technology-World: biomedicine

Could a Genetic Test Predict the Risk for Suicide?

Scientists are hunting for the genetic basis of suicide and developing suicide DNA tests. No one could have predicted that Oscar-winning comedian Robin Williams would kill himself.Or could they?When someone commits suicide, the reaction is often the same. It’s disbelief, mixed with a recognition that the signs were all there. Depression. Maybe talk of ending one’s life.Now, by studying people who think about committing suicide, as well as brains of people who actually did, two groups of genome researchers in the U.S. and Europe are claiming they can use DNA tests to actually predict who will attempt suicide.While claims for a suicide test remain preliminary, and controversial, a “suicide gene” is not as fanciful as it sounds. The chance that a person takes his or her own life is in fact heritable, and many scientific teams are now involved in broad expeditions across the human genome to locate suicide’s biological causes.Based on such gene research, one startup company, Sundance Diagnostics, based in Boulder, Colorado, says it will begin offering a suicide risk test to doctors next month, but only in connection with patients taking antidepressant drugs like Prozac and Zoloft.The Sundance test rests on research findings reported by the Max Planck Institute of Psychiatry in 2012. The German researchers, based in Munich, scanned the genes of 898 people taking antidepressants and identified 79 genetic markers they claimed together had a 91 percent probability of correctly predicting “suicidal ideation,” or imagining the act of suicide.It’s well known that after going on antidepressants, some people do begin thinking about killing themselves. The risk is large enough that a decade ago the U.S. Food and Drug Administration slapped a warnings on antidepressant pills, saying they “increased the risk … of suicidal thinking and behavior” in children and young adults.“The number of completed suicides is not large, but none of us want our loved one to be at risk. You wouldn’t play roulette if it was your child,” says Sundance CEO Kim Bechthold, who licensed the test idea from Max Planck. She says the DNA tests will be carried out on a saliva sample.Given how many people take antidepressants, the market for a suicide test could be big. In the U.S., about 11 percent of Americans 12 years and older take antidepressants, according to a 2011 estimate by the U.S. Centers for Disease Control and Prevention.For now, however, experts say there are good reasons to view any suicide test with skepticism. Genome studies often turn up apparent connections that later are found not to mean much. Dozens of genes have been linked to suicide, but none in a truly definitive fashion.<ASIDE class=ad-left>“I don’t think there are any credible genomic tests for suicide risk or prevention,” says Muin J. Khoury, head of the Office of Public Health Genomics at the U.S. Centers for Disease Control and Prevention. According to the CDC, suicide is the 10th most common cause of death in the U.S.,  accounting for 39,518 deaths in 2011.What is certain, says the CDC’s Khoury, is that suicide runs in families. On its list of suicide risk factors, the CDC lists family history first, followed by mistreatment of children, prior suicide attempts, and depression.That family connection is what makes scientists certain that genes are involved. In 2013, for instance, Danish researchers looked at 221 adopted children who later in life committed suicide. They found that their biological siblings, raised in different households, were five times as likely to also commit suicide as other people. Identical twins are also more likely to both kill themselves than are two non-identical twins.Altogether, epidemiologists believe that 30 percent to 55 percent of the risk that someone takes their own life is inherited, and the risk isn’t linked to any specific mental illness, like depression or schizophrenia.That means suicide probably has its own unique genetic causes, says Stella Dracheva, a pathologist who studies the brains of suicide victims at the Icahn School of Medicine at Mount Sinai in New York. “Suicide is a very complex condition, but there is a lot of evidence that it has a biological base,” she says. “There is something different in people who commit suicide.”In her view, that means it’s worth searching for suicide genes and that a DNA test is also theoretically plausible. She says a test would be particularly useful among veterans or other groups at unusually high risk of harming themselves.A person’s life history still has more to do with whether it ends in suicide than genes do. Virginia Willour, a geneticist at the University of Iowa who studies suicidal thinking among bipolar patients, says environmental factors are especially important in preventing suicide. Getting medical treatment, an involved family, and religious beliefs all cut the chance of suicide dramatically.Willour’s grandfather was bipolar and killed himself. “I chose to research suicidal behavior because I knew the impact. His suicide was a constant reminder and presence in my childhood,” she says.The pain and disbelief surrounding suicide only raises the stakes for scientists claiming they can predict it. The latest report of a possible suicide test came in July from Johns Hopkins University, in Baltimore, where geneticists published a report saying that the presence of alterations to a single gene could predict who will attempt suicide with 80 percent accuracy.Johns Hopkins has filed a patent on a suicide test, and the university is attempting to license it.That research, carried out by Zachary Kaminsky, an assistant professor of psychiatry at Johns Hopkins, began on a collection of a small number of brains of suicide victims held by the National Institutes of Health. Instead of looking just at DNA, they studied patterns of methylation, a type of chemical block on genes that can lower their activity. They found that one gene, SKA2, seemed to be blocked often in the suicide brains. They later found the same gene block was common when they tested the blood of a larger number of people having suicidal thoughts.“We seem to be able to predict suicidal behavior and attempts, based on seeing these epigenetic changes in the blood,” says Kaminsky. “The caveat is that we have small sample sizes.”Kaminsky says that following the report, his e-mail inbox was immediately flooded by people wanting the test. “They wanted to know, if my dad died from suicide, is my son at risk?” he says. They didn’t understand that the type of DNA change he identified probably isn’t the inherited kind, but instead may be the result of stress or some other environmental factor.Kaminsky’s publication has drawn some criticism from scientists who say his conclusions were based on thin evidence. They say more data is needed. “It’s a striking finding, but as always, when you look at complex genetics, you need replication. Time will tell if it [stands up],” says Willour.The bigger problem, says Dracheva, is that there are simply not enough brains of suicide victims to study. Unlike studies of diabetes or schizophrenia, where scientists can call on thousands or tens of thousands of patients, suicide studies remain small, and their findings much more tentative.It’s because they don’t have DNA from enough people who committed suicide that researchers, including those at Hopkins and Max Planck, have had to try connecting the dots between DNA and whether or not people have suicidal thoughts. Yet there’s no straight line between the contemplation of suicide and actually doing it.“Who doesn’t think about killing themselves?” says Dracheva.Gain the insight you need on genomics at EmTech MIT. Register today<img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmEm4ZHN9xN-c0hzukd_9AG9D59kcHeAYnIky0KcYfnnU6m3bGr8rN2asLsLL2m-LTatc3RPikt8cvlhsZUP0xusUsZQUE7-zdnpyT0vRUhdLUu40WJZX6yduLwj42hodrKq6K6LFKfesP//">

Could a Genetic Test Predict the Risk for Suicide?

Scientists are hunting for the genetic basis of suicide and developing suicide DNA tests. No one could have predicted that Oscar-winning co...

Recommended from Around the Web (Week Ending August 30, 2014)

A roundup of the most interesting stories from other sites, collected by the staff at MIT Technology Review. Robots with Their Heads in the Clouds UC Berkeley’s Ken Golden on robots, the cloud, and why Google is building a driverless car. —Nanette Byrnes, senior editor, Business ReportsThis Is Uber’s Playbook for Sabotaging Lyft Amazing! Uber wasn’t pranking Lyft with cancelled calls; it was the shadow of a secretive driver recruiting effort. —Jason Pontin, editor in chief and publisherThere’s No Hope for Amazon’s Fire Phone Away it goes to join the great pile of Kins in the sky. —Rachel Metz, IT editor, Web & social mediaThree Things You Didn’t Know About the Arachnids That Live on Your Face Just look at this mite that lives in our pores. —Tom Simonite, senior editor, ITAmerica’s Tech Guru Steps Down—But He’s Not Done Rebooting the Government The man who rebooted Healthcare.gov embarks on a new mission to Silicon Valley in an effort to revive federal technology infrastructure. —Tom SimoniteFerguson Reveals a Twitter Loop We like to think of Twitter as an important source of breaking news from eyewitnesses. Sometimes it is. But in Ferguson, a lot of what’s being tweeted is wrong. —David Talbot, chief correspondentWho’s in the Office? The American Workday in One Graph This interactive graph allows you to compare employee work days by job category. —J. Juniper Friedman, associate Web producer

Recommended from Around the Web (Week Ending August 30, 2014)

A roundup of the most interesting stories from other sites, collected by the staff at MIT Technology Review . Robots with Their Heads in th...

