biotech

Your whole genome for $5000

In yesterday's NY Times:

The cost of determining a person’s complete genetic blueprint is about to plummet again — to $5,000.

That is the price that a start-up company called Complete Genomics says it will start charging next year for determining the sequence of the genetic code that makes up the DNA in one set of human chromosomes. The company is set to announce its plans on Monday.

...

[T]he cost of DNA sequencing has dropped by a factor of 10 every year for the last four years, a faster rate of decline than even for computers, Dr. [George] Church said.

That's just incredible. I suppose if you just paid for Knome to do it for $350,000, you'd feel pretty burned...

Knome, a company that offers to provide consumers with their DNA sequence, charges $350,000. But that is a retail price that includes not just the sequencing costs but also the analysis of the data and the customer service.

Complete Genomics will not offer a service to consumers. But it will provide sequencing for consumer-oriented companies like Knome.

Knome is already exploring farming out its sequencing to Complete Genomics. “We anticipate we’d be able to significantly drop our price,” said Jorge C. Conde, the chief executive of Knome, which is based in Cambridge, Mass.

Heh. What are "the analysis of the data and the customer service" worth? I mean, since the SNP-handling companies like 23andMe can do all that and the sample for a few hundred bucks. It's not like the whole genome is giving you any better information yet, and all that information is going to be public.

Sequencing now is a commodity for scientists researching microbial genomes, but a boutique product for people. In five years, it will be a commodity for people, and you'll be able to get it from many companies for a few hundred dollars, and one or two for $49.95. Maybe Google Health will do it for free (remember, Google's founder Sergey Brin is married to a founder of 23andMe, Anne Wojcicki).

So companies will try do differentiate themselves based on the other information they provide---what are you at risk of contracting? What will your kids look like? Where did your ancestors live?

There are obvious difficulties with that strategy. There's nothing proprietary there --- all the good information is public, and the people acquiring the good information don't work for any of these companies (yet). Plus, very few of the genetic variants have a strong enough effect on health outcomes to be worth communicating. It's like the wet lab equivalent of Tarot cards.

Reporters that are dipping their toes into the industry are already making note of the basic problem of the fortune teller: Different fortune tellers give you different stories. Companies that do direct-to-consumer genotyping are already facing this problem: the "risk variants" reported by one company's results may differ from those reported by another company's results, for the same customer.

I think we can foresee a couple of probable consequences of these problems, as the industry develops. First, companies will need a way to set their offerings apart from the public domain. They will bundle their genotypes or sequence data within a proprietary format so that customers can't (easily) make comparisons themselves. That will also help to deal with the problem of different "reports" from different companies. If you can't take your data elsewhere, you won't be able to get another story.

Second, they will offer up their large datasets to qualified researchers. That wouldn't be unusual -- many researchers consult for industry. With thousands of individuals, there will be the potential to do many kinds of surveys that are now difficult with data acquired publicly. These kinds of results and studies won't be proprietary, because their results won't be accepted without peer reviewed publications. But they may set companies apart in terms of mindshare and advance the particular emphases of their offerings. I expect that the company that advances the fastest will be the one that gathers in the coolest stable of young scientists to do association work and population history.

It's a very good time to get into this field and set yourself apart, because it's about to go public in a big way.

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Popular Science has a short article covering recent research into European population structure:

To the delight of genealogy buffs like me, scientists recently announced in the journal Nature that they can trace European ancestry to within 192 miles by analyzing tiny inherited markers in DNA. That means someday we'll need look no further than our own genes to locate our motherlands.

The study, and another much like it in a recent issue of Current Biology, harnessed the stream of human genetic data now being gathered by pharmaceutical companies. Using modern “gene chip” technology, researchers can screen 500,000 units of DNA at once. The companies use the data to investigate the genetic basis for adverse drug responses. But population geneticists are taking advantage of the high-resolution databases too, scouring them for trends in human evolution that are otherwise hard to find.

That's me, I guess. They're calling it a "DNA GPS", which is pretty clever.

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If you're interested in athletic performance and genetics, read Daniel Macarthur on ACTN3, sprinting, and Jamaica:

At this point I probably should confess to having a more than casual interest in this story: I was one of the authors on the first study showing an association between this gene and elite athlete status back in 2003, and this gene has been the central focus of my research for a good part of the last six years.

