Biologist George Church, examining a molecular model.

George Church, the geneticist behind the Personal Genome Project, is envisioning a package deal: get your genome sequenced, and he and his collaborators will develop a line of induced pluripotent stem cells (IPS) from your tissue, so in the future, you’ll be able upgrade your system with organs and tissues bearing both your genes and special extras like genes from centenarians. It’s combining stem cells with gene therapy. In an interview with Church, David Ewing Duncan over at Technology Review asks him to elaborate. Why does he think this science fiction scenario is in our near future?

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When people talk about how genetics testing is paving the way for personalized medicine, there’s a subtext that’s not always made clear: that’s personalized medicine for Northern Europeans and their descendants. Non-whites are hugely underrepresented in most collections of genomes, which means if you’re Asian or African, it’s hard to say what genetic predispositions you might have to certain diseases, or how you will react to drugs that target certain forms of enzymes, for example.

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What’s the News: When personal genotyping service 23andMe was founded in 2006, most people were understandably focused on the benefits and the dangers of knowing your chances of getting an incurable disease. But a major part of the company’s business plan was eventually leveraging their users’ information to explore the genetic basis of disease.

With more than 100,000 people now in their database, 23andMe has been turning that into a reality. They’ve just published their first paper focusing on the origins of disease, pinpointing two new areas of the genome involved in Parkinson’s.

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Already, researchers have imagined and built ways to detect one-in-a-billion cancer cells in a person’s bloodstream in order to catch cancer in the act of spreading. Now, that technology is a little closer to moving out of the lab.

Mehmet Toner and colleagues from Massachusetts General Hospital, the brains behind the tech, announced an agreement with a subsidiary of Johnson & Johnson to begin commercial development of their “liquid biopsy.”

The microchip is dotted with tens of thousands of tiny posts covered with antibodies designed to stick to tumor cells. As blood passes over the chip, tumor cells separate from the pack and adhere to the posts. Scientists are wagering that this type of test, if successful, might also detect cancer early in its course, predict the odds for a recurrence, and assess a patient’s general prognosis. [Healthday News]

Toner’s team developed the prototype of the test back in 2007, and for the last several years have refined the extreme sensitivity needed to catch stray cancer cells roaming the bloodstream.

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It may not be as miraculous as turning water into wine, or as wealth-generating as turning dirt into gold, but we still think this is a very cool trick: Researchers have transformed mature skin cells directly into mature blood cells. Crucially, this was done without reverting the cells to a flexible, “pluripotent” stage in which the cells can grow into any form.

The technique, described in Nature, could lead to lab-grown blood cells for transfusions and transplants for people with bone marrow diseases. Researchers think this new process may be safer than previous methods.

By skipping the pluripotent step, the researchers believe they have skirted the risk that the replacement cells might form dangerous tumors. [Los Angeles Times]

The research team, lead by Mickie Bhatia, coaxed the skin cells into becoming blood cells via a harmless virus that carried a gene called OCT4 into the cells–this reprogrammed the cells, turning their developmental clock back part of the way. Then the cells were incubated in a mixture of cell-stimulating proteins, called cytokines, which directed them on their new paths as either red blood cells, white blood cells, or platelets. The ability to grow a specific kind of blood cell has exciting clinical possibilities.

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Is it medicine, or is it not?

In May, the University of California, Berkeley unveiled its “Bring Your Genes To Cal” program. The idea was, Berkeley’s 5,500 or so incoming freshman would have the option to have their DNA tested for three particular characteristics: Their metabolism of folate, tolerance of lactose, and metabolism of alcohol. Though the program was limited, it raised privacy hackles. And now the State of California has ruled: This is a medical test, and Cal can’t do it unless it’s in a clinical setting.

Mark Schlissel, UC Berkeley’s dean of biological sciences and an architect of the DNA program, said he disagreed with the state Department of Public Health’s ruling that the genetic testing required advance approval from physicians and should be done only by specially-licensed clinical labs, not by university technicians. The campus could not find labs willing to do the work and probably could not afford it anyway, Schlissel said. He also contended that the project deserved an exemption from those rules because it was an educational exercise [Los Angeles Times].

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The Food and Drug Administration has a message for the personal genomics revolution: slow down.