The History Inside Us

Every day our DNA breaks a little. Special enzymes keep our genome intact while we’re alive, but after death, once the oxygen runs out, there is no more repair. Chemical damage accumulates, and decomposition brings its own kind of collapse: membranes dissolve, enzymes leak, and bacteria multiply. How long until DNA disappears altogether? Since the delicate molecule was discovered, most scientists had assumed that the DNA of the dead was rapidly and irretrievably lost. When Svante Pääbo, now the director of the Max Planck Institute for Evolutionary Anthropology in Germany, first considered the question more than three decades ago, he dared to wonder if it might last beyond a few days or weeks. But Pääbo and other scientists have now shown that if only a few of the trillions of cells in a body escape destruction, a genome may survive for tens of thousands of years.In his first book, Neanderthal Man: In Search of Lost Genomes, Pääbo logs the genesis of one of the most groundbreaking scientific projects in the history of the human race: sequencing the genome of a Neanderthal, a human-like creature who lived until about 40,000 years ago. Pääbo’s tale is part hero’s journey and part guidebook to shattering scientific paradigms. He began dreaming about the ancients on a childhood trip to Egypt from his native Sweden. When he grew up, he attended medical school and studied molecular biology, but the romance of the past never faded. As a young researcher, he tried to mummify a calf liver in a lab oven and then extract DNA from it. Most of Pääbo’s advisors saw ancient DNA as a “quaint hobby,” but he persisted through years of disappointing results, patiently awaiting technological innovation that would make the work fruitful. All the while, Pääbo became adept at recruiting researchers, luring funding, generating publicity, and finding ancient bones.<ASIDE class=ad-left>Eventually, his determination paid off: in 1996, he led the effort to sequence part of the Neanderthal mitochondrial genome. (Mitochondria, which serve as cells’ energy packs, appear to be remnants of an ancient single-celled organism, and they have their own DNA, which children inherit from their mothers. This DNA is simpler to read than the full human genome.) Finally, in 2010, Pääbo and his colleagues published the full Neanderthal genome.That may have been one of the greatest feats of modern biology, yet it is also part of a much bigger story about the extraordinary utility of DNA. For a long time, we have seen the genome as a tool for predicting the future. Do we have the mutation for Huntington’s? Are we predisposed to diabetes? But it may have even more to tell us about the past: about distant events and about the network of lives, loves, and decisions that connects them.EmpiresLong before research on ancient DNA took off, Luigi Luca Cavalli-Sforza made the first attempt to rebuild the history of the world by comparing the distribution of traits in different living populations. He started with blood types; much later, his popular 2001 book Genes, Peoples, and Languages explored demographic history via languages and genes. Big historical arcs can also be inferred from the DNA of living people, such as the fact that all non-Africans descend from a small band of humans that left Africa 60,000 years ago. The current distribution across Eurasia of a certain Y chromosome—which fathers pass to their sons—rather neatly traces the outline of the Mongolian Empire, leading researchers to propose that it comes from Genghis Khan, who pillaged and raped his way across the continent in the 13th century.Thing reviewedNeanderthal Man: In Search of Lost Genomes by Svante Pääbo Basic Books, 2014But in the last few years, geneticists have found ways to explore not just big events but also the dynamics of populations through time. A 2014 study used the DNA of ancient farmers and hunter-gatherers from Europe to investigate an old question: Did farming sweep across Europe and become adopted by the resident hunter-gatherers, or did farmers sweep across the continent and replace the hunter-gatherers? The researchers sampled ancient individuals who were identified as either farmers or hunters, depending on how they were buried and what goods were buried with them. A significant difference between the DNA of the two groups was found, suggesting that even though there may have been some flow of hunter-gatherer DNA into the farmers’ gene pool, for the most part the farmers replaced the hunter-gatherers.Looking at more recent history, Peter Ralph and Graham Coop compared small segments of the genome across Europe and found that any two modern Europeans who lived in neighboring populations, such as Belgium and Germany, shared between two and 12 ancestors over the previous 1,500 years. They identified tantalizing variations as well. Most of the common ancestors of Italians seem to have lived around 2,500 years ago, dating to the time of the Roman Republic, which preceded the Roman Empire. Though modern Italians share ancestors within the last 2,500 years, they share far fewer of them than other Europeans share with their own countrymen. In fact, Italians from different regions of Italy today have about the same number of ancestors in common with one another as they have with people from other countries. The genome reflects the fact that until the 19th century Italy was a group of small states, not the larger country we know today.<BLOCKQUOTE class=pullquote readability="6">In a very short amount of time, the genomes of ancient people have facilitated a new kind of population genetics. It reveals phenomena that we have no other way of knowing about.</BLOCKQUOTE>Significant events in British history suggest that the genetics of Wales and some remote parts of Scotland should be different from genetics in the rest of Britain, and indeed, a standard population analysis on British people separates these groups out. But this year scientists led by Peter Donnelly at Oxford uncovered a more fine-grained relationship between genetics and history. By tracking subtle patterns across the genomes of modern Britons whose ancestors lived in particular rural areas, they found at least 17 distinct clusters that probably reflect different groups in the historic population of Britain. This work could help explain what happened during the Dark Ages, when no written records were made—for example, how much ancient British DNA was swamped by the invading Saxons of the fifth century.The distribution of certain genes in modern populations tells us about cultural events and choices, too: after some groups decided to drink the milk of other mammals, they evolved the ability to tolerate lactose. The descendants of groups that didn’t make this choice don’t tolerate lactose well even today.MysteriesAnalyzing the DNA of the living is much easier than analyzing ancient DNA, which is always vulnerable to contamination. The first analyses of Neanderthal mitochondrial DNA were performed in an isolated lab that was irradiated with UV light each night to destroy DNA carried in on dust. Researchers wore face shields, sterile gloves, and other gear, and if they entered another lab, Pääbo would not allow them back that day. Still, controlling contamination only took Pääbo’s team to the starting line. The real revolution in analysis of ancient DNA came in the late 1990s, with second-generation DNA sequencing techniques. Pääbo replaced Sanger sequencing, invented in the 1970s, with a technique called pyrosequencing, which meant that instead of sequencing 96 fragments of ancient DNA at a time, he could sequence hundreds of thousands.Such breakthroughs made it possible to answer one of the longest-running questions about Neanderthals: did they mate with humans? There was scant evidence that they had, and Pääbo himself believed such a union was unlikely because he had found no trace of Neanderthal genetics in human mitochondrial DNA. He suspected that humans and Neanderthals were biologically incompatible. But now that the full Neanderthal genome has been sequenced, we can see that 1 to 3 percent of the genome of non-Africans living today contains variations, known as alleles, that apparently originated with Neanderthals. That indicates that humans and Neanderthals mated and had children, and that those children’s children eventually led to many of us. The fact that sub-Saharan Africans do not carry the same Neanderthal DNA suggests that Neanderthal-human hybrids were born just as humans were expanding out of Africa 60,000 years ago and before they colonized the rest of the world. In addition, the way Neanderthal alleles are distributed in the human genome tells us about the forces that shaped lives long ago, perhaps helping the earliest non-Africans adapt to colder, darker regions. Some parts of the genome with a high frequency of Neanderthal variants affect hair and skin color, and the variants probably made the first Eurasians lighter-skinned than their African ancestors.Ancient DNA will almost certainly complicate other hypotheses, like the African-origin story, with its single migratory human band. Ancient DNA also reveals phenomena that we have no other way of knowing about. When Pääbo and colleagues extracted DNA from a few tiny bones and a couple of teeth found in a cave in the Altai Mountains in Siberia, they discovered an entirely new sister group, the Denisovans. Indigenous Australians, Melanesians, and some groups in Asia may have up to 5 percent Denisovan DNA, in addition to their Neanderthal DNA.In a very short amount of time, a number of ancients have been sequenced by teams all over the world, and the growing library of their genomes has facilitated a new kind of population genetics. What is it that DNA won’t be able to tell us about the past? It may all come down to what happened in the first moments or days after someone’s death. If, for some reason, cells dry out quickly—if you die in a desert or a dry cave, if you are frozen or mummified—post-mortem damage to DNA can be halted, but it may never be possible to sequence DNA from remains found in wet, tropical climates. Still, even working with only the scattered remains that we have found so far, we keep gaining insights into ancient history. One of the remaining mysteries, Pääbo observes, is why modern humans, unlike their archaic cousins, spread all over the globe and dramatically reshaped the environment. What made us different? The answer, he believes, lies waiting in the ancient genomes we have already sequenced.There is some irony in the fact that Pääbo’s answer will have to wait until we get more skillful at reading our own genome. We are at the very beginning stages of understanding how the human genome works, and it is only once we know ourselves better that we will be able to see what we had in common with Neanderthals and what is truly different.Christine Kenneally is the author of The Invisible History of the Human Race, to be published in October.

