Category: Personal Genomics

Laura Hercher convinces me there is no non-self interested case for genetic paternalism

By Razib Khan | January 16, 2013 12:56 am

Over at David Dobbs’ weblog Laura Hercher has a guest post up with the heading The Case for Selective Paternalism in Genetic Testing. Here are some relevant sections:

Which brings me back to this issue of paternalism. I agree that it makes no sense to put up obstacles for inquisitive and motivated individuals who wish to query their genome for information, however laced with uncertainty or peril. But forgive us if our first thoughts are often about how to help (yes, and to protect) the patients we see, in the medical setting. Science literacy is rare. The desire to use web-based tools to analyze their own DNA sequence is vanishingly rare. And a sentence like “Your risk of type II diabetes is decreased by the allele that you carry, in a gene that accounts for an estimated 1.5% of the heritability of the disease” is regularly interpreted as “You will not get type II diabetes.” So we worry about the effect that getting this information may have on the people who live where the sky is blue and the sun is yellow. Sue us.

So, yes – more information, not less, is the way of the future, for so many reasons. But I will throw in a plea for understanding that sometimes the opposition is not merely protecting an information fiefdom, but responding to their own previous experience. Sometimes, I get a little protective. I guess that’s paternalism. I plead guilty – guilty, with an explanation.

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Buyer beware in ancestry testing!

By Razib Khan | December 18, 2012 12:20 am

Over at Genomes Unzipped Vincent Plagnol has put up a post, Exaggerations and errors in the promotion of genetic ancestry testing, which to my mind is an understated and soft-touch old-fashioned “fisking” of the pronouncements of a spokesperson for an outfit termed Britain’s DNA. The whole post is worth reading, but this is a very grave aspect of the response of the company:

…The main reason is that listening to this radio interview prompted my UCL colleagues David Balding and Mark Thomas to ask questions to the Britain’s DNA scientific team; the questions have not been satisfactorily answered. Instead, a threat of legal action was issued by solicitors for Mr Moffat. Any type of legal threat is an ominous sign for an academic debate. This motivated me to point out some of the incorrect, or at the very least exaggerated, statements made in this interview. Importantly, while I received comments from several people for this post, the opinion presented here is entirely mine and does not involve any of my colleagues at Genomes Unzipped.

From what I can gather this firm is charging two to three times more than 23andMe for state-of-the-art scientific genealogy, circa 2002. So if you can’t be bothered to read the piece, it looks like Britain’s DNA is threatening litigation for researchers having the temerity to point out that the firm is providing substandard services at above-market costs. Plagnol’s critique lays out point-by-point refutation of assertions, but the interpretation services on offer seem to resemble nothing more than genetically rooted epic fantasy. A triumph of marketing over science.

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$99 for 1 million markers

By Razib Khan | December 11, 2012 10:18 am

Looks like 23andMe has a new $99 price point. If so, that’s 100 markers per cent! (here’s the press release)

1) Privacy: Yes, this a privacy risk. 23andMe is fundamentally an IT company, and IT companies mess up. But I am confident that within 10-15 years genetic information is going to be pretty easy to get anyhow. Your data will be in too many places for any expectation of privacy.

2) Cost/worth it: That is dependent on your income. If you are willing to spend $100 on a nice meal, I think $100 for 1 million markers is an excellent proposition. The markers never depreciate, though in the near future you will you get sequence data which will supersede them.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: 23andMe

Can your genes be patented?

By Razib Khan | November 30, 2012 9:30 pm

Court to Decide if Human Genes Can Be Patented. So it seems a group of middle aged to very aged lawyers will decide the decades long Myriad Genetics saga. My position on this issue is simple: if you are going to award patents, they must be awarded to acts of engineering, not discoveries of science. See Genomics Law Report for more well informed commentary.