Personal DNA tests have been available for years now from companies like 23andMe and Pathway Genomics, and the direct-to-consumer tests have sold briskly even while the companies tried to sort out whether or how their systems would be regulated by the FDA. Then last month, Pathway took the next big step, offering to sell their tests over the counter in the nation’s largest drugstore chain, Walgreens.

For the FDA, that was one step too far, and it began to make noise about regulation. Now the agency’s leader in this field, Alberto Gutierrez, has sent official letters to all the major personal DNA-testing companies saying it intends to regulate the tests as medical devices, and that the companies must provide evidence of their scientific validity.

The letters, posted on the F.D.A. Web site on Friday, say the companies must apply for approval or discuss with the agency why certain test claims do not require such approval. But the letters stop short of saying the tests must be taken off the market until they are approved. Dr. Gutierrez said in an interview that it would be unfair to remove the tests from the market because the agency had not clearly told the companies that the devices needed approval [The New York Times].

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When Walgreens, the nation’s biggest drugstore chain, announced last week that personal genomics tests would join diet soda and pregnancy tests in its aisles, we gave some reasons that might not be such a great thing. We weren’t the only ones concerned: The Food and Drug Administration said it would investigate the tests, and now Congress is involved. It opened an investigation into personal genomics tests yesterday.

House Committee on Energy and Commerce, chaired by Rep. Henry A. Waxman, just sent out official requests for information to the big three personal genomics companies—23andMe, Navigenics, and Pathway Genomics.

Waxman’s interest was piqued by the move—quickly rescinded last week after the FDA objected—by Pathway to sell its DNA-collection kits in Walgreen’s drugstores. The letters ask the companies for information on, among other things, how they analyze test results to determine someone’s risk for any disease or drug response, and how accurately the DNA tests identify genetic risks [Newsweek].

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While you’re down at the drug store picking up toothpaste and sleeping pills, why not have your DNA tested? Walgreens says that this month it will become the first drug store to offer personal genomics tests in its store. For the low, low price of $20-30 you can pick up a kit to take a sample of your own saliva, which you mail off to Pathway Genomics, a company partnering with Walgreens.

Customers can then go Pathway’s Web site and order tests. Pathway says the tests — for drug response, “pre-pregnancy planning” and “health conditions” — start at $79 and run up to $249 for all three [AP].

With the personal genomics trend continuing to accelerate, this was perhaps an inevitable development. But the fact that personal tests are going into drug stores doesn’t mean that personal tests are as readily reliable or regulated as the rest of the tests and medications that fill the aisles.

1. The FDA is not pleased.

The Pathway test has not been approved by the Federal Drug Administration. In a statement after announcing this deal, Walgreens washed their hands of responsibility in this regard, saying Pathway assured them that the product didn’t require FDA approval. The FDA, however, does not agree.

In a statement, the FDA said it has regulatory authority over all lab-developed tests. “As new technologies become available and are marketed directly to consumers, FDA will consider all regulatory options,” the agency said. “Consumers should understand that the claims made by a company with an unapproved test have limitations and that they should not be making important medical and lifestyle decisions without first consulting a health care professional” [Wall Street Journal].

The FDA isn’t the only public body worried about these tests. Here in New York, where DISCOVER is located, we won’t be able to run down to Walgreens and pick up a DNA test. The state considers these to be medical tests, and medical tests require a license. When personal genomics companies first began to spring up, New York State issued nearly 40 cease-and-desist orders in 2007 and 2008. It’s still going to take some time to sort out the legality of who can look into your genome.

2. Can you actually learn anything useful?

Remember, only six years have passed since the human genome was fully sequenced. Incorporating personal genomics into medicine is moving fast, but it’s still in the early stages.

In most cases, the current level of DNA scanning technology and science is unable to offer meaningful predictions about the risk that a person will get a disease. “It is a really wonderful form of recreation,” said Scott R. Diehl, a geneticist at the University of Medicine and Dentistry of New Jersey. But as for applying it to health care, he said, “It’s very premature” [The New York Times].

The tests by personal genomics companies like 23andMe and Pathway look at particular point mutations that scientists think to be associated with diseases like Alzheimer’s or cystic fibrosis. Making clear predictions from a person’s DNA, though, will require not only a further understanding of what genes are linked to what diseases, but also how those genes interact with environmental factors, lifestyle choices, and each other, as our reporter found out in 2008 when having her DNA examined by several of the most prominent companies.

All that knowledge won’t come fast, or cheap.