The History Inside Us

Every day our DNA breaks a little. Special enzymes keep our genome intact while we’re alive, but after death, once the oxygen runs out, the...

Terahertz Chip Identifies Short Strands of DNA

<img alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKR5zvIiUtq6UPyBuaTo7x6UsY0ik4RzgsWwlx7QhoRML7s_xE0A75cJ4gaMjzbl4tG_FZdQTe9NQTDpCp4nMUhxrupvDN6nETyUH7Ovn395EUEby-cO_1PqHuQmKHf01IphHWU_Sv2MKJ//"> Take a short, single strand of DNA, zap it with terahertz waves and watch how it vibrates. Voila, a machine that can detect DNA sequences. <img alt="" height="356" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzLo0_T7UnufwM1iKxgHpANlpSkKkKPCrdpbTRljspbtizW2FMQcV5BO2zqtfYFNM3aYxsXLC-99fLwps7iTaeBeLMWOic2Hdodyt9e-UJgzdS7X-z1cVmk8ZSI_ko9MGX8ngjVNvYp-DZ//" width="616"> One of the more significant practical challenges currently occupying molecular biologists is to find better ways of identifying short strands of DNA. Called oligonucleotides, these strands of nucleotides are hugely useful in processes such as genetic testing, forensics and DNA amplification.But identifying the strands is a somewhat laboured business. Almost every detection method relies on fluorescent dyes and markers that can be picked up by optical sensors providing a useful but indirect indication of the molecules that are present.But molecular biologists would like a better system that measures the characteristics of the molecules involved and so provides direct evidence of the sequence of nucleotides. Indeed, various research teams are working on such systems, some with significant success.Today, Andrey Chernev at St Petersburg Academic University in Russia and a few pals say they have invented an entirely new way of identifying oligonucleotides using terahertz radiation. “Our results demonstrate a new method for label-free, real-time oligonucleotide characterisation,” they say.An oligonucleotide is a short single-stranded DNA or RNA molecule usually consisting of fewer than a hundred or so bases. The sequence of these bases determines the type of oligonucleotide. So the ideal detection mechanism would reveal this sequence.Chernev and co’s idea is based on the way these molecules resonate. They say that the sequence of bases in an oligonucleotide determines the way in which the strand resonates at frequencies in the terahertz range. Their idea is to capture a single oligonucleotide in a cavity filled with terahertz waves that stimulates this resonant behaviour.They begin by producing a signal as close as possible to the resonant mode. By measuring the output from this cavity, they can determine when the input spectra exactly matches the resonant modes of the molecule. That tells them exactly what sort of oligonucleotide they have.That’s the theory and they have tested it using a device they call a silicon nanosandwich, a quantum well of p-type silicon surrounded by barriers doped with boron. This produces terahertz radiation inside the well where the oligonucleotide is deposited at a concentration that allows a single molecule to enter.They have tested the device on two oligonucleotides, one that was 50 bases long and the other that was 100 bases long and characterised their unique resonances. That allows them to distinguish between the two oligonucleotides with relative ease at room temperature.But this is just a first step. What is needed next is an entire library of the unique signatures associated with every oligonucleotide. That should be possible. Chernev and co aim to start by analysing the resonances of each of the monomer and dimer molecules that make up oligonucleotides. The signatures from these should provide a kind of alphabet from which to work out the resonances of more complex polymers.That is an interesting approach. But this is a crowded area in which lots of good ideas are competing to become the standard technique for identifying the molecules of life quickly and cheaply. Chernev and co will have their work cut out to prove that their method is better than the others that are emerging. But it certainly has potential and so is one to watch for the future.Ref: http://arxiv.org/abs/1407.6520 : DNA Detection By THz Pumping

Terahertz Chip Identifies Short Strands of DNA

Take a short, single strand of DNA, zap it with terahertz waves and watch how it vibrates. Voila, a machine that can detect DNA sequences....

What Else Could Smart Contact Lenses Do?

Besides health tracking, contact lens technology under development could enable drug delivery, night vision, and augmented reality. Last week Google and Novartis announced that they’re teaming up to develop contact lenses that monitor glucose levels and automatically adjust their focus. But these could be just the start of a clever new product category. From cancer detection and drug delivery to reality augmentation and night vision, our eyes offer unique opportunities for both health monitoring and enhancement.“Now is the time to put a little computer and a lot of miniaturized technologies in the contact lens,” says Franck Leveiller, head of research and development in the Novartis eye care division.<ASIDE class=ad-left>One of the Novartis-Google prototype lenses contains a device about the size of a speck of glitter that measures glucose in tears. A wireless antenna then transmits the measurements to an external device. It’s designed to ease the burden of diabetics who otherwise have to prick their fingers to test their blood sugar levels.“I have many patients that are managing diabetes, and they described it as having a part-time job. It’s so arduous to monitor,” says Thomas Quinn, who is head of the American Optometric Association’s contact lens and cornea section. “To have a way that patients can do that more easily and get some of their life back is really exciting.”Glucose isn’t the only thing that can be measured from tears rather than a blood sample, says Quinn. Tears also contain a chemical called lacryglobin that serves as a biomarker for breast, colon, lung, prostate, and ovarian cancers. Monitoring lacryglobin levels could be particularly useful for cancer patients who are in remission, Quinn says.Quinn also believes that drug delivery may be another use for future contact lenses. If a lens could dispense medication slowly over long periods of time, it would be better for patients than the short, concentrated doses provided by eye drops, he says. Such a lens is not easy to make, though (see “A Drug-Dispensing Lens”).The autofocusing lens is in an earlier stage of development, but the goal is for it to adjust its shape depending on where the eye is looking, which would be especially helpful for people who need reading glasses. A current prototype of the lens uses photodiodes to detect light hitting the eye and determine whether the eye is directed downward. Leveiller says the team is also looking at other possible techniques.Google and Novartis are far from the only ones interesting in upgrading the contact lens with such new capabilities. In Switzerland, a company called Sensimed is working on a contact lens that measures the intraocular pressure that results from the liquid buildup in the eyes of glaucoma patients (see “Glaucoma Test in a Contact Lens”). And researchers at the University of Michigan are using graphene to make infrared-sensitive contact lenses—the vision, as it were, is that these might one day provide some form of night vision without the bulky headgear.A Seattle-based company, Innovega, meanwhile, has developed a contact lens with a small area that filters specific bands of red, green, and blue light, giving users the ability to focus on a very small, high resolution display less than an inch away from their eyes without interfering with normal vision. That makes tiny displays attached to glasses look more like IMAX movie screens, says the company’s CEO, Steve Willey. Together, the lens and display are called iOptik.Plenty of challenges still remain before we’re all walking around with glucose-monitoring, cancer-detecting, drug-delivering super night vision. Some prototypes out there are unusually thick, Quinn says, and some use traditional, rigid electronics where clear, flexible alternatives would be preferable. And, of course, all will have to pass regulatory approval to show they are safe and effective.Jeff George, the head of the Novartis eye care division, is certainly optimistic about Google’s smart lens. “Google X’s team refers to themselves as a ‘moon shot factory.’ I’d view this as better than a moon shot given what we’ve seen,” he says.Hear more from Google at EmTech 2014. Register today<img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOAs_rW3z70yzhq8ZKhFt-K7tMKJyt1zaD80CMu3XVm_JMtrPvF9fNwAENR1sFQ5BKAxvZmVlT1mLhTzhvrUWytKVKe-6EkOcjZrF6qWx8RY8X_riZp-fKzXOtl4l0flC2B_LeAHirBw27//">