...

It is almost certainly true that Usain Bolt carries at least one of the "sprint" variants of the ACTN3 gene, but then so do I (along with around five billion other humans worldwide). Indeed, I'm fortunate enough to be lugging around two "sprint" copies - but that doesn't mean you'll see me in the 100 metre final in London in 2012.

Larry Moran comments on the Gene Wiki. (If you haven't read about it, check out this AP article, or the PLoS Biology paper). Larry has written before about the errors in sequence databases and how hard it is to fix them, he's one of the people with the most practical experience trying to find ways to remove errors.

His posts are a good way to learn about the limits of these resources. I've seen several cases where incorrect data made it into a database and proliferated through the literature. These cases are extremely hard to root out once they get in. Errors are inevitable -- sometimes things just aren't the way they look. The wiki concept does provide a chance to fix things, or at least a place for annotations of existing errors, as long as credible people are doing the annotations.

I think that the baseline may have the potential as a foundation for a wiki about recent selection on human genes.

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Cybernetics and the brain-controlled robot

An interesting story from Popular Mechanics about progress in cybernetics, titled "Mind control stories." It starts with the macaque controlling a robot arm by brain implants, and then considers the future:

For Miguel Nicolelis, a professor of neuroscience at Duke University Medical Center, the backbone of mind-machine interfaces is the ability to analyze neural activity. Sure, the system demonstrated at Pitt in May accessed information from 100 neurons at once. But Nicolelis’s lab has managed five times that amount, with data coming from up to 10 different brain structures.

For me, this is the most interesting part:

The main purpose of the walking robot experiment was to demonstrate just how precisely brain activity could be translated, but it produced another interesting result: It actually took less time for the brain signal to travel from the monkey in North Carolina to the robot in Japan than it took to go from the primate’s brain to its own muscles. At any given moment, then, the bot was receiving the command to walk before the monkey’s body did.

I've been reading Ray Kurzweil's book, and it has always seemed to me that a fundamental barrier to the development of effective neural implants is bandwidth: Human brains have evolved to use inputs and outputs at the speed of language, not the speed of electronics. So this idea of accelerating real-world responses and feedback by wiring may suggest substantial plasticity with respect to bandwidth.

I think I'll lecture on this topic in my "Biology of Mind" course this fall.

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Genetic Future comments on news from the Wellcome Trust Sanger Institute:

At the current rate (which is rapidly increasing) the Sanger is churning out more DNA sequence every two minutes than was generated by the entire research community from 1982-1987. This obscene rate of data generation has been enabled by the development of next-generation DNA sequencing platforms, which can each churn out one human genome equivalent in less than a week.

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Daniel Macarthur, of Genetic Future, reviews the amount of information required to store genomic information. Naturally, you'd probably think it was around 12 billion bits (2 bits per base pair), but sequencing technologies and the availability of references from other people make things a little more complicated.

This interesting quote about the raw image files generated by the Illumina platform presents some of the range of complications:

Almost as soon as these images are generated they are fed into an algorithm that processes them, creating a set of text files containing the sequence of each of the fragments. The image files are then almost always discarded. Why are they discarded? Because, as you will see in a minute, storing the raw image data from each run in even a moderate-scale sequencing facility quickly becomes prohibitively expensive - in fact, several people have suggested to me that it would be cheaper to just repeat the sequencing than to store these data long-term.

An accurate read requires lots of redundant bits, which adds up to lots and lots of data storage. If these are winnowed down to a real "best" sequence, then you're back to 12 billion bits (=1.5 gigabytes), more or less. Of course, most of that sequence is redundant and may be significantly compressed. And if you compare with a reference sequence, really a small amount of information is sufficient to distinguish your genome compared to the reference. Anyway, all this is explained at the link.

Becoming bionic

A couple of months ago, the Washington Post ran an article by Michael Chorost, who has written a book about his experience with a cochlear implant. I meant to link it at the time, but got it lost on a different computer. The book is titled, Rebuilt, with alternate subtitles in paperback and hardcover editions. The Post article is titled, "Confessions of a Bionic Man":

My implants don't aid my hearing. They create my hearing.

