DIY DNA research

February 2, 2009 4:29 AM

Hugh Reinhoff has sequenced his daughters DNA at home attempting to diagnose her unique genetic mutation.

Although most parents don't have his background, he also started a website to bring together the parents of children with undiagnosed disorders, and doctors who are interested in the area. At least one family has found their answers through the community already.

posted by jacalata (22 comments total)

I wonder what the ethical ramifications of publishing the results of his research would be.

As a student in the biomedical sciences whose specific interest is in neurogenetics, I am tempted to create an account on this website just to contribute as someone who, while it'll be a few years before I get my PhD, has some useful knowledge and might be able to fill in a few gaps as regards resources (I noticed he didn't include links to NIH's Office of Rare Diseases department).

If enough word gets out about this, Reinhoff could make a huge dent in figuring out the problems of these children.
posted by kldickson at 4:54 AM on February 2

I wonder what the ethical ramifications of publishing the results of his research would be.

What prompted this question?
posted by DU at 5:19 AM on February 2

I wonder what the ethical ramifications of publishing the results of his research would be.

What prompted this question?

It looks more like a rhetorical statement.
posted by P.o.B. at 5:44 AM on February 2

Probably this:

Rienhoff first asked Lee to do the DNA sequencing. But Lee declined on bureaucratic grounds. Professors who wish to work with human genetic material need clearance from their university's institutional review board. This onerous approval processes can take months, and there was no guarantee Lee would get the OK.

There's been a lot of unethical science: scaring kids to turn them into stutterers, Tuskegee, Buck v. Bell "eugenics", etc. So strong IRBs are necessary. But something's gotten out of hand if IRBs are essentially preventing scientists from reading something. Taking a generic sample is so risk-free we even allow cops and other laymen to do it; once a mouth swab or blood sample's been taken, there's no further even negligible risk to a patient other than non-anonymous disclosure and that only because insurance company gate-keeping.

We are on the cusp of being able to do individualized medicine, by sequencing genomes and comparing those to parents and to the general population. Since much of this will be able to be automated, the price will come down; and to the extent that better knowledge of each patients' biological processes can allow to eschew the inappropriate and pinpoint better therapies for them sooner and even in the advance of symptoms, it has the potential to make health care less expensive. Academic medicine needs to be embracing, not frustrating this. Medical bureaucrats need to streamline procedures, not get in the way.
posted by orthogonality at 5:47 AM on February 2 [3 favorites has favorites]

A while back I was using my vacuum and noticed someone's hair was wrapped up in the roller; probably my old roommate's. I though, "Heh, if I believed in Voodoo or something like that I could take their hair and gain power over them." Then I realized that within my lifetime that's actually going to work when I could take their hair and run it through my $100 Home Gene Machine and see if they had any genetically-determined weaknesses I could exploit. Future's gonna be interesting.
posted by TheOnlyCoolTim at 5:57 AM on February 2 [1 favorite has favorites]

Do you know why I love the 21st century? Because we have news headlines that could double as narration boxes in Spider-Man.
posted by The Whelk at 6:39 AM on February 2 [15 favorites has favorites]

Perhaps someone more involved than I can tell us about it, but biological colleagues, toxicologists, in my case, are starting to get hesitant about new research projects, not because they can't get funding (always a problem), equipment (ditto) or people (ditto, but thanks for sending us your best and brightest, BRIC countries!), but because it is very, very difficult to move samples from one lab to another. Like years-long process to source a new cell line, for example.
posted by bonehead at 7:27 AM on February 2

DIY DNA at home?
I'm thinking low-cost DNA sequencing for health insurance underwriting will be a growth industry over the next few years.
posted by Thorzdad at 7:31 AM on February 2

I'm thinking legislation prohibiting health insurance from requiring DNA before insuring with be within the next few years. Isn't the whole point of insurance to pool risk to protect individuals from uncontrollable variables?
posted by mrstrotsky at 8:02 AM on February 2 [1 favorite has favorites]

Taking a generic sample is so risk-free we even allow cops and other laymen to do it

The risk isn't that someone's swab is going to infect your mouth - the risk is that, with your DNA sequence published, each new genetic infirmity that's discovered is a new chance that you might never be able to change health insurance providers again...