What Else Could Smart Contact Lenses Do?

Besides health tracking, contact lens technology under development could enable drug delivery, night vision, and augmented reality. Last we...

Three Questions for J. Craig Venter

Gene research and Silicon Valley-style computing are starting to merge. <ASIDE class=img-left><img alt="J. Craig Venter" height="299" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrHm52DcU0dbTrJ4OOzfpYLb5fGACwImBpOLIyVXcrqT7r9Qy1CKO-2ufqR2YImHYIm3sIOs7PMw8xXBDq9sePdJKH2zTDEt0Cu437E0XQ2PnTVbCWp3vdkK0aj7IKFOzdfdWis3sITHSg//" width="299"> <ASIDE class=caption-left>J. Craig VenterGenome scientist and entrepreneur J. Craig Venter is best known for being the first person to sequence his own genome, back in 2001.This year, he started a new company, Human Longevity, which intends to sequence one million human genomes by 2020, and ultimately offer Web-based programs to help people store and understand their genetic data (see “Microbes and Metabolites Fuel an Ambitious Aging Project”).Venter says that he’s sequenced 500 people’s genomes so far, and that volunteers are starting to also undergo a battery of tests measuring their strength, brain size, how much blood their hearts pump, and, says Venter, “just about everything that can be measured about a person, without cutting them open.” This information will be fed into a database that can be used to discover links between genes and these traits, as well as disease.But that’s going to require some massive data crunching. To get these skills, Venter recruited Franz Och, the machine-learning specialist leading Google Translate. Now Och will apply similar methods to studying genomes in a data science and software shop that Venter is establishing in Mountain View, California.The hire comes just as Google itself has launched a similar-sounding effort to start collecting biomedical data (see “What’s a Moon Shot Worth These Days”). Venter calls Google’s plans for a biomedical database “a baby step, a much smaller version of what we are doing.”What’s clear is that genome research and data science are coming together in new ways, and at a much larger scale than ever before. We asked Venter why.How are we doing in genomics?In my view there have not been a significant number of advances. One reason for that is that genomics follows a law of very big numbers. I’ve had my genome for 15 years, and there’s not much I can learn because there are not that many others to compare it to.<ASIDE class=ad-left>Why did you hire an expert in machine translation as your top data scientist?Until now, there’s not been software for comparing my genome to your genome, much less to a million genomes. We want to get to a point where it takes a few seconds to compare your genome to all the others. It’s going to take a lot of work to do that.Google Translate started as a slow algorithm that took hours or days to run and was not very accurate. But Franz [Och] built a machine-learning version that could go out on the Web and find every article translated from German to English or vice versa, and learn from those. And then it was optimized, so it works in milliseconds.I convinced Franz, and he convinced himself, that understanding the human genome at the scale that we are trying to do it is going to be one of the greatest translation challenges in history. How is discovering the connection between genes and disease like translating languages?Everything in a cell derives from your DNA code, all the proteins, their structure, whether they last seconds or days. All that is preprogrammed in DNA language. Then it is translated into life. People are going to be very surprised about how much of a DNA software species we are. Gain the insight you need on genomics at EmTech MIT. Register today<img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJpukIzXd-1MtUaFIHd5YPlFnY6IRUzxN5PD9vySMibEJhHzAT-KfuDGg6wxgVqNyw2_j_oDY6gwarzJqNQOdwjv5a1wp9MZPUHNW6LFd1NpR5KhDbWQkVQ3Bp6om8ZLBluqN7sFrcpuHC//">

Three Questions for J. Craig Venter

Gene research and Silicon Valley-style computing are starting to merge. J. Craig Venter Genome scientist and entrepreneur J. Craig Venter ...