That might take a few years and require sequencing a person’s entire genome, not just sampling selected bits, as the companies do now [The New York Times].

3. Overreaction—and mixed results

As the FDA noted in its statement quoted above, customers must understand the limitations of these tests—and not act too drastically. As DISCOVER’s own Kat McGowan wrote last year, “Another worry is that people may overreact to their results. Someone who has an elevated risk of breast cancer, for example, might take a drastic step like getting a mastectomy, not realizing that the test predicts increased risk, not a particular outcome.”

Then again, if you get curious enough to try multiple tests, you might have the opposite problem. Some curious folks who’ve tried out multiple personal genomics firms have received contradictory answers.

4. The fine print

Even if you don’t act on the information that a personal genetic test brings, it could impact you emotionally to learn about your ancestry or your family (say, if your father wasn’t your genetic father). That’s why the fine print on personal-genomics products is so extensive.

And the ramifications could do beyond the emotional realm. The Genetic Information Nondiscrimination Act of 2008 offers some protection for personal genetic information, but how much is not terribly clear. Things are changing fast in the world of personal genomics, and it may be difficult or impossible to predict the significance, or even risk, of information you learn in 2010. As 23andMe’s terms and conditions notes:

Even if you share genetic information that has no or limited meaning today, that information could have greater meaning in the future as new discoveries are made. If you are asked by an insurance company whether you have learned genetic information about health conditions and you do not disclose this to them, this may be considered to be fraud.

5. Ready for the shelves?

Still, though, why shouldn’t you have the choice of whether to test your own genome? You get to test yourself in other health capacities:

Drug stores already carry a variety of diagnostic tests, like those for pregnancy, cholesterol and blood sugar. When some of these tests were introduced, there was controversy about whether consumers could test themselves.

Although broader in scope, Pathway’s test is not the first DNA-based analysis to be sold in drug stores. Sorenson Genomics began selling a paternity test through Rite Aid stores in late 2007. Sorenson has sold more than 100,000 tests through Rite Aid and other major pharmacy chains since then, according to Jacob Moon, a spokesman for the company [The New York Times].

But personal genomics is a different ballgame. Paternity tests and pregnancy tests bring you clear yes-or-no answers; they don’t evaluate complicated, multifactorial questions like those that personal DNA tests try to answer. And that complexity may be more than consumers bargained for.

Related Content:
DISCOVER: How Much Can You Learn from a Home DNA Test?
DISCOVER: Your Genome, Now Available for a Relative Discount
Gene Expression: Creative Destruction in Personal Genomics
Gene Expression: Personal Genomics Is Dead; Long Live Personal Genomics

Image: flickr / twodolla

Doctors who are torn over how aggressively to treat a cancer patient, not knowing whether a tumor has fully regressed or is coming back, might someday be able to find out just by testing the patient’s blood. In a study forthcoming his week in Science Translational Medicine, John Hopkins researchers say they have tested a way to spot the “fingerprint” of cancer–the changes to the DNA inside cells that make up cancerous tumors.

Jeffery Schloss of the National Human Genome Research Institute, who wasn’t involved in the study, likened the approach to drawing a map. Sequencing the letters of the genetic code would be akin to plotting every house in a large neighborhood. The Hopkins team was looking only for neighborhoods—in particular, neighborhoods out of place compared with where they would be in normal tissue [Wall Street Journal]. The researchers in the study looked at tissue from people with breast or bowel cancer, and found multiple DNA rearrangements in each of the samples of cancerous tissue.

In each patient, the genetic changes in the cancerous cells amount to a unique marker of the patient’s tumor, the researchers say. Using blood samples from two of the colorectal cancer patients, they found the test was sensitive enough to detect this marker or “fingerprint” DNA that had been shed by tumours into the bloodstream [BBC News].

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Linda De Croock, a Belgian woman who had her throat crushed in a car accident a quarter-century ago, received one of the odder-sounding organ transplants we’ve ever heard: For two years, De Croock had a dead man’s windpipe growing inside her arm. Reporting in the New England Journal of Medicine, her doctors say they successfully implanted the donated trachea in her forearm and then moved it from there to where it belongs.