What I hear is, quite literally, a computer simulation of real sound. The day my first implant was activated in 2001, voices sounded bizarre; the radio might as well have been in Esperanto. That was because the software couldn't reproduce all the aspects of a normal auditory system. Still, I learned how to recognize consonants and vowels again by listening to books on tape. Now I can turn on the radio and hear it all but effortlessly.

In 2005, I got new software that made music sound brighter and clearer. The software's improved frequency resolution enabled me to distinguish between tones that had sounded identical before. It was a simple upload; no surgery was necessary.

Chorost also maintains a blog, discussing the themes of the book and his experiences promoting it. He provides an interesting account of his experiences conversing and interacting (sometimes uncomfortably) with deaf advocates of signing:

One burly fellow with enormous wrists introduced himself to me as having been in the classroom during a two-hour debate I had at Gallaudet last year with Dirksen Bauman’s students. That debate had the feel of history, of titanic forces clashing: the passion of the deaf community colliding with a technology that penetrates and transforms everything it meets. I’d spoken with candor. I’d said, Look, ninety-six percent of the deaf children born in this country are born to hearing parents. Offered a technology that lets their child hear, what do you think they’re going to choose? But I’d also said that sign language and the community sustained by it are precious, and that their disappearance would be a tragedy. I offered no easy answers, because I had none. Everyone was unsettled. Nothing was settled. At the end of the debate I felt worn out and anxious. Anxious, because I wondered if I had alienated them. I had wanted to build bridges, and I wondered if I had.

I happen to be reading Ray Kurzweil's book, and this article (and blog) make a more tangible example than many of the speculations that Kurzweil provides. It is sort of a best-case example, considering that a cochlear implant is intended to exploit brain areas that already exist and are tuned for interpreting auditory information. But the "upgrade" that Chorost describes is an incredible example of the way that technology can be improved once it is enabled.

The road to prophylaxis

Jane Brody writes about hereditary cancers, and genetic testing. It's sort of a self-education kind of piece. The theme is the extreme: radical surgeries that can nearly eliminate the chances of cancers that otherwise would be near-certain:

Dr. Coit described a family in which the father and his father both developed thyroid cancer linked to the RET mutation. The younger man's 6-year-old son was tested and found to carry the same damaged gene. Because the boy was certain to develop thyroid cancer, most likely at a young age, his thyroid was removed. Although the boy will need to take thyroid hormone for the rest of his life, the surgery reduced to zero his chance of developing this often fatal cancer.

The last part of the article is the warning section. Most interesting: Your relatives might sue you if you fail to tell them about your positive genetic test result.

Also, there's a warning about bogus genetic tests, for "what kinds of food to eat" and other stuff. I'll have a bit more about that later -- there are a lot of charlatans out there making hay out of the current rise in genetic testing.

I should point out that the description of these extreme cases does little to educate people about the much more common situation, where a "risk variant" may confer a very slight increased risk of a condition.

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Shining glowing people

Sarah-Kate Templeton of the London Times has reported that a Cornell University group created a genetically-modified human embryo:

The Cornell team, led by Nikica Zaninovic, used a virus to add a gene, a green fluorescent protein, to an embryo left over from in vitro fertilisation.
The research was presented at a meeting of the American Society of Reproductive Medicine last year but details have emerged only after the HFEA highlighted the work in a review of the technology.
Zaninovic pointed out that in order to be sure that the new gene had been inserted and the embryo had been genetically modified, scientists would ideally need to grow the embryo and carry out further tests.
The Cornell team did not have permission to allow the embryo to progress, however.

Another article about the work appears in the New York Times by writer Andrew Pollack:

But the researchers, at Cornell University, say they used an abnormal embryo that could never have turned into a baby.
"This particular piece of work was done on an embryo that was never going to be viable," said Dr. Zev Rosenwaks, director of the Center for Reproductive Medicine and Infertility at NewYork-Presbyterian/Weill Cornell hospital. He said the purpose of the work was stem cell research.
That did not stop some from criticizing the work, saying that the techniques being developed could be used by others to create babies with genes modified to make them smarter, taller, more athletic or better looking. They also said there should have been more public discussion.
"It's an important ethical boundary that scientists have been observing," said Marcy Darnovsky, associate director of the Center for Genetics and Society, a watchdog group in Oakland, Calif. "These scientists, on their own, decided to step over that boundary with no public discussion."