Spotting Cancer in a Vial of Blood

The answers Bert Vogelstein needed and feared were in the blood sample. Vogelstein is among the most highly cited scientists in the world. He was described, in the 1980s, as having broken into “the cockpit of cancer” after he and coworkers at Johns Hopkins University showed for the first time exactly how a series of DNA mutations, adding up silently over decades, turn cells cancerous. Damaged DNA, he helped prove, is the cause of cancer.Now imagine you could see these mutations—see cancer itself—in a vial of blood. Nearly every type of cancer sheds DNA into the bloodstream, and Vogelstein’s laboratory at Johns Hopkins has developed a technique, called a “liquid biopsy,” that can find the telltale genetic material.The technology is made possible by instruments that speedily sequence DNA in a blood sample so researchers can spot tumor DNA even when it’s present in trace amounts. The Hopkins scientists, working alongside doctors who treat patients in Baltimore’s largest oncology center, have now studied blood from more than a thousand people. They say liquid biopsies can find cancer long before symptoms of the disease arise.This particular blood sample, though, was personal. It was from Vogelstein’s brother, an orthopedic surgeon one year younger. He was fighting skin cancer, and the disease was already spreading. There was hope he’d respond to a new type of drug, but the treatment causes swelling, and it’s difficult to tell from an x-ray or CT scan whether the cancer is melting away or not. So Vogelstein used his lab’s new technology. If the cancer DNA had disappeared from the blood, they might celebrate. If it was still there, maybe he could steer his brother to some last-ditch drug.“We tried to guide the treatment. That was the hope, anyway,” says Vogelstein. His voice tightens. He doesn’t say what happened next.The obituary of Barry Vogelstein, born in Baltimore, appeared on July 3, 2013.We’re not winning the war on cancer, and the death of Vogelstein’s brother shows why. Too many cancers are caught when they have become incurable. Each year, $91 billion is spent on cancer drugs worldwide, but most of those medicines are given to patients when it’s too late. The newest treatments, created at staggering expense, cost $10,000 a month and often extend life by only a few weeks. Pharmaceutical firms develop and test more drugs for late-stage cancer than for any other kind of disease.“We as the public and as scientists have been entranced by this idea of curing advanced cancers,” says Vogelstein. “That is society’s Plan A. I don’t think that has to be the case.” There are other ways to reduce cancer deaths: wearing sunscreen, not smoking, and getting screened to catch cancer early. To Vogelstein, all these preventive steps represent “Plan B” because they receive so much less attention and funding. Yet when prevention works, it has better results than any drug. In the United States, the chance of dying from colorectal cancer is 40 percent lower than it was in 1975, a decrease mostly due to colonoscopy screening. Melanoma skin cancer, too, is treatable with surgery if caught early. “We think Plan B needs to be Plan A,” says Vogelstein.<img alt="" height="619" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikpuYUyewaq4zWLQ2CB25OGrHg27eEdt3Bq0R2xJpmgmmdFprqTmyVlAfXEuRw07UiLwFwvA5bVXEMIzskci1FlzDHNRq4nFvdrQVhfNDlcQDyyOh8YgZPg9crYANrff6GP3aNtMG6Bhfb//" width="519"> Bert VogelsteinThe new blood tests could make that possible. For the first time, Hopkins researchers say, they are within reach of a general screening tool that could be used to scan broadly—perhaps at an annual physical—for molecular traces of cancer in people with no symptoms. “We think we’ve solved early detection,” says Victor Velculescu, a Hopkins researcher who runs a lab in the building next to Vogelstein’s.Making such screening a routine practice in medicine will be challenging. One difficulty is that while the test may detect the presence of cancer DNA in the body, physicians might not know where the tumor is, how dangerous it is, or even whether it is worth treating. “We have to be cautious about how we talk about that,” says Daniel Haber, director of the Massachusetts General Hospital Cancer Center. He believes the DNA blood tests are “far from ready” and says very large studies will be needed to prove that they are useful. “There is a huge bar to get over,” he says.Despite such skepticism, the technology is gaining attention. Tony Dickherber, head of the Innovative Molecular Analysis Technologies Program at the National Cancer Institute, says the idea of scanning blood for tumor DNA was “fringe at best” only three years ago. But now labs and companies from California to London are jumping in, producing a stream of improvements to the blood screening technology and new data supporting it. “People are starting to think that [Vogelstein] is right—this could be the best way to do early diagnosis,” he says. “[It] could be done much more widely than other screening technology we have, and you could screen for an incredible range of cancers.”In February, doctors from Hopkins and 23 other institutions provided the largest survey yet of their findings. They studied the tumors of 846 patients with 15 different types of cancer. They found tumor DNA in the blood of more than 80 percent of patients with advanced cancers, the kind that have spread, and about 47 percent of those whose cancer was still localized and at the earliest stage. In advanced colorectal cancer, the DNA was always seen. <img alt=" magnified drop of blood" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjasVcNDnNjzQtRn__Yuugqx-eo89pRiAeyuOBq2uRDCvx3hLegX7gNicxTRcoUzm_qC-G_PQ3KeulOCW5OqhIvO324JNjdnDJT5DsZuUo1W4wvua1J3HvCMlH8OjXiDrzgcJ4cO_ACDpQb//"><BLOCKQUOTE class=pullquote readability="7">For the first time, Hopkins researchers say, they are within reach of a general screening tool that could be used to scan broadly—perhaps at an annual physical—for molecular traces of cancer in people with no symptoms.</BLOCKQUOTE>The results might not at first appear impressive. A test that misses half the time? The benefit is that the tests are “exquisitely specific,” according to Velculescu. If you do have tumor DNA, it appears, so far, that you also have cancer. That could give DNA screening the edge over current tests for prostate and breast cancer, which frequently produce false positives. “It’s normal to have circulating DNA in the blood; it is not normal to have circulating DNA that matches a tumor,” says Stefanie Jeffrey, chief of surgical oncology research at Stanford University.To Vogelstein, the blood tests mean it may be possible to catch more than half of cancers early on, and potentially cure them with surgery. “If there were a drug that cured half of cancer you’d have a ticker-tape parade in New York City,” he says.Early DaysPresident Nixon’s War on Cancer was launched in 1971, when Vogelstein was in medical school. Years of frustration followed as drugs failed to make much of a dent in cancer deaths. What has changed is that now we know what causes cancer. Vogelstein’s work in the 1980s, carried out with colleague Kenneth Kinzler, helped demonstrate the crucial role of mutated genes in the disease. And scientists have now assembled a list of more than 150 genes that appear to be the key drivers. Even though cancer’s genetic landscape is complex, all the DNA mutations do one thing: they allow some cells to keep multiplying when normal cells would die. The resulting imbalance is cancer.For pharmaceutical companies, this insight and the gene list have been the launching point for billion-dollar efforts to develop new drugs for advanced cancers. But to Vogelstein, the knowledge that DNA mutations cause cancer has always also meant something different: that it should be possible to spot the telltale changes early on, well before the disease is usually diagnosed. And in oncology, it’s a truism: the sooner you detect cancer, the better your chances.Consider colorectal cancer, the type Vogelstein has studied most closely. It begins with a single mutation to a gene called APC. Yet it takes on average 30 years from that point for the cells to acquire several other DNA mutations they need in order to spread and kill. About 600,000 people die from colorectal cancer each year. “Nearly all of them will die only because their cancer was not detected in the first 27 years of the tumor’s existence,” Vogelstein says. “That is a huge window to intervene in this process.”The problem has been that until the blood tests, there was no very easy way to look for these mutations. Vogelstein has been working on early-detection schemes since the 1990s, when he began looking for tumor DNA in urine and stool, using the laborious methods available at that time. He believes prevention and screening still receive too little attention, putting him, even now, in an “absolute minority” of researchers. He estimates that 100 times as many research dollars go toward drugs as toward these strategies.This may explain why, despite his preëminence, Vogelstein seems to have a chip on his shoulder. The Hopkins research group, which includes several other well-known researchers, is quick to publish new ideas, but it often makes the effort to shoot down scientific concepts that are trendy elsewhere. Any young scientist who want to work there, according to the lab’s traditions, must first present his or her earlier scientific work while wearing a Burger King crown.