Craig Venter's Genome

The genomic pioneer bares his genetic code to the world.

By Emily Singer

Personal genomes: Genomics pioneer Craig Venter (above) has sequenced his entire genome and released it to the world.

Credit: J. Craig Venter Institute

Five years ago, Craig Venter let out a big secret. As president of Celera Genomics, Venter had led the race between his company and a government-funded project to decode the human genome. After leaving Celera in 2002, Venter announced that much of the genome that had been sequenced there was his own. Now Venter and colleagues at the J. Craig Venter Institute have finished the job, filling in the gaps from the initial sequence to publish the first personal genome.

His newly released genome, published today in the journal PLoS Biology, differs from both of the previous versions of the human genome (one from Celera, the other from the Human Genome Project) in that it details all of the DNA inherited from both mother and father. Known as a diploid genome, this allows scientists to better estimate the variability in the genetic code. (In a genome sequence generated from a conglomerate of different individuals, some variations are lost in the averaging.) Within the genome of 2.810 billion base pairs, scientists found 4.1 million variations among the chromosomes; 1.2 million of these were previously unknown. Of the variations, 3.2 million were single nucleotide polymorphisms, or SNPs, the most well-characterized type of variation, while nearly one million were other kinds of variants, including insertions, deletions, and duplications.

Venter's genome will join that of another genomic pioneer, James Watson, codiscoverer of the structure of DNA. (See "The $2 Million Genome.") Announced in June, Watson's genome was sequenced by 454, a company based in Branford, CT, that's developing next-generation sequencing technologies. (For more on 454's technology, see "Sequencing in a Flash.")

Venter's and Watson's genomes are likely just the first in an upcoming wave of personal genomes, a crucial step in the advent of personalized medicine: the ability to tailor medical treatments to an individual's genetic profile. (See "The X Prize's New Frontier: Genomics.") Venter has already explored some of his genome, discovering that he carries genetic variations that put him at increased risk for Alzheimer's disease, heart disease, and macular degeneration. He says that he's been religiously taking statins, cholesterol-lowering drugs, ever since.

Venter talks with Technology Review about what lies ahead for his genome.

Technology Review: Why did you decide to embark on this project?

Craig Venter: The genome we published at Celera was a composite of five people. To put it together, it became clear that we had to make some informatics compromises--we had to leave out some of the genetic variation. We knew the only way to truly understand the genome would be to have the genome of one individual. Rather than starting from scratch, we decided to take what we had from the Celera genome and add more sequence. The goal was to get an accurate reference sequence from a single individual.

TR: How does your genome sequence add to what we know from the Human Genome Project?

CV: The government labs sequenced and assembled a composite haploid genome from several individuals [meaning it included a DNA sequence from only one of each chromosome pair]. There was the assumption back then that having half of the genome was all that was needed to understand human complexity. But it's become clear that we need to see the composite of the sets of chromosomes from both the mother and father to see the variation in the genome.

This genome has all the insertions and deletions and copy-number differences. That gives us a very different view.

TR: What's the most exciting finding so far?

CV: For me, the most exciting finding is that human-to-human variation is substantially higher than was anticipated from versions of the human genome done in 2001. If fact, it might be as much as tenfold higher: rather than being 99.9 percent identical, it's more like 99 percent identical. It's comforting to know we are not near-identical clones, as many people thought seven years ago.

TR: How will scientists use your genome sequence?

CV: It will serve as a reference genome. This is probably the first and last time anyone will spend the time, money, and energy to sequence a diploid genome using highly accurate Sanger sequencing. Future genomes, like those from 454 or George Church's Personal Genome Project, will be layered onto [existing] data, adding to the completeness of this genome. (See "The Personal Genome Project.") [The traditional Sanger sequencing method, used for the Human Genome Project and to generate Venter's sequence, generates longer pieces of DNA than do newer methods, such as that used by 454, making it easier to assemble the overlapping pieces.]

TR: James Watson released a version of his own genome earlier this summer. How is yours different?