I don't really have any comments, but I wanted to point to these stories because I've been teaching a class that addresses these issues. Also, it strikes me that the opposition is poorly stated -- expressing an aversion to "smarter, taller, more athletic or better looking" children doesn't make much sense on its face.

One possible interpretation, that people may be forced to use such technologies if they want their children to remain competitive (the "private school" problem) won't carry much weight with most people, who don't feel such pressure now despite the many ways that people may invest in their children. Another, that such technologies may have "unforeseen side effects" (that is, the Frankenstein problem) doesn't argue against the technologies in general, it merely suggests an appropriate amount of caution.

Anyway, this discussion demands a longer post, and I just wanted to point to these articles.

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"Blood Matters" review

The NY Times is running a review by Jennifer Senior of the new book, Blood Matters, by Masha Gessen. The book details Gessen's journey through modern-day genetics and medicine. She learns that she carries a mutation to the BRCA1 gene conferring a very high breast cancer risk, and is then faced with figuring out what to do about it.

Gessen suddenly became part of "a cancer caste" (her term), a "previvor" (the community's term) with terrible choices to make posthaste. Specifically, she had to decide whether to keep her breasts and ovaries or have them prophylactically removed....So Gessen ditches the counselors and the doctors and instead tries to collect information from a wider, more eccentric variety of sources. A sympathetic nurse scientist at the Dana-Farber Cancer Institute concedes that close surveillance might be a reasonable alternative to surgery for some women. Nancy Etcoff, a psychologist at Harvard Medical School and the author of "Survival of the Prettiest," a study of the evolutionary importance of beauty, points out that while breasts are central to female attractiveness, attractiveness and happiness are barely correlated. Most memorably, an instructor in a psychology and economics class at Harvard attempts to "express life in numbers" for Gessen on an Excel spreadsheet, assigning values to living with cancer, living without cancer and living with the stench of a cancer threat. Though she rejects some of his findings -- I will not say what Gessen ultimately chooses to do -- she leaves his office feeling light, unburdened: "I jumped on my bicycle and sped home, making currents in the puddles, getting soaked, feeling strong and a little silly and generally like my life had a utility of 100 a year, possibly even more, now that I also felt that much more competent for being able to put a number on the value of riding in the rain."

I'm looking forward to reading this book.

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Should we want to live longer?

I've been lecturing about various genetic enhancement strategies in my genetics course the last two weeks. Today's lecture concerned clinical trials for gene therapy, but I have also talked about cloning, pharmacogenomics, genetic testing, GMO's and other aspects of biotechnology.

I ask my students to explore and engage with moral and ethical arguments. For example, we discussed whether there could be changes that would objectively be improvements in human biology. If so, are there moral or ethical objections that might apply to them? I don't think students are often asked to think in these ways, certainly not in basic science courses, so I am always interested to see where the conversation will go.

One of the topics last week was life extension. I can make a reasonable case that living longer (say, an average increase of 10 years) would be an objective improvement in human biology. The opposite case, dying 10 years earlier, seems like it would be an objective detriment.

I won't elaborate on my students' conversation along these lines -- that being limited to class -- but I wanted to give the story as a prologue, before linking to this op/ed by bioethicist Arthur Caplan, on the topic of life extension.

In this case Caplan does a good job expressing common sense (something not always true of Caplan's writing):

That said, arguments that we should not live a lot longer because we will grow decrepit are simply silly. No one proposes that we spend a lot of money on biomedical research to pursue a longer life of decrepitude and suffering. The idea behind radical life extension is that we live a decent quality of life for a lot longer. If all that is in store is frailty and mental decline, then the debate is over before it starts. But that is not what the debate is really about.
As for violating some natural limit if we live a lot longer -- what limit? We have already doubled our lifespan since the days of the Hittites, Israelites, Greeks, Babylonians and Egyptians, all of whom were lucky to make it to 35. Are we already living unnatural, and thus immoral, lifespans?