<ASIDE class=img-left><img alt="" height="251" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjVqJdJTQ-CeYwCnVvbC_P2HthrEIhEFsaeSOsf1_ji1Sno8MX3juDXk6exNROa4PdIm8gPa1efcSmRyc-8XoLsBZLjx1z6UbidUprItzUKl8nQq9Nfr0Ic8uNQS2qkZNF6UomRw5Ea-zMO//" width="274"> <ASIDE class=caption-left>Luis DiazThe lab’s work on the blood tests has been led by Luis Diaz, an oncologist who has become Vogelstein’s protégé. He hit on the idea of testing blood for cancer DNA in 2005, while researching whether a flesh-eating bacterium could be used to eradicate tumors. The work involved transplanting human cancers into mice, and Diaz recalls that he “needed a way to monitor the tumors in the mouse without killing it.” He and a colleague decided that they might be able to do that with a blood test. Soon they saw the level of human DNA bouncing down and up as the treatment worked or failed. If they could monitor DNA from a human tumor in mice, wouldn’t it work in humans, too?The idea wasn’t entirely new. It’s been known since 1948 that free-floating DNA circulates in our veins and arteries. It’s normally a waste product of dead cells. But tumors also shed DNA into the blood. The portion of DNA in the blood that comes from tumors can be as high as 87 percent in a person dying from cancer, but often the amount is vanishingly small.When Diaz began looking at the question, all this was not yet fact but muddy possibility. To develop the liquid biopsy, the Hopkins scientists first had to invent ways to pick out the tumor DNA from an overwhelming background of normal DNA. Working with blood donated by patients with colorectal cancer whom Diaz was treating in Baltimore, the researchers initially tracked only four cancer genes. Yet they could see that the tumor DNA in the blood would disappear quickly—even within a day—after these patients had surgery or drug treatments. Healthy control subjects never tested positive. “We realized this test can ask and answer the question ‘Do I have cancer?’” says Diaz.Hopkins believes its test may be more sensitive than any tool doctors have now—at least for cancers that are too small to be seen with an imaging machine. Vogelstein estimates that a tumor has to contain at least 10 million cells, making it about as big as the head of a pin, to shed a detectable amount of DNA. To be visible on an MRI, by contrast, a tumor needs to be about 100 times that size, containing at least one billion cells.The Hopkins physicians have begun using the DNA tests in an effort to determine whether malignant cells remain behind in patients whose tumors have been surgically removed. Working with Peter Gibbs, an Australian oncologist, they have scanned blood samples from 250 patients who have been operated on for early-stage colon cancer. Most of these people will turn out to be cured, but up to 30 percent are expected to suffer a relapse because not all the tumor cells were removed. The problem is that doctors don’t know which patients will relapse. “The surgeon will say, ‘Don’t worry—we got it all,’” says Diaz. “It’s frustrating to me, because then I have to tell the patient, ‘We don’t really know if you are cured.’” Survivors can get caught in a state of limbo, uncertain whether their disease is coming back, possibly in a more dangerous form. And the situation can drag on for years.<BLOCKQUOTE class=pullquote readability="10">Patients could be frightened, doctors uncertain how to act. “The idea of screening healthy people and telling them ‘Oh, look, there is cancer somewhere but we don’t know where it is’—well, that would be the death of the whole [idea],” says one oncologist.</BLOCKQUOTE><img alt=" magnified drop of blood" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhn8XVOvc6UhSrV5QRBl9IVrzPgBGdB4mASBnOZFcKOVOtS_Gvrpm1Uv5ET8g8TIngQH8iTH1CzSyicqMGx9xJaZQxhCUlCBQQarHF12tuCvhuaUnlBvuahKnlVNtDisWIKtD3ariZakQVJ//">The patients in Australia are checked for tumor DNA in their blood six weeks after surgery. So far, the researchers say, they have correctly identified about half the people who later relapsed. In the future, says Vogelstein, these patients could be flagged to receive chemotherapy, probably saving at least a third of them. Yet the limits of the test are also apparent, since it still missed half the patients whose cancer later reappeared.Diaz says this may be because whatever cancer cells remain aren’t giving off enough DNA to detect. “We may have hit the biological limits,” he says. However, the cancer DNA could rise to detectable levels over time, and retesting patients periodically could pick that up. Even though Hopkins’s testing remains experimental, Diaz says he has enough confidence in it to tell some patients they are still sick and others that they are probably healed. “Six to eight weeks later, we can tell them if they are cured,” he says. “It’s very satisfying.”Mass ScreeningVogelstein says his ultimate goal is to turn the blood tests into a way to routinely screen everyone for cancer. The Hopkins researchers believe they have a version of the test that can do that. Instead of tracking a few key cancer genes, they sequence a person’s entire genome using DNA from the blood sample. This lets them count how often chunks of genetic material are misplaced or appear scrambled. A large amount of rearranged DNA is a molecular side effect seen only on the chromosomes of cancer cells—a tip-off that cancer is present. But a full genome sequence is still expensive. “If a person has cancer, you don’t mind spending $5,000 on a DNA test. But you can’t have a test that costs $1,000 that you can do at an annual physical,” says Vogelstein. “The goal is to get the technology cheap enough to use in screening.”That could take time. The cost of DNA sequencing has been falling very rapidly, yet a $100 genome—the price that might be low enough for a general screening test—could be 10 years away. In the meantime, Hopkins has begun several studies, mostly on individuals predisposed to cancer, to determine whether the techniques can catch tumors early in healthy people. One involves 800 people at risk for pancreatic cancer. In these unusual cases, people have cysts on the pancreas that sometimes turn into cancer but sometimes don’t. The clinical trial began following patients in 2012, and the researchers will get their first look at the results late this year.Pancreatic cancer is a good test case for early screening. It’s not a very common cancer, but it’s the fourth-highest cause of cancer deaths in the United States, because it’s cured only 4 percent of the time. If detected very early, before it spreads, the survival rate rises to about 25 percent. (Apple founder Steve Jobs died of a different type of pancreatic cancer, called a neuroendocrine tumor, at age 56.)But extending the DNA tests to everyone is an enormous leap. Haber, the Mass. General oncologist, says the technology, as currently conceived, might tell a doctor if cancer is present. But unlike an imaging scan or a biopsy, it could leave you guessing where in the body it is. Patients would be frightened, doctors uncertain how to act. “The idea of screening healthy people and telling them ‘Oh, look, there is cancer somewhere but we don’t know where it is’—well, that would be the death of the whole [idea],” Haber says.Medicine has a precedent of handling predictive tests poorly. Consider the PSA test, which detects a protein linked to prostate cancer. Not only does the test produce false positives a majority of the time, but some of the tumors it actually detects are so slow-growing that they aren’t worth treating. Millions of men have ended up getting treated for cancers that ultimately wouldn’t have affected them. By one estimate, for every 47 men who had their prostates removed, a single cancer death was avoided. Studies by researchers at Dartmouth College suggest that mammography also leads to overdiagnosis and overtreatment. About 25 percent of breast cancers discovered, and treated, would not have caused any symptoms. “You test everyone and end up treating people for diseases that would never have mattered, either because they wouldn’t have progressed or because people die of something else,” says Jonathan Skinner, a health economist at Dartmouth. “The downside of early screening can be very high.”<ASIDE class=ad-left>At Hopkins, however, Velculescu says he’s hopeful that mass DNA screening for cancer will become a reality. “If you can’t make a difference, then maybe you would want to remain ignorant,” he says. “But I can’t imagine that knowing about cancer wouldn’t help patients. Maybe we won’t dramatically act on every piece of information. Maybe we don’t do anything. But with these tests, it would be so easy to keep doing them and say to the patient, ‘Let’s see how it develops.’”So far, companies aren’t talking loudly about broad screening for cancer in seemingly healthy patients. For now, Personal Genome Diagnostics, a diagnostic testing startup that Diaz and Velculescu founded, and several competitors, like Boreal Genomics and Guardant Health, offer liquid biopsies only to patients who are fighting late-stage cancer. For those patients, the tests might reveal whether a treatment is working in time to try something else if it’s not. Another valuable use of the technology is to track the specific DNA mutations driving a patient’s tumors. Since many new cancer medications are “targeted”—they block specific molecular processes—patients get them only if their tumor is the kind expected to respond. Doctors can already use DNA tests on chunks of tumor obtained through tissue biopsies. But the noninvasive blood tests could be easier and safer, allowing patients to be evaluated more frequently. Since cancer DNA is constantly mutating, that could help patients switch drugs when appropriate.To Helmy Eltoukhy, the CEO of Guardant, liquid biopsies are “a huge idea” with many applications. For commercial and medical reasons, his company so far is marketing the tests only to people who have cancer. But he says early screening tests are on his company’s road map. “It’s obviously the Holy Grail,” he says. “Imagine the applications, and that is what we are working on.”I asked both Vogelstein, who is 65, and Velculescu, who is 44, if they had ever tested themselves. Both said no. Yet overall, men in the United States have a 40 percent chance of developing cancer sometime, and the odds rise with age. If these researchers haven’t sought the screening, it seems questionable that the broader public will be eager to do it either. For a screening test to be performed widely as a public health measure, the entire medical community will have to participate, and that will take a great deal of time.Vogelstein isn’t naïve. We’ll still need new drugs to treat people who develop cancer anyway. But he remains convinced that the best way to beat late-stage cancer is to prevent it from happening. When I offered my condolences to Vogelstein on the death of his brother, he waved them aside. “This is why we do the work,” he says. “A hundred years from now, when cancer and death from cancer is a lot less common, a lot of that is going to be due to early detection, not because we can cure a body riddled with tumors.”This story was updated on August 13 to clarify that Steve Jobs did not have the kind of pancreatic cancer that Hopkins researchers are trying to detect in the trial of 800 patients.