CATEGORIZED UNDER: Personal Genomics

Back to crunching personal genomic data

By Razib Khan | November 22, 2012 12:54 am

Many months ago I told some of my friends that I’d run analyses of their 23andMe data, and report it back to them. A year ago I made the same promise to some of my readers. But life got in the way, and I’ve been very busy. I’m working on scripts to make the whole process efficient for me (if you want to know, I’m trying to get the output to be easy to merge many runs with CLUMPP and then produce DISTRUCT type outputs; I’ve done this with other Admixture outputs, but for various reasons the labeling gets messed up with my ‘personal’ project). But I’ve decided to at least start pushing some of the results live. I won’t be putting it in this space, probably razib.com. But I thought I would get your attention first. I know a lot of ID’s are missing, but I’ll add them later when I can find anything. And yes, I need to get back to African Ancestry too (that site was infested with a backdoor, so I had to yank it). This is all rather basic stuff, but I just don’t have the time to do things in a manual fashion, and the scripts I have for population sets don’t transfer over when I want to give individual friend results as well as population results.

The results in tabular format are here. And all individual results are here. In terms of the tech details, ~140,000 SNPs, ~3000 total individuals in the data set, at K = 11. I will probably be reporting K = 12 to K = 25 from now on (I’m just going to get 10> replicates and merge them).

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It takes a village, and guidelines

By Razib Khan | November 5, 2012 11:46 am

A week ago I posted on a rather scary case of medical doctors withholding information from a family because they felt that it was in the best interests of the family. I objected mostly because I don’t have a good feeling about this sort of paternalism. Laura Hercher has a follow up. She’s not offering just her opinion, but she actually made some calls to people who were involved in the case. From what I can gather in her post the issue that triggered this outrage (in my opinion, it’s an outrage) is that for these particular tests informed consent was simply not mandatory. Since they didn’t have the consent a priori, the doctors had to go with their judgement.

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One girl, one exome

By Razib Khan | October 22, 2012 12:22 am

Interesting story in The San Jose Mercury News, Open-source science helps San Carlos father’s genetic quest:

“We used materials that are public, freely available,” said Rienhoff, a physician and scientist, as Beatrice frolicked nearby. “And everything we’ve learned we’ve put back out there, in the public domain. It’s for the patient’s good, and the public good.”

Born with small, weak muscles, long feet and curled fingers, Beatrice confounded all the experts.

No one else in her family had such a syndrome. In fact, apparently no one else in the world did either.

Rienhoff — a biotech consultant trained in math, medicine and genetics at Harvard, Johns Hopkins and the Fred Hutchinson Cancer Research Center in Seattle — launched a search.

He combed the publicly available medical literature, researching diseases, while jotting down each new clue or theory. Because her ailment is so rare, he knew no big labs or advocacy groups would be interested.

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CATEGORIZED UNDER: Personal Genomics

GEDmatch needs funds!

By Razib Khan | October 21, 2012 11:51 pm

I noticed today that GEDmatch is trying to raise funds to cover the cost of their web services. What are those services? Basically if you get raw data back from direct-to-consumer genotyping firms GEDmatch allows you to run further analytics. You can do some of these yourself…but most people aren’t going to know how to convert their files into pedigree format and use PLINK. As genotype data becomes more and more common there’ll be more need for analytic services like GEDmatch, whether for profit or for fun.

One can imagine a near future where much of the work can be offloaded to desktop applications (e.g., Promethease does this for traits and diseases). But the problem is that there is greater returns to the analysis when you aggregate the source data into huge agglomerations, and if people are doing their own analyses on their own systems that’s not going to happen (the GWAS information in Promethease uses aggregated information implicitly with the studies they rely on). This is why GEDmatch and openSNP are important.

In any case, if you have used GEDmatch and wish to give, this would be a good time.

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AncestryDNA is now accepting the necessity of raw data downloads

By Razib Khan | October 15, 2012 1:02 am

The Legal Genealogist points me to the fact that AncestryDNA is now going to work on allowing users to download their data. Here’s the specific section:

AncestryDNA believes that our customers have the right to their own genetic data. It is your DNA, after all. So we’re working to provide access to your raw DNA data in early 2013, which includes related security enhancements to ensure its safety during every step of the process. Moving forward, we plan to add even more tools and improvements for our customers, and any new features will be available to all AncestryDNA members.

If the rights of the customers to own their own data were so important to them they should have front-loaded this feature. As it is, they didn’t, and as many bloggers noted the firm had stated they didn’t have plans to unroll this feature in the near future. What changed? I don’t know the details, but I suspect they realized that many of us who complained in the past were going to continue to complain constantly. Combined with the contrast with its competitors, like 23andMe, and I assume they realized this just wasn’t going to solve itself if they ignored it. The key here is follow up. I’ll assume “early 2013″ is no later than March 31st (the first 1/4th of the year). If AncestryDNA doesn’t have the feature out by then I’ll assume they’re not serious, and will begin trying to make sure that their deficits come up high on Google searches again.