He also argues that it is not vain or indulgent to want to live longer, because others may wish you could live longer (children, grandchildren) even more than yourself. Those are good arguments, and it is hard to come up with a coherent argument against the idea that people should extending their lives if they want to do so (again, assuming that there is no unacceptable trade-off of increased pain and suffering).

UPDATE (2008/04/30): Arthur Caplan writes:

I would demur from the view expressed on your blog. I think all Caplan's writings are eminently sensible.

Heh. I think I've been just been served...

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Einstein's brain and Watson's genome

This week's Nature includes a report on the sequencing of James Watson's complete genome by a new process developed by 454 Life Sciences. I just had to convey this gag-inducing quote from the news article's conclusion:

James Watson is a brilliant scientist with a remarkable life story. He both laid the deep scientific foundations for genomic biology and devoted much of his life -- through his teaching, his leadership and the sheer force of his personality -- to building this science to its current productive state. Along the way, he stepped on more than one landmine. Future historians will find him a rich and elusive subject. Perhaps, informed by the advanced genetics of their day, they will scrutinize the data left behind by Wheeler et al. for clues to why he was the way he was. However, I suspect that they will have to rely instead, as historians do today, on what Watson wrote, said and did during his lifetime rather than on the order of the base pairs in his genome.

Oh, brother.

References:

Olson MV. 2008. Dr. Watson's base pairs. Nature 452:819-820. doi:10.1038/452819a

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Zimmer on E. coli and bioterror

I very much liked Carl Zimmer's Slate piece about foodborne pathogens and their lessons for defending against bioterrorism. Zimmer has a book about E. coli coming out later this spring, and he visits the topic of the 2006 outbreaks of an especially virulent strain.

This worrisome trend led a team of scientists based at Michigan State University to take a look at the DNA of the bacteria. The researchers compared bacteria from recent outbreaks with hundreds of others samples and published the results last Monday. The scientists drew an evolutionary tree based on the differences in the bacteria's genes. One branch of the tree -- the one that caused the spinach and lettuce outbreaks in 2006 -- is significantly more likely to make people sick than the others. And they found that this lineage has been exploding in recent years. In 2002, it accounted for 10 percent of the E. coli cases recorded in Michigan. In 2006, it accounted for 46 percent.

Whole-genome sequencing found large deletions and insertions of hundreds of genes in the newer virulent clade. Zimmer brings our attention to the complexity of the mechanisms that determine virulence. At present, science still can't predict how these genes will affect the pathogens. On this grounds, one may argue that the prospects are low that an enemy state or mad scientist will soon be able to create such a dangerous strain deliberately.

But this is not grounds to celebrate, since nature is busily creating dangerous strains for us. Natural selection does not design its products in a single leap of invention, but it sifts many millions of variants much more efficiently than any human laboratory.

I think that the last paragraph contains the essential lesson.

But this ignorance [of which genes must be altered to make a killer pathogen] is not cause for much comfort. Even if we don't need to worry about synthetic bacteria just yet, we do need to worry about new pathogens evolving right in our own backyard (or, rather, our own feedlots and factory farms). As things stand, we become vaguely aware of these bacteria only once they've been sickening and killing for years.

Sure, it may be difficult to engineer a more virulent pathogen for bioterror. But it is pretty easy to use the ones we already have. The evil genius is much less a threat than nature. And a saboteur looking to replicate small-scale terror on the order of the D. C. sniper may find hundreds of victims by contaminating one line of the vast American food web.

Defending against this kind of terror is the same task as defending against nature.

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The future of genetics is corny

Elizabeth Pennisi's story about maize genomics is a good reminder for why biology will continue to grow in importance toward our understanding of human history:

With $9.1 million from the Mexican government, Jean-Philippe Vielle-Calzada of the National Laboratory of Genomics for Biodiversity in Irapuato and his colleagues have decoded a native "popcorn" strain grown at elevations above 2000 meters. Although still in more than 100,000 pieces, the sequence has revealed many new genes, he reported. This variety's genome "will be of tremendous value in terms of understanding the evolution of [maize] domestication," he says.