CV: There has been nothing published yet on his genome, so we have no idea. But as I understand it, in contrast to really assembling a genome, they sequenced short fragments that are layered onto the sequence assembled at the NIH. So there are a lot of technical differences, but until it's published, we won't really know.

TR: You've had sections of your genome in the public domain for several years now. Any second thoughts about putting the entire high-quality sequence out there?

CV: No. And I applaud Watson for doing this as well. A key part of the message here is that people should not be afraid of their genetic codes or afraid to have other people see them. That's in contrast to the notion that this is dangerous information that should be kept under lock and key. We're not just our genetic code. There is very little from the code that will be 100 percent interpretable or applied.

TR: Have you searched your genome for disease-related mutations?

CV: Yes. I have a book coming out in October called A Life Decoded where I look at many variants and try to put them in context of my life. For example, I have a high statistical probability of having blue eyes, but you can't be 100 percent sure from my genome that I have them. The message is that everything in our genomes will be a statistical uncertainty. We're really just in the first stages of learning that.

Previous published genomes don't represent anyone, so we can't interpret human biology based on these. But now we can start to make human-genome inferences. We'll need tens of thousands to millions of genomes to put together a database that would allow interpretation of multiple rare variants and what they mean. That will take decades.

TR: How much did the project cost?

CV: The goal was not to see how cheaply we could sequence a genome; it was to see how accurately we could do it. It was clearly a multimillion-dollar project over the years.

Source: http://www.technologyreview.com

"Personalized" Embryonic Stem Cells for Sale

A company offers to generate and store stem cells from leftover IVF embryos.

By Emily Singer
Stem-cell insurance: A company called StemLifeLine offers to generate embryonic stem cells (shown above) from leftover embryos created for in vitro fertilization. The cells could potentially be used for future medical treatments, although no embryonic-stem-cell-based treatments exist yet.
Credit: David Scharf, Science Photo Library

It's a new, rather dicey form of life insurance. A company in California called StemLifeLine has announced that it will offer a service to generate stem cells from excess frozen embryos stored after in vitro fertilization (IVF). The company promises a huge potential payoff: the cells could one day be used to treat disease in the buyers or in their families. But the service is already garnering criticism from some scientists and ethicists who say that without current medical uses for those cells, there's no point in people paying for them.

"I think the company's website overly hypes what may be possible," says Lawrence Goldstein, director of the stem-cell research program at the University of California, San Diego. "They are almost guaranteeing that therapies are around the corner, and now is the time to start banking stem cells, but that strikes me as premature for the field."

The new service is meant to take advantage of a growing interest in the field of regenerative medicine. Stem cells from adult blood or umbilical-cord blood are already used to treat some diseases, including sickle-cell anemia and several forms of leukemia. But these cells are largely limited to treating blood-related disorders and can't be grown in large numbers. Embryonic stem cells, on the other hand, can be coaxed to form virtually any type of cell in the body and can theoretically be replicated indefinitely. Scientists are developing ways to use them to replenish cells lost or damaged in ailments such as diabetes, Parkinson's disease, and heart disease. But as of now, those treatments are limited to the lab: no embryonic stem-cell-based therapies are approved for human use.

Couples who have had children via IVF are often left with extra embryos--and the rather difficult decision of what to do with them. As of 2003, an estimated 400,000 embryos remained in cryopreservation in the United States. Embryos can be donated to research or to other couples, destroyed, or left languishing in frozen storage. According to Ana Krtolica, StemLifeLine's CEO, the inspiration to form the company came from requests from clients at IVF clinics who were donating their embryos to research but wanted to know if they would have access to those cells if they were ever needed. (The answer is no.)

"We had a patient whose husband is a paraplegic," says Russell Foulk, a member of StemLifeLine's advisory board andmedical director of the Centers for Reproductive Medicine, a private clinic with offices in Nevada and Idaho. "They wanted to have a child and were excited about the possibility of creating neural cells from the extra embryos."