Blogs and word of mouth matter a lot in this domain. I convinced James Miller, author of Singularity Surviving, to get his parents genotyped this weekend. Also, after more than two years of harassment a friend who works at Google finally got typed, and will be sending me his data.

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Dienekes and ADMIXTOOLS

By Razib Khan | October 8, 2012 7:55 pm

Less than a month ago I pointed to the release of ADMIXTOOLS. Unfortunately, though I have a desktop at home devoted purely to my personal genomic hobbies I haven’t been able to free up the time on weekends to start doing my own analysis. This is pretty pathetic, and sometimes I get a little depressed at how little usage there is of all the great scientific software released into the public domain. But in case you haven’t seen it, I want to point you to Dienekes Pontikos’ posts using ADMIXTOOLS. Frankly, my personal experience with this sort of thing tells me to hold off on any judgement until I’ve used the software package and gotten a feel for its tendencies. But until those of us with aspirations manage to get some blocks of time together Dienekes has the field all to himself.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: ADMIXTOOLS

Fear not the gene!

By Razib Khan | October 4, 2012 12:33 am

John Hawks points me to a critique of NPR coverage of personal genomics. In defense of NPR they seem like Physical Review Letters in comparison to other media, such as the BBC. But I do wonder what the causality here is. Does the media lead us to the proposition that “genetics is scary”? Or is it the public which demands these stories?

Meanwhile, as some are expressing worry, technology keeps pushing forward:

A faster DNA sequencing machine and streamlined analysis of the results can diagnose genetic disorders in days rather than weeks, as reported today in Science Translational Medicine.

Up to a third of the babies admitted to neonatal intensive care units have a genetic disease. Although symptoms may be severe, the genetic cause can be hard to pin down. Thousands of genetic diseases have been described, but relatively few tests are available, and even these may detect only the most common mutations.

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I am free of rare homozygous recessives! (well, perhaps)

By Razib Khan | September 30, 2012 4:11 pm

I got a notification today from Ian Logan that he set up a page on my genotype using a method which detects rare homozygous SNPs in the ~1 million markers I put up from my 23andMe results. My raw data is online, so anyone can analyze it. Here is the summary of my results:

The program finds about 50 ‘rare/uncommon’ SNPs from the 900,000+ tested by 23andMe.

The are no ‘homozygous-recessive’ results (surprisingly, as 1-2 might be expected).

There are a list other individuals, and sure enough most of them do have a rare recessive homozygous locus or two. I assume that ascertainment bias (the technology finding variation in Europeans better than non-Europeans in most cases) wouldn’t result in my case, because I should have less variation, not more (less variation would presumably result in more homozygous recessives). So I am thinking it may simply be that because I’m from a population with greater genetic variation (South Asians) I am less likely to yield a homozygous recessive.

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Ancestry.com's AncestryDNA won't give you your raw data

By Razib Khan | September 16, 2012 9:18 pm

CeCe Moore points me to an “interesting” fact I had not noticed about Ancestry.com‘s AncestryDNA service (which is not open available to everyone right now):

I re-emphasized to John the importance to the genetic genealogy community that AncestryDNA release our genetic data to us. I mentioned that my colleagues and I were happy to discover that Ken Chahine’s statements to the Presidential Commission for the Study of Bioethical Issues in Washington D.C. on August 1st were in line with our belief that our genetic data belongs to us (video and transcript). During the second session, Dr. Chahine stated that “the customer retains ownership of their DNA and data”. However, we feel that AncestryDNA’s policies do not currently reflect this. John reiterated what I have been told before, which is that they are genuinely considering the best way to deliver this data to us. In response to my persistence, John told me that they are aware that this is important to me, but that they have to take into consideration everyone’s feedback, not just mine. As a result, giving us access to our genetic data is not at the top of their list of priorities. He explained that they read lots of feedback and do a significant number of surveys and focus groups in order to determine what is most important to their customers and, by that process, their priorities are dictated….

