic fibrosis" and "surprise, you have a gene that we think maybe means you need a particular type of nutritional supplement that we'd be happy to sell you". For the latter, well, if they have studies that back it up, great. If not, it's just like any other hokum.
posted by Sequence at 1:51 PM on March 19

There is a very strong tendency in popular culture to regard genetic sequencing as a literal transcription of the elements that constitute yourself, but this is not a very good representation of the truth.

Like any chunk of code that constitutes a program, there's a lot of stuff that isn't being currently used. There are redundant copies, old revisions, total junk. There are entire sections that look like they're working but in another section of the code you can see how that library isn't even being accessed by anything else, it's just running in circles around itself. Maybe it's being blocked.

Maybe there was an error but the code was unaffected, or only minimally affected.

Your genetic report can show that your genes are trashed, but you never have any problems. There are a lot of back up systems in the human body, and we haven't mapped it all out yet. If that's even possible. The reverse is true as well, your report could show that there's never been any correlation between your sequence and a certain disease, and you have a roaring case of cystic fibrosis.

This is just a very long way of saying that in general, anything you will be able to find is not going to affect the entirely clinical diagnosis of autism, or the treatment. Similarly with chronic illness, although with the exception of a very few, very rare, and very debilitating diseases that generally have no cure or treatment.

And with the exception of very, very few doctors nobody is going to have the faintest idea what you're talking about when you come in with some esoteric gene report. Because, as I said, it's not useful information. Yet.

However, who knows what the future will hold. I certainly hope that we see great things from genetics, but so far there's been a lot of promise and a lot of really problematic technical issues preventing developments from reaching any clinical import.
posted by hobo gitano de queretaro at 1:57 PM on March 19 [4 favorites]

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