The technology to derive these cells is not new. Scientists at StemLifeLine use a similar procedure to that employed by research scientists for almost a decade, although the StemLifeLine scientists have refined it so that the resulting cells are fit for human use. For less than $10,000 (actual price depends on the collaborating IVF clinic), clients can send in their excess embryos and, in return, receive a line of stem cells that have been "quality assured," meaning they have been checked for the molecular markers that signify that the cells can be differentiated into multiple cell types. The company received certification as a tissue bank from the state of California last month, and it's in the process of generating cell lines for its first group of clients.

However, critics say that the service is premature. Extra embryos can remain in frozen storage for years. And in the case of the paraplegic man, no treatments using neural stem cells are yet available. "There is no reason to take your embryos out of cryopreservation and make a line of stem cells and then freeze them again until the technology is available to actually use them," says Eric Chiao, a stem-cell biologist at Stanford's Institute for Stem Cell Biology and Regenerative Medicine, in Palo Alto.

Chiao and others argue that by the time scientists have figured out how to use embryonic stem cells as therapies, they will likely have developed better ways of generating the stem cells themselves, possibly using cloning, in which scientists would generate perfectly matched stem cells from an adult cell of the patient to be treated. "My offspring would be better off if they used cloning to generate stem cells for themselves," says Arthur Caplan, an ethicist at the University of Pennsylvania. "In America, the best thing you can do is take the money you would have used and invest it in an insurance policy to maximize the likelihood that your kid will have health insurance someday."

Krtolica counters that because it takes two to three months to generate the cells, it's better to have them ready before an approved use in case a client needs them immediately.

Stem-cell scientists also say that StemLifeLine's description of its product as "personalized" stem cells is misleading. As with organ transplants, cell transplants require that the immune profile of the transplanted cells match the host as closely as possible. Scientists generally use the term personalized stem cells to refer to a type of stem cell not yet possible to create: those generated through cloning, making them a perfect genetic match to the donor. Cells made from discarded embryos would not be a perfect match to family members, says Doug Melton, codirector of the Harvard Stem Cell Institute, in Cambridge, MA. "This would be like having stem cells from a sibling, so immunosuppression is still an issue."

The prospect of generating stem-cell lines from embryos is likely to ignite new ethical arguments over embryonic stem cells. Critics of embryonic-stem-cell research oppose generating stem cells from embryos for any reason. But this service could spark growth of a practice that some find even more problematic: the creation of embryos solely as a source of cells. For example, some people might want to undergo IVF expressly for the stem cells, not to have a child. Krtolica says that she hasn't yet fielded any such requests but that ultimately, it would be up to the fertility clinics. Foulk, for one, says he would perform IVF under these circumstances.

Source: http://www.technologyreview.com

Electric Fields Kill Tumors

A promising device uses electric fields to destroy cancer cells in the brain.

By Katherine Bourzac

Zapping tumors: Brain-cancer patients in a trial for a portable device that sends a weak electric field into the brain must wear electrodes almost constantly. One patient in a pilot clinical trial for the device, who still had cancer after radiation, chemotherapy, and surgery, experienced a complete recovery. The MRI at top shows a tumor on the left side of this patient’s brain before treatment. The MRI at bottom, taken after eight months of treatment, shows no tumor.
Credit: Yoram Palti, NovoCure (top image); Proceedings of the National Academy of Sciences (bottom MRIs)

An Israeli company is conducting human tests for a device that uses weak electric fields to kill cancer cells but has no effect on normal cells. The device is in late-stage clinical trials in the United States and Europe for glioblastoma, a deadly brain cancer. It is also being tested in Europe for its effectiveness against breast cancer. In the lab and in animal testing, treatment with electric fields has killed cancer cells of every type tested.

The electric-field therapy was developed by Yoram Palti, a physiologist at the Technion-Israel Institute of Technology, in Haifa, who founded the company NovoCure to commercialize the treatment. Palti's electric fields cause dividing cancer cells to explode while having no significant impact on normal tissues. The range of electric fields generated by the device harms only dividing cells. And since normal cells divide at a much slower rate than cancer cells, the electric fields target cancer cells. "An Achilles' heel of cancer cells is that they have to divide," says Herbert Engelhard, chief of neuro-oncology in the department of neurosurgery at the University of Illinois, Chicago.