In an imaginary free market full of perfectly shared information, that would be just something else to insure for: I pay you a premium, and instead of paying health-care costs that I incur now, you contract to pay future costs based on whatever genetic problems I discover now. As we start learning more and more about what our DNA means, though, I think the lemon problem is going to make such insurance impossible: who's going to insure your genetic code based on the fact that you totally pinky-swear that you haven't already looked at it and found something bad?
posted by roystgnr at 8:40 AM on February 2

mrstrotsky said, Isn't the whole point of insurance to pool risk to protect individuals from uncontrollable variables?

There is already a model for discrimination based on purely empirical statistical models: car insurance. The US supreme court just greenlighted gender based insurance pricing, and age and other non-driving related variables have been factored in for years.

DNA is a much more precise tool than this. You can bet that the American insurance lobby will push for this, and hard. I am afraid that the reality depicted in the movie Gattaca is not going to be far from the truth.

The insurance companies are going to do everything they can to wring every last dollar out of every soul and take every opportunity to wring every penny out of every situation. The time to resolve this issue in favor of ordinary people is now upon us, and we must act before big money does.
posted by Xoebe at 9:01 AM on February 2 [1 favorite has favorites]

If she dies and he doesn't find anything or find it in time, it's going to break his heart.
posted by Brandon Blatcher at 9:12 AM on February 2

If she dies and he doesn't find anything or find it in time, it's going to break his heart.

Yeah, I'm afraid he's looking for a needle in a haystack; in fact, it could be a green needle, a red needle, and a blue needle that need to all be in the haystack together to produce her symptoms and he can never identify it with an "n" of one. It's his only hope for his daughter, though, and if I were he, I would also be doing what he's doing. A father's love...
posted by Mental Wimp at 9:28 AM on February 2

All the sequencing in the world isn't going to help much if it's a copy number variation. I'm surprised he didn't start with that after the negative findings from the traditional genes.
posted by greatgefilte at 9:30 AM on February 2 [1 favorite has favorites]

Taking a generic sample is so risk-free we even allow cops and other laymen to do it

This raises an interesting question: do/should we have the right to be interrogated in a sort of clean-room bubble that leaves no genetic traces of ourselves with the police?

Police need a warrant to confiscate our personal property as evidence, right? If hair and dead skin cells are our personal property, but we "leave" that property at the police station (say, a hair falls out while in an interrogation chair), do the police no longer need a warrant to gather that hair as evidence? Is the unintentional shedding of dead cells the legal equivalent of throwing stuff in your street-side trash barrel (which I believe is fair game to police)?

In other words, when is our genetic material no longer considered our property?
posted by TimeTravelSpeed at 10:11 AM on February 2 [1 favorite has favorites]

It's a fascinating and heartbreaking story - with all the stories about parents of sick children who turn to quackery and unscientific treatments to try and help their children, it's nice to hear about one who turns to their knowledge of science, but heartbreaking because I'm not sure he's going to find anything. He might find a single base-pair change which explain sit, and he's going about it the right way by ruling out anything present in the parents, but what if it is a copy number change? Or a different methylation pattern? Or a change in the expression of the gene, something in the promoter, or an enhancer element miles away? Even if he does find something, with no other patients with the same disease he would have a hard time showing it was the cause. Maybe his best hope is to find another child with the same disease through his website.

I did find one part of the article somewhat strange, though:
The job was daunting: The printouts contained data for approximately 20,000 base pairs, and there was no feasible way to automate the hunt for variants.

I'm not sure why he couldn't just do a sequence alignment and find any variation from the reference without sifting through the printouts.
posted by penguinliz at 10:39 AM on February 2

Maybe he'll come upon some accidental discovery along the way, and, though his daughter tragically succumbs to her condition, he'll go on to have a life spanning hundreds of thousands of years, eventually riding a tree in a magic bubble towards a supernova in an attempt to prolong his existence.
posted by kaibutsu at 10:42 AM on February 2

If she dies and he doesn't find anything or find it in time, it's going to break his heart.

Think about what he'd feel if he didn't even try.

My son's got kidney disease. My daughter's got Crohn's Disease. It's basically obvious there's some genetic commonality (my sister-in-law has Crohn's, too) and when the price comes down, I can tell you that we will indeed be sequencing their genes and seeing what we can see.