 

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The ecstasy and agony of prenatal information

By Razib Khan | September 16, 2012 6:34 pm

Slate reposts a piece from New Scientist, Do You Really Want To Know Your Baby’s Genetics? It is arranged as a series of questions which might arise from the new information. For me my frustration with this sort of discussion is rooted in reviewing old articles about “test-tube babies” in major newspapers from the 1970s and early 1980s. Today in vitro fertilization is banal and commonplace, but many of the same concerns were voiced back then which you see cropping up now in regards to personal genomics. My issue is not concern as such, but its inchoate character. It is not uncommon for me to encounter people pursuing postgraduate work in science who express the opinion that “it’s scary,” the “it” being genetic information. When further queried the fear is generally layers upon layers of formless disquiet, some confusion about the specific details, as well as a default stance toward the “precautionary principle.”

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Consent and genomics

By Razib Khan | August 26, 2012 5:15 pm

Interesting story in The New York Times, Genes Now Tell Doctors Secrets They Can’t Utter:

One of the first cases came a decade ago, just as the new age of genetics was beginning. A young woman with a strong family history of breast and ovarian cancer enrolled in a study trying to find cancer genes that, when mutated, greatly increase the risk of breast cancer. But the woman, terrified by her family history, also intended to have her breasts removed prophylactically.

Her consent form said she would not be contacted by the researchers. Consent forms are typically written this way because the purpose of such studies is not to provide medical care but to gain new insights. The researchers are not the patients’ doctors.

But in this case, the researchers happened to know about the woman’s plan, and they also knew that their study indicated that she did not have her family’s breast cancer gene. They were horrified.

“We couldn’t sit back and let this woman have her healthy breasts cut off,” said Barbara B. Biesecker, the director of the genetic counseling program at the National Human Genome Research Institute, part of the National Institutes of Health. After consulting the university’s lawyer and ethics committee, the researchers decided they had to breach the consent stipulations and offer the results to the young woman and anyone else in her family who wanted to know if they were likely to have the gene mutation discovered in the study. The entire family — about a dozen people — wanted to know. One by one, they went into a room to be told their result.

“It was a heavy and intense experience,” Dr. Biesecker recalled.

Around the same time, Dr. Gail Jarvik, now a professor of medicine and genome science at the University of Washington, had a similar experience. But her story had a very different ending.

She was an investigator in a study of genes unrelated to breast cancer when the study researchers noticed that members of one family had a breast cancer gene. But because the consent form, which was not from the University of Washington, said no results would be returned, the investigators never told them, arguing that their hands were tied. The researchers said an ethics board — not they — made the rules.

Dr. Jarvik argued that they should have tried to persuade the ethics board. But, she said, “I did not hold sway.”

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Beware of the ancient of days!

By Razib Khan | August 23, 2012 1:29 am

By now you have probably read in The New York Times, or on the blogs, about the new paper in Nature which reports on the empirical trend toward the children of older fathers carrying more de novo mutations. Really all you need is this figure:

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CATEGORIZED UNDER: Personal Genomics

Yes we should (prenatal sequencing)

By Razib Khan | August 13, 2012 11:22 pm

Obsession. I’ve been obsessed with many things in my life, from specific women to sundry topics. But I’ve never known obsession until I had a child. Perhaps others are not like me, but the monomaniacal need to know as much as you can about your future child as soon as possible gripped me early on. Even today I want to know as much about her as I can. This is why I had her genotyped at two months, and this is why I plan to have her whole-genome sequenced as soon as it is feasible. This doesn’t mean that I put much stock in the power of individual prediction. Rather, even if the returns are marginal even the smallest tidbit of knowledge about my child is precious to me.

This is why I’m left scratching my head when I see pieces which moot concerns about whole-genome sequencing of fetuses. Obviously some people will go for it, and some people will not. It won’t be very cheap, nor will it frankly tell you that much on a per base pair basis as a function of the cost. But it will tell you something, and depending on the coverage (ergo, how accurate the sequence is going to be at the end of the day) you keep the information you get. Imagine, for example, that it would cost $5,000 for 10X coverage. Would you go for it? I would. Why? How much does the average American car cost? $30,000 dollars. A car is very useful, but it’s a depreciating asset. A genome will never depreciate, it won’t degrade. In fact, as more research gets done its utility will only increase! If people are willing to pay >$5,000 for a high end gaming box, and not be perceived as crazy, why should genophiles be seen to be wild-eyed weirdos?