Oh, and if you're interested in biology, consider the potential experiments from this:

Another resource introduced at the meeting will help ... sort out how genes interact. The agribusiness giant Syngenta announced it was making available 7500 lines of corn, each representing a B73 genome with a single piece of DNA bred into it from one of the 25 strains of the Maize Diversity Project. Taken together, the lines incorporate all the genetic diversity of those strains but make it easier to understand the activity of particular genes. The community has long awaited these tools, says Brutnell: "They are really going to revolutionize the way we do genetics."

I'd say. Imagine 7500 twins, all identical except for a unique piece of DNA spliced in from some other person. Except with corn, it's not 7500 twins, its 7500 experimental plots full of twins. Now, see what they all do!

References:

Pennisi E 2008. Corn genomics pop wide open. Science 319:1333. doi:10.1126/science.319.5868.1333

The cloning of the bulls

Here's an AP story about cloning bullfighting bulls. Yes, I know, "bullfighting bulls" is redundant, but what else are you supposed to call them? I suppose corrida bulls.

The story adds to last year's discussion about horse cloning (horserace horse cloning?). But here the main theme is the affection that owners have for their bulls:

"I am extremely fond of this bull," del Rio said at his ranch in this town outside Madrid, watching 16-year-old Alcalde graze with some of his latest offspring -- mere toys next to their prolific, half-ton father. "He has given us tremendous satisfaction."

This has become quite the going concern:

ViaGen spokesman Ben Carlson confirmed the orders from del Rio and Fernandez, but would not comment on pregnancies or expected birth dates. Carlson said the breeders would pay standard cattle cloning prices: $17,500 for the first calf, $15,000 for the second, $12,500 for the third and $10,000 for the fourth and beyond.
ViaGen has cloned about 300 mammals, including show pigs, rodeo horses and bucking broncos, since its founding in 2002. But this is the world's first go at cloning the breed that takes on matadors in the deadly minuet of bullfighting.

The common strain between the bulls and the horses is the time you have to wait to see if your careful breeding made any difference:

Even in its traditional mode, bull breeding is a slow, hit-or-miss business. Studs are crossed with cows carefully selected for feistiness through simulated fights in the ring, albeit without bloodshed. Then the rancher has to wait a few years for the resulting bull to grow up, and see if it has the right stuff.

They're worried that the clones won't have the same qualities as the originals; calling it all an experiment.

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"I'd rather spend my money on my genome than a Bentley"

Amy Harmon profiles Dan Stoicescu, a Swiss-living millionaire who has become the first paying customer of the genome-sequencing company, Knome.

Mr. Stoicescu said he worried about being seen as self-indulgent (though he donates much more each year to philanthropic causes), egotistical (for obvious reasons) or stupid (the cost of the technology, he knows, is dropping so fast that he would have certainly paid much less by waiting a few months).
But he agreed to be identified to help persuade others to participate. With only four complete human genome sequences announced by scientists around the world -- along with the Human Genome Project, which finished assembling a genome drawn from several individuals at a cost of about $300 million in 2003 -- each new one stands to add considerably to the collective knowledge.
"I view it as a kind of sponsorship," he said. "In a way you can also be part of this adventure, which I believe is going to change a lot of things."

"Sponsorship" seems like a good way to look at it, as long as they don't start including companies' names in the sequence, like "Pepsi" on a high school scoreboard!

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DNA testing and health insurance

Amy Harmon brings several patients' stories to this article, "Fear of insurance trouble leads many to shun or hide DNA tests."

In some cases, doctors say, patients who could make more informed health care decisions if they learned whether they had inherited an elevated risk of diseases like breast and colon cancer refuse to do so because of the potentially dire economic consequences.
Others enter a kind of genetic underground, spending hundreds or thousands of dollars of their own money for DNA tests that an insurer would otherwise cover, so as to avoid scrutiny. Those who do find out they are likely or certain to develop a particular genetic condition often beg doctors not to mention it in their records.
Some, like Ms. Grove, try to manage their own care without confiding in medical professionals. And even doctors who recommend DNA testing to their patients warn them that they could face genetic discrimination from employers or insurers.

According to the article, many people are choosing to pay out of pocket for genetic tests to avoid insurance or medical involvement. If this precedent becomes more common -- people paying for single-disorder tests -- then companies that offer genome-wide SNP typing may have an easy time growing their market.

