Where can I get a specific gene tested for mutations/polymorphisms?

December 3, 2006 7:13 PM

Where can I get a specific gene tested for mutations/polymorphisms?

I do part-time research on a health syndrome I have. My recent readings have led me to believe that I have a mutation/polymorphism of a particular gene. I'm wondering where I could get my DNA screened for abnormalities of this gene. This is not at all one of the standard clinical tests that doctors order. I understand that it's very easy to resequence a gene these days, but I'm wondering what kinds of places are willing to do it on a patient's request. That is, a university genetics lab has the equipment to do it, but it might not have the human subject protocols, or might have a policy of not doing experiments that are not related to the lab's research.

I know that "ask your doctor" is the standard sage advice, but I long ago exhausted my GP and specialist's knowledge.

Thanks!

posted by wireless to health & fitness (17 comments total)

I'm not sure where you can do it--but i'm in med school and a genetics nut--so you mind saying what you have? and why you think so? thanks
posted by uncballzer at 7:33 PM on December 3, 2006

You could email the people who are researching the syndrome you think you have and ask them about this. Their email addresses will be printed in their journal articles on the subject. These can be easily located by searching Pubmed, although depending on the journal you may not be able to access the full text if you are doing this from home - I am assuming you have access to a University library or some such. You should still be able to find their home-pages now you know their name and institution, and email addresses will be there.

People who are researching genetic diseases will often be interested in finding novel mutations that cause the disease. You have not provided enough information for us to guess whether this will be the case for your syndrome. In any case, labs that are already working on this gene are the way to go; nobody else will be interested.

I would imagine, however, that there is a whole lot of red tape involving genetic counselling, referrals from your doctor to an appropriate specialist, etc etc that will be necessary. I don't know much about that stuff, I only sequence mutations from fruit flies.
posted by nowonmai at 7:53 PM on December 3, 2006

Many hospitals have genetic counselors now, sometimes associated with the Peds or Reproductive Health departments.
posted by gramcracker at 7:58 PM on December 3, 2006

Contact some researchers studying your gene (as nowonmai suggested). They'll certainly have the human protocol taken care of and would be interested. In lieu of that, contact a local molecular anthropologist, who are used to working with human subjects and have passed the IRB. They may not have the right enzymes to work with, but would probably be glad to 1. do it if you pay for the chemicals or at least 2. refer you to a friend that would be interested.
posted by The Michael The at 8:03 PM on December 3, 2006

Your actual best bet would be to have a friend who ran or worked in a lab, who would be willing to do the work for you off the record (probably providing you pay for the relatively inexpensive primers and sequencing reactions, probably under $100 for a single gene). Not that I myself would ever do this of course...

The second best option would be to follow nowonmai's advice and contact researchers working on your disease. If those researchers already have an IRB protocol (review board that must approve all collection and uses of human patient data) that covers sequencing of patient DNA, you have a shot. Otherwise, the lab probably isn't going to jump through the very considerable hoops to get approval to sequence your gene(s). But it never hurts to contact them.

I know that various companies offer commercial genetic testing (Genzyme, for example). I'm not sure if they only offer a particular set of tests (cystic fibrosis, brca cancer genes, etc) or if they will develop a custom test for you. Googling some combination of "genetic counseling" and "gene sequencing" might get you the contact information for more companies.

However, if the gene you think you might have a mutation in does not already have well-established polymorphisms, just knowing your code without any context won't be too helpful.
posted by twoporedomain at 8:16 PM on December 3, 2006

I do not recommend having another person do this work under the table. If you go that route, make sure that they are cleared to work with human tissues. Yeah it'd be great to figure this out and I'm sure your friend would get a kick out of the actual work, but all that fun goes right out the window when people get fired for working with tissue they're not supposed to, or when the head of a lab questions why his grant money is paying for a project he never wanted to do.

If you do find a willing and qualified lab it should be pretty darn straight forward and simple to sequence your gene. As mentioned above that may not actually give you any information if the disease causing mutations are not already known.
posted by Science! at 8:58 PM on December 3, 2006

You could email the people who are researching the syndrome you think you have and ask them about this. Their email addresses will be printed in their journal articles on the subject.

I third this advice very much. If your syndrome involves genetic polymorphisms then I'd be surprised if someone isn't researching them. Any authors working in the field should be able to tell you what work is gong on and who is doing it. If you're having trouble finding full pdfs of applicable articles drop me a line (email is in profile), I have great journal access myself or can direct you to a couple of livejournal groups which can help.

Just as an example I'm studying Inflammatory Bowel Disease and the group I work with is genotyping people like crazy. We're very interested in finding more participants for our studies, and the people involved get good information out of it also (and as an aside, anyone with any form of IBD in NZ not involved in the NuNZ study, contact me *grin*).