Spotting Cancer in a Vial of Blood

The answers Bert Vogelstein needed and feared were in the blood sample. Vogelstein is among the most highly cited scientists in the world....

Chinese GMO Research Outpaces Approvals

The fact that China hasn’t approved any commercial GMO planting since 2009 reflects public fears. <ASIDE class=img-left><img alt="Chinese farmer" height="299" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6EDt5MGGKmweWFOSPDHGLtYMvQeMUGVPkHEZjuDUvqyc2DYc1_NuVGDq_Oj5LpNxGTdf3FJr0HcAABj1C7pqwpL8UfgkHTw8E6-GClicKCyckxeSgKnkQCUo5L_xP1BHowmcZjy5gPpIB//" width="299"> <ASIDE class=caption-left>Growing future: China is the world’s largest producer of wheat; here a farmer harvests from fields in Jiangsu province. Despite recent research advances, such as a new strain of wheat that resists destructive mildew (see “Chinese Researchers Stop Wheat Disease with Gene Editing”), commercial planting of genetically modified food crops has stalled in China, the world’s most populous nation and one with a fast-tightening food supply.In 2009, the nation’s Ministry of Agriculture issued a so-called safety certificate to two strains of insect-resistant rice, known as Bt rice, pioneered by Qifa Zhang, a scientist at Huazhong Agricultural University in Wuhan. The ministry also approved a type of corn that helps livestock digest phosphates.Before that, a few minor crop varieties were approved for commercial planting. But to date only an insect-resistant cotton and a virus-resistant papaya have been commercially planted on a large scale in China.The rice approval seemed to have hit a public nerve. Rumors spread in social-media chat rooms that homegrown GMOs and the nation’s vast imports of GMO grains posed health and environmental dangers. (Military officials in one Chinese province even recently banned GMO-sourced cooking oil from troops’ food supply.) “We need the GMOs, but we face severe issues so far in China, meaning the public fears. This is a problem,” says Dafang Huang, former director of the Institute of Biotechnology within the Chinese Academy of Agricultural Sciences.Meanwhile, the government is also trying to wean itself from imports by building its ownseed-producing capacity for GMO corn and soybean at state companies such as DBN, which runs a biotech center in Beijing.Long-term food security trends are worrisome. China is home to 1.3 billion people. Its population is rising, its available arable land is slowly decreasing, and yield per acre has stayed essentially flat over the past decade. “It’s going to be hard to increase the food supply with the traditional crop technology,” adds Huang, who spent time planting wheat during the Cultural Revolution.Against a nationalist and popular backlash, none of the modified rice is officially planted, though reports of illegal plantings abound. Strictly speaking, even though rice has a biosafety certificate, it needs a final step, called varietal trials. “For the varietal trials for all major crops except cotton, there are no government guidelines on how to do it. It seems the government is not in a rush. It probably has more challenging issues on its hands, so this is not one to deal with at the moment,” says Xing-Wang Deng, who heads a joint research center for plant molecular genetics and agricultural biotech at Peking University and Yale. Deng was one of the prominent experts China lured back to establish labs in China under a government plan called the “1,000 Talent Program.”Despite the regulatory uncertainties, Chinese researchers have quintupled their output of plant science papers in the past decade amid annual funding increases that are the envy of counterparts in other nations. “We can do research—we have enough of financial support—but I don’t know if Chinese scientists can produce the product. The government should give us clearer guidelines or information on which direction we could go further,” says Caixia Gao, who heads a gene-editing research group at the State Key Laboratory of Plant Cell and Chromosome Engineering at the Institute of Genetics and Developmental Biology in Beijing.<ASIDE class=ad-left>Gao cowrote a recent paper on how to confer mildew resistance in wheat using new genome-editing methods. The trick avoids creating transgenic crops because it doesn’t involve inserting genes from other organisms. As such she hopes the technology can sidestep much of the controversy surrounding transgenic crops.These recent advances in the lab—plus the certainty of future food supply pressures—could quickly turn things around, Huang adds. “I am cautiously optimistic about the GMO development in China,” he says.And if China decides to open the doors to new commercial plantings, the impact could be vast. The country’s size guarantees that any action will reverberate in global markets and research labs. “What we can do is just wait for approval from the government. And probably we can do more research work,” says Huang.Some research has shown big benefits in China from the planting of pest-resistant cotton, which produces a substance toxic to a major pest, the bollworm. Bollworm populations have been sharply reduced not only in cotton by in nearby nontransgenic crops including corn, peanuts, and soybeans, cutting the need for pesticides while not affecting beneficial insects. But the news is not all good; a secondary pest not sensitive to the toxin has become more prevalent, suggesting that GMOs are no panacea. Gain the insight you need on emerging technologies at EmTech MIT. Register today<img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjraA2ApAEXsN9a6xv4WdX2ZBuAaEyuAe0trO9Q0P4jiNOJFAXjhdQzSUV8oTA3gcNSaq6h-EYIY_c9P7C7q560kgPWw96IEphRmN5Q5CUmo-yHhDNTDXz9pEHPYiHfDJFmEYzT30e_l5UG//">

Chinese GMO Research Outpaces Approvals

The fact that China hasn’t approved any commercial GMO planting since 2009 reflects public fears. Growing future: China is the world’s la...

Challenges Remain for Technologies to Fight Ebola

Efforts to contain Ebola in West Africa suffer from a lack of effective tools to treat and prevent the disease, although several are in development. <ASIDE class=img-left><img alt="" height="299" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjH8M-5Mr5VRWofNZDJlRj5lZrbB5zY6gR2Mav5a7W3gBny1RmgckByUoZPFCic7HAult__i7lJnfdgvUYViBFCelN3v0gU8bALylNm8PS6mgMITnDkYAaWFsMWa_dbtzyr6T8ne9I67K7U//" width="299"> <ASIDE class=caption-left>Viral load: A micrograph of the Ebola virus.Technologies that might prevent the spread of Ebola beyond West Africa are under development, and work could accelerate if the outbreak continues to worsen. But even if a vaccine were available today, deploying it could prove surprisingly difficult.As of last week, the Ebola outbreak had claimed the lives of 88 percent of the more than 1,000 people who had contracted the virus. The virus causes fever, headache, sore throat, and other symptoms, followed by vomiting and diarrhea. It can lead to internal and external bleeding, and often death.Ebola has affected relatively small populations in Africa since it was discovered in the 1970s. There has therefore been little incentive for companies to invest in developing treatments or vaccines, experts say. One treatment that has shown promise in animals but has not yet been tested in humans is called ZMapp—a combination of three monoclonal antibodies manufactured in tobacco plants by Mapp Biopharmaceuticals in San Diego. These antibodies are designed to mimic the antibodies the human body naturally produces as part of an immune response that’s typically disabled by the Ebola virus. The monoclonal antibodies attach to a part of the Ebola virus and trigger an immune response that neutralizes any virus particles floating around in the body to keep them from doing additional damage.Samaritan’s Purse, the organization that employs one of the American Ebola patients, says that two American patients received this experimental serum while in Africa. MIT Technology Review was not able to reach Mapp Biopharmaceuticals or the Emory Hospital where the patient is being treated for comment. Several Ebola vaccine candidates are also in development, including one developed by the National Institute for Allergy and Infectious Diseases’ Vaccine Research Center that has shown promise in monkeys and has been fast-tracked for human testing this fall. The vaccine works by inserting two Ebola genes into a cell that helps to generate an immune response, allowing the body to recognize and fight the disease in the future.<ASIDE class=ad-left>Even if a vaccine is approved, however, one challenge would be figuring out who to vaccinate. “It’s not going to be all of Africa,” says Stephen Calderwood, chief of the Division of Infectious Disease at Massachusetts General Hospital. “It’s going to be in response to a specific outbreak and within a specific population that is at high risk, for example health-care workers.”Furthermore, some reports say that there has been reluctance among patients in West Africa to accept care from Western doctors, stemming from a lack of trust in these health professionals.Ebola is difficult to study because it occurs sporadically within small populations, compared to diseases like malaria or HIV. Animal models are used to help research the disease, and have offered clues as to why certain patients survive. For example, scientists have detected differences in the responses of monkeys that survive Ebola and those that die, such as the high prevalence of a subset of immune cells called neutrophils in the latter group, says John Connor, associate professor of microbiology at Boston University School of Medicine. “I’d say we’re in the middle of the story right now in understanding what the relevance of that is and why that’s the case,” he says.