This one I hadn't heard about:

When the Equal Employment Opportunities Commission sued the Burlington Northern Santa Fe Railway for secretly testing the blood of employees who had filed compensation claims for carpal-tunnel syndrome in an effort to discover a genetic cause for the symptoms, the case was settled out of court in 2002.

That is creepy.

It seems likely that the insurance risk fear will be addressed soon by legislation:

The Genetic Information Nondiscrimination Act, which passed the House of Representatives by a wide margin last year, would prohibit insurers from using genetic information to deny benefits or raise premiums for both group and individual policies. (It is already illegal to exclude individuals from a group plan because of their genetic profile.) The bill would also bar employers from collecting genetic information or using it to make decisions about hiring, firing or compensation. But it has yet to reach the Senate floor.

The article deals with both kinds of fears -- the fear of insurance consequences, and the fear of testing itself. It ends with a woman who feared being tested for the BRCA1 mutation so much that she chose surgery to remove her ovaries. Before a double mastectomy, she had the testing anyway -- and learned that she did not carry the risk allele after all.

UPDATE (2008-02-24): Hsien-Hsien Lei picks up the story also, and adds a perspective from Britain:

Two years ago, Cancerbackup found in a survey of regional genetics centers that waiting time for appointments to receive a BRCA genetic test can be as long as nine months with a further wait of 1 to 2 years for results. In some ways, this could be construed as discrimination in that other forms of testing are probably taken more seriously and performed more speedily.

She also provides a raft of links to other blogs that have posted on the Harmon story.

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Hunting for your child's DNA doppelganger

Maybe you believe you have an identical twin somewhere. Or if not a twin, at least someone who looks a lot like you, a doppelganger. Someone who looks like you, sure. But maybe also someone whose life has curiously paralleled your own.

There are parents who would like nothing more than such a doppelganger for their children. Amy Harmon reported last month on some of them -- parents of children with rare novel mutations.

Every person is born with a handful of new deleterious mutations. Chances are you will never notice yours. Their effects may be small, and many are recessive, needing two copies to show their bad effects -- and of course, since they're new, you only have one copy. If you have children, you will pass half your new mutations to each of them, and they will have their own new ones.

Such new mutations do not cause a large proportion of the recognized Mendelian genetic disorders. The most common disorders are caused by mutations that have been passed down in families over many generations. Some, like the X-linked hemophilia inherited by the descendants of Queen Victoria, have been recognized from pedigrees of relatives. A few are much older. For example, nearly all cases of variegate porphyria in South Africa result from an allele that arrived in Cape Town in 1688. Three hundred years of Afrikaner porphyria have been tracked through pedigrees to one woman, Ariaantje Adriaanse, who carried the mutation.

If your child has a well-known Mendelian disorder, chances are you can find a support group -- possibly locally, but certainly on the internet. These support groups have become very important resources, with everything ranging from dietary advice, results with distinct combinations of treatments, to forums for commiserating about other people's reactions to their kids' unique needs. Some of the recognized Mendelian disorders are often caused by new mutations: for example, half of all cases of neurofibromotosis (roughly 1 in 10,000 people) result from new mutations.

But there are a large set of new mutations that only occur in a tiny fraction of births. Many have only recently been discovered, as genome-wide screens for variation have become possible. Harmon's report focuses on a few of these kids.

A decade ago, these kinds of mutations were unrecognizable, and kids were lumped into broad categories like "developmentally disabled." The most obvious such category is "autism spectrum," which as the name "spectrum" implies, includes a variety of developmental challenges and a range of outcomes. As Harmon's article points out, geneticists are slowly unraveling the different causes of autism. A small fraction of cases result from these rare new mutations, such as 16p11.2.

These genetic results have started to allow families to find other children who are genetically and phenotypically similar to their own. Even if treatments or interventions are not available, this can give parents some idea about the course of their childrens' future development. That's a step forward for some families who can't find their ground easily in the large pool of children on the autism spectrum. What things may be effective with some developmental pathways may have no effect at all on others.