I'd also like to second this spot-on comment:
However, if the gene you think you might have a mutation in does not already have well-established polymorphisms, just knowing your code without any context won't be too helpful.
Individual genomics still has a long way to go, and often times knowing the underlying polymorphism doesn't help us yet. Also many syndromes and disorders are multigenic and complex, there may be a whole bunch of things going on.
posted by shelleycat at 9:20 PM on December 3, 2006

You might be able to find a genetic/genomic core facility to help you. I know our lab routinely does this sort of thing for doctors who suspect a particular gene harbours a mutation in one of their patients. I would either call or have your physician call a local genome core (Google 'dna core facility') and ask if they could arrange the sequencing. They'd probably charge for reagents and technician time, but I'm sure it could be done.
posted by greatgefilte at 9:53 PM on December 3, 2006

Also, what everyone else is saying about the questionable significance of any mutations/polymorphisms that haven't been documented. Unless it's something obvious.
posted by greatgefilte at 10:19 PM on December 3, 2006

Thanks for the amazing replies so far! Those are some great ideas.

Good point about the polymorphisms being known; I should have mentioned this. There are in fact well established polymorphisms for this gene (it's for a particular nerve receptor). However, nobody is studying this receptor as it relates to my condition, although I have a strong suspicion that it is involved in my particular case.
posted by wireless at 10:38 PM on December 3, 2006

Have you seen a clinical geneticist? I'd imagine a proper specialist would be very interested in what you have to say.
posted by altolinguistic at 2:06 AM on December 4, 2006

However, nobody is studying this receptor as it relates to my condition, although I have a strong suspicion that it is involved in my particular case.

This does not sound like you have a strong basis for your hypothesis. You are being very vague here, but if the syndrome and the gene have not previously been connected then it might be difficult to get people to take you seriously.
posted by nowonmai at 6:42 AM on December 4, 2006

So what you're saying is that there's no research being done on the connection of your unnamed gene to your unnamed condition? Well, there won't be any clinical studies to enroll in, in that case. I mean, you could contact any of the labs studying the gene or the condition and see if they can give you more information. If there's been no prior connection of the gene with your condition, it's most likely that if you do get a response from someone, they'll be telling you why the two aren't connected.

I want to know what makes you think you know more than the people doing the research!
posted by Mr. Gunn at 7:37 AM on December 4, 2006

Thanks for the last few replies.

>I want to know what makes you think you know more than the people doing the research!

I don't; I said I think it is involved in my particular case, not for others who have this condition.

For several reasons, including not wanting to give out personal genetic information on the internet, I don't want to turn this into a discussion on the merits of my hypothesis. Apologies to those who are curious.
posted by wireless at 9:19 AM on December 4, 2006

What is your goal in learning this information?

If the polymorphism is present, what will the effects and benefits be of learning this information? What decisions will this information help you make?

If the polymorphism is absent, what will the effects and benefits be of learning this information? What decisions will this information help you make?
posted by ikkyu2 at 10:23 AM on December 4, 2006

It sounds like what you want is an Orphan Disease Testing Center such as the one at UCLA.
posted by euphorb at 12:05 PM on December 4, 2006

You don't mention your gender or marital/partner status, but you might want to try one of the many pre-natal or pre-conception genetic screening centers. Tell the doc you're considering getting (you or your partner) pregnant, and you need the gene screened to try to prevent passing it on to your kid, i.e. you're thinking about doing IVF and pre-implantation genetic screening of all the embryos to avoid having to pass it on to the next generation. They might not want to help you, but they might want to help your hypothetical kid.

Be warned, though, that even for known and well-studied genetic syndromes that have identifiable gene mutations, that doesn't mean anyone actually tests for them! I went to an eminent genetic counselor at UCLA recently to learn if pre-implantation screening was available for hereditary spherocytosis, which I have (thanks to a de novo mutation) and which I'd rather not pass on to my kids, if possible. The doc said that not only has no one done that kind of screening yet, but only one lab on the planet even offers the genetic screen, and it's somewhere in Europe, or possibly Russia. Also, it would be ridiculously expensive to do the screening. So, it's gonna be an old-fashioned roll of the dice for my future kids, and we'll just hope they get lucky and inherit some other, better, gene from me, like decent height.

And that's all for a fairly common disorder, 1 in 5000. So an even rarer disorder like yours is a longshot, but I guess it's worth a try.

Good luck! And make sure you publish your results somwhere if you're right. No use hoarding data that could help other people with your condition.
posted by Asparagirl at 4:43 PM on December 6, 2006