See, everybody thinks you can just go to the doctor and they can help. But let me tell you -- gastoenterologists haven't got a clue. We took our daughter to a pediatric gastroenterologist, he gave us a diagnosis, and his "treatment" was $400-a-month medication to hold her over until they'd have to start cutting bits of her intestines out.

Instead, we started reading. And we discovered that there are alternative ways of dealing with Crohn's Disease. So far, she has been symptom-free for a year and a half, has resumed growing, and isn't, you know, bleeding internally any more. The secret? Cut out all complex carbohydrates.

Let me tell you about how society looks at a family who cuts out complex carbohydrates. That means no sugar, no wheat, no potatoes, no soft drinks, no juices that you didn't juice yourself, no processed foods at all, no processed meats, no fricking processed nothing. With everybody around you treating you like you're an idiot for sending your kids to school with cauliflower again. But you know what? My daughter's intestines haven't been cut up yet, and she is symptom-free now. (Also, I've lost twenty pounds and my blood pressure is down. But that's another story.)

With the boy, we've had less success, but we stopped attempting any conventional treatment after our second try with steroids made him far worse again. (It's an idiosyncratic reaction; most nephrologists just plain deny that it's possible, but you know, I believe what I can see.)

On our last visit to his nephrologist, though, he told us we should just continue doing whatever it is we're doing, because our son is stable and outwardly healthy, and he doesn't have anything better to offer right now. The lab results tell us that the inflammation is still active in his kidney, but it probably isn't getting worse. (The only way to know for sure would be another biopsy, so we're not in a hurry.)

Conventional medicine has not brought us these successes, however limited they might be. And we have run the gamut with doctors -- we've seen seven nephrologists in three countries. One of them flat-out-told us, "Well, you might as well get used to the side effects of steroids, because he'll be on them permanently after his transplant." (We didn't actually pay her. I consider that a win.) The attitudes of professional physicians to anyone with the temerity to do their own research are familiar to me, in other words.

We may never find out the key to our son's kidney disease. There may not even be a key. But we're damned if we're not going to keep trying. So I am more heartened than you can imagine to read this FPP.
posted by Michael Roberts at 12:28 PM on February 2 [6 favorites has favorites]

I'm thinking legislation prohibiting health insurance from requiring DNA before insuring with be within the next few years. Isn't the whole point of insurance to pool risk to protect individuals from uncontrollable variables?

Already happened in the US. 2008 saw the passage of a law that prevents employers and insurance companies from forcing genetic testing, and discriminating against any conditions (potential or otherwise) found through genetic screening. http://www.geneticalliance.org/ws_display.asp?filter=policy.leg.nondiscrim

I was quite surprised such a common sense law past without an onslaught of discrimination cases to go before it. For once, the government seemed proactive about protecting its citizens from bullying corporations. And under the Bush administration. Who would have thunk it?
posted by [insert clever name here] at 12:39 PM on February 2

I thought he had actually sequenced her DNA at home, but he really didn't. Most of the work was done at labs outside his home. Also he didn't assemble her entire genome, he just sequenced portions of it that he hoped would have the mutated genes. This is not to discount his efforts, just that for one second, it seemed we were a lot farther along in science than I'd thought.

I think it's fascinating that two of the best technology inventions of the last 50 years or so, DNA sequencing and better computer search/pattern matching algorithms (Google, but also the alignment algorithms) have dovetailed into a project like this. All he can do is try, but it's really awesome that we have the tools available to do this type of research as individuals. I agree penguinliz, I don't understand why he can't BLAST his daughters genes against Ensembl either.
posted by bluefly at 3:38 PM on February 2

I don't understand why he can't BLAST his daughters genes against Ensembl either

He probably did and the reporter didn't get it. Happens all the time in science reporting.
posted by Sublimity at 5:12 PM on February 2

Conventional medicine has not brought us these successes, however limited they might be.

I try to keep this mind every time I seek care: All medicine is alternative medicine. Any therapy or diagnostic technique, based only on theory and without hard proof of efficacy in human beings, is as speculative as any non-Western medical approaches. Until someone can go into a lab with only chemicals and come out with a baby, theory is only a guideline and doesn't justify any medical practice.
posted by Mental Wimp at 11:56 AM on February 3