For three families, the impulse to find others in the same situation was immediate.
A few months before the Lanes crossed the state to meet Taygen's chromosomal cousin, Jennie Dopp, a mother in Utah, was scouring the Internet for families with "7q11.23," the diagnosis that explained her son's odd behavior and halting speech.
"I want someone to say `I know what you mean,'" Ms. Dopp told her husband, "and really mean it."
Noa Ospenson's parents flew from Boston to South Carolina for a meeting of 100 families with children who, like Noa, are also "22q13." Hoping for more information about their daughter's diagnosis, they emerged as lifetime members of what they call "Noa's tribe."
For each of them, a genetic mutation became the foundation for a new form of kinship.

This formulation of kinship is more real than many that anthropologists study, because here there is a real connection between gene sequences, although not a "genetic" one in the traditional sense of origins. But there are many forms of analogical kinship in human societies. It is natural, perhaps, the extent to which we are adopting new gene-centered forms of kinship -- from adoptees using genetics to search for their biological relatives, to genealogy buffs sending their DNA to find their distant genealogy buff kin.

For the families described in this story, it is really a case of trying to find a lost part of their own child's biological story. The very things that make their children different from their kin may make them similar to someone else's children. In many cases, finding such connections can be an enormous relief.

The results are not always happy, though:

And then they went to the biennial meeting of 22q13 families in July 2006. But that first day, in Greenville, S.C., they wondered if they had made a mistake.
Few of the children, even the handful of teenagers, were toilet trained. Some had never gained the use of their hands, which had stiffened into a claw-like shape. Many were chewing on rubber tubes or "chew rags," to keep them from shredding their clothes.
Ms. Perlson, a communications consultant, and Mr. Ospenson, a computer analyst, attended sessions on one of the genes that Noa is missing, which codes for a protein crucial to neurological development. They learned about the health problems, like seizures and kidney failure, that Noa might face in her 20s. The window onto her future was hard to digest.

It's a good article, following a number of these stories. I think it's an important view of today's human genetics -- not only are we increasing our knowledge of the origins of common mutations, but we are also increasing the number of rare ones that we know about. Ten years ago, few imagined that these structural gene variants could be an important element of human variation. Now we know that insertions and deletions of genes may account for an important fraction of phenotypic variation in humans.

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Rolling and the health care challenges of the disabled

The New England Journal of Medicine is carrying an article by researcher Gretchen Berland, which describes her work documenting the health access needs of the wheelchair-bound:

By the time Galen Buckwalter's physician knocked on the exam-room door, Buckwalter's video camera had been recording for nearly 40 minutes. He had booked the appointment because his shoulders were hurting, and the camera recorded his view of the examination table, the comments he made while waiting and, eventually, a largely transactional and superficial exchange with his physician. Two weeks later, in his home, the camera would record a strikingly different take on his shoulder pain -- a growing problem that, Buckwalter worried aloud, might cost him even more of his cherished independence.
As an internist, I was disturbed by the contrast between those two scenes, the second revealing the depth of Buckwalter's concerns and fears, none of which were apparent during the conversation with his doctor. In the later tape, Buckwalter's struggle is palpable. If such stark contrasts are common, how much do I really know about my own patients? Probably far less than I care to admit.

She doesn't call it medical anthropology, but it is a nice example of the use of new ethnographic methods (in this case, video observation) to document social interactions. I think it would be a great article for introductory courses; it provokes a range of reactions. Berland describes the film that she made from some of the video, titled Rolling, and the reactions to the problems faced by one of the covered subjects, an MS patient named Vicki Elman:

Rolling has been shown in many venues, perhaps most memorably One World Berlin, a human-rights film festival. After one screening there, several audience members -- some from the German disability community, others Berlin health care providers -- approached Elman. Having seen her experiences in the United States, they had some advice: Stay here.
It was tempting to contemplate that a move might alleviate some of her problems, but Elman had built her life in Los Angeles, not Berlin. Still, I savored that moment, because other viewers were less sympathetic, convinced that the responsibility for change lay with Elman, Buckwalter, and Wallengren. At a meeting of a state medical society, a physician asked whether the participants were taking antidepressants: it might make things feel less difficult, he advised. At one screening, a medical student even inquired whether the participants had considered having their legs amputated, in order to make transfers from their wheelchairs easier.

I know I have a lot of readers interested in the medical aspects of human variation who might not notice an article in NEJM. This one helps to illustrate the ways that cultural anthropological methods can be valuable.

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