Even after chemotherapy, radiation therapy, and surgery, about 85 to 90 percent of glioblastoma patients' cancer still progresses, and their survival rates are low, says Engelhard. He has about 10 glioblastoma patients enrolled in the trial, which is testing the unusual treatment in patients for whom all other approaches have failed. Engelhard says that the results are encouraging but that it's too early to comment on the treatment's efficacy.

The electric fields' different effects on normal and dividing cells mostly have to do with geometry. A dividing cell has what Palti calls "an hourglass shape rather than a round shape." The electric field generated by the NovoCure device passes around and through round cells in a uniform fashion. But the narrow neck that pinches in at the center of a dividing cell acts like a lens, concentrating the electric field at this point. This non-uniform electric field wreaks havoc on dividing cells. The electric field tears apart important biological molecules, such as DNA and the structural proteins that pull the chromosomes into place during cell division. Dividing cells simply "disintegrate," says Palti.

Palti, who for years has been studying the effect of electric fields on cancer and normal cells, says that he has verified this mechanism in computer models and experiments in the lab. "The physics are solid," says David Cohen, associate professor of radiology at Harvard Medical School.

Patients in the glioblastoma clinical trial wear the device almost constantly, carrying necessary components in a briefcase. A wire emerging from the briefcase connects to adhesive electrodes covering the skull. Alternating electric fields pass through the scalp, into the skull, and on to the brain. The Food and Drug Administration approved the device for late-stage clinical trials for glioblastoma following promising results from a pilot study in 10 patients, one of whom had a complete recovery.

One exciting result from his studies, says Palti, is that there is "excellent synergy between electric-field treatment and chemotherapy." In an unpublished lab study of several types of cancer, he says, adding electric-field treatment makes several chemotherapeutics more effective at lower doses. NovoCure is now conducting a pilot trial in Europe in which patients begin electric-field treatment in conjunction with chemotherapy when they are first diagnosed with glioblastoma. The results are preliminary, but, Palti says, "I strongly believe that the combination treatment will ... enable one to reduce the chemo doses to levels where their side effects will be significantly reduced."

Palti says that after more than 200 cumulative months of electric-field treatment in several patients, there have been no side effects beyond irritation of the scalp. "So far, toxicity seems to be low," says Engelhard. This stands in stark contrast to chemotherapy and radiation, which cause many side effects, including nausea, hair loss, and fatigue.

One worry is that the electric-field treatment could affect healthy cells that are dividing. The electric fields emerging from the electrodes can't be focused, says Cohen, and although they are primarily concentrated in the brain in the glioblastoma trial, they may also reach other parts of the body where cells are dividing. Cells in the bone marrow, for example, multiply at a great rate to create red blood cells and immune cells. But Palti says that the electric fields have no effect on blood-cell counts. The bone and muscle surrounding the marrow appear to protect the cells..

It's unclear how long patients will need to wear the device. "We're hesitant to stop treatment, because the consequences could be severe," says Palti, although one patient whose cancer has disappeared has stopped wearing the device. Patients must go to the clinic twice a week to have their heads shaved so that their hair doesn't interrupt contact between the scalp and the electrodes. The device itself costs only about $1,000 to manufacture, but replacing the electrodes twice a week is expensive.

Engelhard says that he got involved with the NovoCure clinical trial because the electric-field treatment is "radically different" from all existing cancer treatments. For patients with recurrent glioblastoma and other deadly forms of cancer, there are few options. "Researching and testing new therapies for this type of patient is very important," says Engelhard.

The Invisible Hearing Aid

A fully implantable device is poised to change the world of hearing loss--but is it worth the risks that are associated with the required surgery?