While the arm might seem a questionable place to put a windpipe, the point was to acclimate her body to the new organ and get her off anti-rejection drugs. Doctors at Belgium’s University Hospital Leuven implanted the donor windpipe in De Croock’s arm as a first step in getting her body to accept the organ and to restart its blood supply. About 10 months later, when enough tissue had grown around it to let her stop taking the drugs, the windpipe was transferred to its proper place [Canadian Press]. Since De Croock’s own tissue has grown around the windpipe, her body no longer considers it foreign and dangerous. A year has passed since the surgery to move the windpipe from her arm to her throat, and the doctors report she is doing well.

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There’s nothing like the round number at the start of a new decade to get everyone prognosticating (yes, we know some of you are in the crowd that says the new decade doesn’t begin until 2011; OK, fine). To predict what the scientific scene will be like in 2020, the journal Nature brought in experts from 18 fields. Though the collection doesn’t encapsulate the “world of tomorrow” feel of, say, the old Omni magazine, it’s still packed with sunny (and scary) forecasts. Some show lingering uncertainty, some unbridled optimism, and some give warnings to the world to make a much-needed course correction. Here are five we thought were particularly telling.

1. In 2020, Google defines your reality (even more than it does already).

Peter Norvig, Google’s director of research, tackles the question of where search will be a decade hence. Advanced, he says, but also troublesome: Most searches will be spoken rather than typed, and designers will be experimenting with search systems that read your brain waves. “Users will decide how much of their lives they want to share with search engines, and in what ways”—such is Norvig’s polite description of a world with even less digital privacy than today’s.

What search engines give you back will change, too. Particularly, he says, they will come up with a way to judge relevance and quality that doesn’t rely on popularity: “Thus, a site that claims that the Moon landings were a hoax and seems to have a coherent argument structure will be judged to be lower quality than a legitimate astronomy site, because the premises of the hoax argument are at odds with reality.”

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The genomes of lung and skin cancer have been decoded by scientists at the UK-based Wellcome Trust Sanger Institute near Cambridge, which is the first time an entire cancer gene map has been created.

The scientists say they have pinpointed specific DNA errors that may cause tumors in these two cancers, both of which have direct known causes—smoking for lung cancer and sun exposure for skin cancer. Researchers predict these maps will offer patients a personalized treatment option that ranges from earlier detection to the types of medication used to treat cancer. The genetic maps will also allow cancer researchers to study cells with defective DNA and produce more powerful drugs to fight the errors, according to the the study’s scientists [CNN]. News reports are heralding the new research as revolutionary, however it will be years, perhaps decades, before the full implications of the work are understood.

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DeCode Genetics, a genome sequencing and drug development company, found out the hard way that predicting disease risk simply by reading someone’s genes isn’t so straightforward. On Tuesday, deCode filed for chapter 11 bankruptcy protection in Delaware. The company’s financial problems have also raised some troubling questions about genetic privacy.

DeCode’s mission was to uncover genetic risk factors for common diseases and to develop personal genome scans so individuals could learn their risk. DeCode quickly became the leader in the worldwide race to identify the causes of common disease. The company’s researchers discovered mutations linked to schizophrenia, heart disease, diabetes, prostate cancer and many other illnesses. Its approach was to identify the mutations first in Icelanders and then to confirm them in other populations [The New York Times]. Iceland was seen as an ideal spot for genetic studies, because the population was fairly isolated and the country has excellent medical and genealogical records. However, the company’s early successes did not translate into dollars, in part because the mutations they found only account for a small percentage of the overall incidence of a given disease.

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“People ordered genomes for Christmas” [The New York Times], says the chief executive of the personal gene-sequencing company Knome, commenting on the recent increased demand for his company’s services. Now, Knome is partnering with the non-profit X Prize Foundation to auction its complete genome scan service on eBay. Bidding will open at $68,000—far below Knome’s current price of $99,000. The auction starts Friday and will continue for 10 days. The highest bidder will walk away with a full readout of their gene map, along with a complete interpretation of their genetic details [CNN].

The auction is essentially a publicity stunt [The New York Times] for the company, and is set to begin Friday in order to coincide with DNA Day, the anniversary of the discovery of the double helix structure. Proceeds will benefit the X Prize Foundation, an educational institute offering a $10 million prize for the sequencing of 100 genomes in 10 days for less than $10,000 per genome. Knome and other personal genetics companies claim that besides identifying risk of diseases, sequencing can also determine an individual’s potential reaction to certain drugs and pick out those that may be ineffective or even toxic…. Genomics plays a critical role in the move towards personalized medicine [CNN].

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