Of course the natural objection is that I’m discussing a problem which doesn’t exist. I wish this were so, but there’s a whole bioethics industry whose bread & butter is to trade in flimsy and specious reasoning, which might appeal to politicians who are will to purchase specious reasoning for purposes of their demagoguery. For example, As Prices for Prenatal Genome Sequencing Tests Fall, Researchers Worry About Consequences for Families in a Real-Life ‘Gattaca’:

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CATEGORIZED UNDER: Bioethics, Personal Genomics
MORE ABOUT: Prenatal Screening

23andMe discount code (again)

By Razib Khan | August 9, 2012 11:57 pm

At this point if you have spare cash why not shell out $300 for a raw copy of your genotype? (yes, I know 23andMe provides other services) I’m sure many readers spend $100 on nice meals now and then. That’s one day. Your genotype won’t ‘depreciate’ in a literal sense, and more practically until whole-genome sequencing gets affordable within the next decade (i.e., < 10 years) 1 million SNPs is a pretty good deal. And not to be morbid, but it is probably best to get older family members typed now (though if they have had hospital stays you can probably later retrieve genetic material, it will be a bureaucratic pain).

The reason I’m posting this now though is that I received a notification about a $50 discount code from 23andMe. Here it is: YHPRD7. It’s valid for the next few days. $50 isn’t trivial for most people, so perhaps it will prompt a few here to go and purchase.

CATEGORIZED UNDER: Personal Genomics, Uncategorized
MORE ABOUT: 23andMe

Regulate the diet industry!

By Razib Khan | August 3, 2012 10:15 am

Brandom Keim leaves this comment:

It’s easy to see genomic data regulation in romantic narrative terms — The plucky little guys who want to be free! The big, bad institutions who want to control them! — and it’s also a trap. Interpreting genomic information in a medically useful way is very, very complicated. It’s easy to do badly — and people may make life-altering decisions based on bad information.

Gene-testing companies already have a track record of offering tests unsupported by unsupported by clinical evidence, such as CYP450 testing to determine antidepressant dosage. A let-the-market-regulate-itself, buyer-beware approach isn’t any more desirable than it would be for new drugs.

We’re discussed this before. The shorter perspective from me is that on principle I don’t object to regulation, but when viewed across the constellation of things which our government regulates, I don’t see the case for direct-to-consumer genomic services being monitored closely. A result from 23andMe will not kill you, though it may lead to a sequence of actions which may kill you. But this is unfortunately a problem with the whole diet industry, which is often based on unsupported fads and fashions, and has a much larger social impact. Nutrition is very complicated with incredible real life consequences, and yet regulating it would frankly be a fool’s errand. You may destroy the American diet publishing industry, but you can’t prevent internet message boards. Similarly, the SNP-chip results themselves are commodities, and with client and server analytic software proliferating in the next few years the reality is that the market will regulate itself! And unfortunately, the impact on peoples’ lives will be the same, for good or bad, as the diet industry.

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Genetic counseling and conflict of interest

By Razib Khan | July 14, 2012 9:33 pm

Article in The New York Times:

Genetic testing raises some vexing ethical questions, like whether it will cause unnecessary anxiety or lead to more medical procedures, including abortions.

Now, as the number of tests and the money to be made from them are exploding, another question is being asked by professionals in the field themselves. Is it ethical for genetic counselors, who advise patients on whether to undergo testing, to be paid by the companies that perform the tests?

While it might not always be immediately obvious to patients, some counselors offering them advice in hospitals and doctors’ offices work for the commercial genetic testing companies, not for the hospitals or doctors themselves.

Conflict of interest in anything medical is pretty bad. On the other hand, medical care is expensive. But I want to add something here: the pre-natal screens by Genzyme are really, really, bad value-for-cost. For example, a non-insurance “sticker price” of thousands of dollars for 200 traits. Speaking from personal experience here. Also, don’t think you can ever get genetic material sent to Genzyme back. I called and tried this for a few months, and there was no response (I wanted to do typing of tissue myself).

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Genetic Testing
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