By Michael Chorost

Listen in: Otologics’s fully implantable hearing aid is countersunk into the skull so that it lies flush along the surface underneath the skin and muscle.
Credit: Otologics

Hearing aids help millions of people, but many resist them because they think wearing one carries a social stigma. Hearing aids also have serious lifestyle limitations: the hearing impaired can't wear them while showering or swimming, and most models are hard to wear while sleeping. Now, a new kind of hearing aid that aims to overcome these problems is in clinical trials. It's invisible and waterproof because all of its circuitry--including its battery and microphone--is in the user's head.

Developed by Otologics, of Boulder, CO, the device picks up sound with a microphone implanted underneath the skin behind the user's ear. The signal is processed by electronics and sent to a tiny vibrating piston implanted against the small bones in the middle ear. The bones transmit the vibrations to the inner ear, which encodes them as nerve impulses and sends the information to the brain.

"You can have a more normal life," says Otologics's CEO José Bedoya. "You can be exposed to environments in which hearing aids have difficulty operating properly." He also suggests that implantation creates a psychological bond with the device that is life enhancing. "Individuals implanted with the system have said that it becomes a part of you--there's a greater sense of security."

The device is powered by a battery that is recharged when the user places a small radio transmitter against his or her head for 60 to 90 minutes. The transmitter is held to the skin by a magnet in the implant. An inductive coil in the implant converts the radio energy to electricity and recharges the battery with it. The battery can stay inside the body for at least five years, according to the company, before it needs to be replaced. The implanted components are hermetically sealed together to protect against leaks, so the electronics, microphone, and inductive coil are replaced as well. However, the piston in the middle ear remains in place.

The results of a phase I clinical trial of the hearing aid were reported in the August 2007 issue of Otolaryngology--Head and Neck Surgery. Twenty subjects with moderate to severe hearing loss were implanted in one ear. (Seventeen of the subjects had worn conventional hearing aids prior to the study.) The subjects did somewhat worse than with the hearing aid they had previously worn: their ability to hear a range of single-frequency tones dropped between 5 and 12 decibels, and mean word-recognition scores dropped from the low 80 percent range to the high 60 percent range.

On the other hand, a satisfaction survey found that the subjects felt that the device not only improved their hearing, but also sounded more natural than their old hearing aid. The authors of the study speculated that new processing algorithms would improve the test results. Otologics has indicated that it is already working on this.

A key challenge in developing a fully implantable hearing aid is designing a microphone that will work effectively under the skin. Bedoya notes that the properties of human skin change throughout the day with the user's hydration levels and other factors, and he hinted that the company is developing technology to detect those changes and adjust to them. He also points out that the location of the microphone behind the ear is an important factor that can be fine-tuned.

Outside experts see significant progress being made in implantable microphone design. Joseph Roberson, an ear surgeon and the CEO of the California Ear Institute, in Palo Alto, CA, says, "I listened to a good-fidelity musical signal received by an implantable microphone positioned under half an inch of raw steak." The functional outcome of the Otologics device, he says, is "roughly equivalent to existing visible external technology."

But critics question whether Otologics can match the performance of conventional hearing aids, and they ask whether the new device is worth the surgical risk and the cost ($19,000 in Europe, excluding the cost of the surgery, versus $6,000 for a high-end conventional aid; the device is available in Europe but still in clinical trials in the United States). Gerald Loeb, a professor of biomedical engineering at the University of Southern California, argues that implanted hearing aids should outperform conventional ones before they can be considered worth the extra cost and risk. He also questions the emphasis on making an invisible device: "How big an issue is it to have a little appliance on your ear when the whole world is walking around with cell-phone headsets and iPod earpieces?"

Nonetheless, the phase I study concluded that the Otologics device "serves as a viable treatment alternative for moderate to severe sensorineural hearing loss." Bedoya says that the company is addressing the problems found by the study and preparing for phase II trials, in which 90 subjects will be tested with a revised device.

Roberson suggests that the device may be most suitable for "alpha adopters ... who are motivated to keep their use of a hearing device a private matter, or those who are intolerant of standard hearing-aid technology." Silicon Valley executives, he thinks, may be first in line.

Michael Chorost is the author of Rebuilt: How Becoming Part Computer Made Me More Human.

Source: http://www.technologyreview.com