Challenges Remain for Technologies to Fight Ebola

Efforts to contain Ebola in West Africa suffer from a lack of effective tools to treat and prevent the disease, although several are in dev...

A Mouse with the Same Cancer as You

For $12,000, a company grafts a patient’s cancer into rodents and tests drugs on them. <ASIDE class=img-left><img alt="" height="299" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDFA8EgWwf_QazDFJ7lYmmTgbj1xhBPKyv0IMa8kBhRPrU_f2z6Fv6z2038sFQJSplnY8SHKSkyJGsnaiGKopHx3-t73xQ3eF9JfR64Z2DiozjgqgL4qd-pmxSdp5xpvVV-J6MlmRRXBoY//" width="299"> <ASIDE class=caption-left>Test tube: Human tumors will grow in this mouse, which has no immune system.At a laboratory in Baltimore, hairless mice kept in racks of plastic crates are labelled with yellow cards, each identifying a person fighting cancer. These mice are cancer “avatars”—the lumpy tumors visible under their skin come from actual patients.The animals serve as personalized, living test tubes. Each mouse will eventually be treated with a different drug and its tumors measured. Results showing which medicine worked best will be sent back to a doctor trying to treat a difficult cancer case.The technology is a twist on personalized medicine that’s being developed by Champions Oncology. The company, based in New Jersey and Maryland, has started offering mouse avatars directly to patients, at a cost of $10,000 to $12,000. Insurance companies don’t yet pay for the technology, which remains experimental.In the service Champions is selling, doctors first remove a piece of a patient’s tumor during a surgery or biopsy. Then they ship it to the company, where it gets grafted under the skin of an immune-deficient mouse. Because the rodents have impaired defenses, the human tumor is able to grow. Parts of it can be removed and implanted in additional mice.The data from the avatars is potentially life-saving, since the choice of what drug to give a cancer patient is often made by guesswork or trial and error. “Generally, the drugs we give to patients are more likely to not work than to work,” says Justin Stebbing, an oncologist at the Imperial College London, who has been involved in medical studies of Champions’s technology. The results from the personalized mice, he says, “give patients an additional layer of confidence.”Cancer avatars are part of a wider effort to carry out experiments on people’s tumors outside their bodies. Some researchers have created fruit flies that share the same gene mutations patients have. Another technology, still in development, looks to capture floating tumor cells from a person’s bloodstream, then grow and test them in culture dishes (see “A Laboratory for Rare Cells Sheds Light on Cancer”). Still further out, scientists have plans to grow mini-organs, complete with an immune system that matches the patient’s (see “Building an Organ on a Chip”).Don Ingber, director of the Wyss Institute for Biologically Inspired Engineering at Harvard University, says these outside-the-body approaches face some similar challenges. For one, cancer cells vary so much that it’s not certain the tumor in the mouse is the same as the one in the person. What’s more, the immune system is closely involved in the body’s response to cancer, but these mice lack one. “I think the real issue is that it’s still a mouse,” he says. Champions, founded in 2007, has successfully grown tumors from more than 350 patients, says company president Ronnie Morris. In June, the company said it would collaborate with the Icahn School of Medicine at Mount Sinai, in New York, to create mouse avatars for an additional 100 breast cancer patients. “On the whole, it seems to yield very convincing data that’s predictive, so it tells you what treatment is going to work ahead of giving these expensive and toxic drugs,” says Stebbing, who has tried the technology with patients suffering from rare or unusual cancers.<ASIDE class=ad-left>Not every graft works. In about 30 percent of cases, Champions hasn’t been able to grow a patient’s tumor in mice. But the biggest limitation to cancer avatars is that tumors grow at about the same speed in a mouse as in a person. That means the avatars won’t be helpful for patients who need to be treated quickly, as is often the case. Morris says it takes four to six months to grow the tumors, treat the mice, and send doctors a report.In a study Stebbing published in April in the journal Cancer, for instance, Champions created avatars for 22 patients with advanced sarcoma. But nine of the patients died before the results were ready. “Within a couple of months after their surgery or biopsy, they get chemotherapy and they pass away,” says Morris. “We build the avatar, but the patient can’t use it.”

A Mouse with the Same Cancer as You

For $12,000, a company grafts a patient’s cancer into rodents and tests drugs on them. Test tube : Human tumors will grow in this mouse, w...

Chinese Researchers Stop Wheat Disease with Gene Editing

Researchers have created wheat that is resistant to a common disease, using advanced gene editing methods. <ASIDE class=img-left><img alt="" height="299" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhGm_JxMvm_WiVFv5GtUwJ8evbwXRIe0saN7ELPaaSHJZJDp6Eys28dyGcsbOpGERrYMmx4RkQWZYWRbCps4_Tjkz5u1ArMnIR79KM2OVDEkYifC-0neHtX4eBeh3t71CrcBVVowH0p36Y//" width="299"> <ASIDE class=caption-left>Seeds of hope: Chinese researchers led by Caixia Gao have developed genetically modified wheat far more able to withstand powdery mildew.Advanced genome-editing techniques have been used to create a strain of wheat resistant to a destructive fungal pathogen—called powdery mildew—that is a major bane to the world’s top food source, according to scientists at one of China’s leading centers for agricultural research.To stop the mildew, researchers at the Chinese Academy of Sciences deleted genes that encode proteins that repress defenses against the mildew. The work promises to someday make wheat more resistant to the disease, which is typically controlled through the heavy use of fungicides. It also represents an important achievement in using genome editing tools to engineer food crops without inserting foreign genes—a flashpoint for opposition to genetically modified crops.The gene-deletion trick is particularly tough to do in wheat because the plant has a hexaploid genome—that is, it has three similar copies of most of its genes. That means multiple genes must be disabled or the trait will not be changed. Using gene-editing tools known as TALENs and CRISPR, the researchers were able to do that without changing anything else or adding genes from other organisms.“We now caught all three copies, and only by knocking out all three copies can we get this [mildew]-resistant phenotype,” says Caixia Gao, who heads a gene-editing research group at the State Key Laboratory of Plant Cell and Chromosome Engineering at the Institute of Genetics and Developmental Biology in Beijing.A paper describing the results appears in Nature Biotechnology.<ASIDE class=ad-left>“This is very, very interesting; it is quite an accomplishment to knock out all three genes at the same time,” says Xing-Wang Deng, who heads a joint research center for plant molecular genetics and agricultural biotech at Peking University and Yale. “And this could be considered as a nontransgenic technology, so that can be very significant. I hope the government would not consider this transgenic, because the end result is no different than a natural mutation.”There are currently no commercially planted varieties of genetically modified wheat anywhere in the world. And while many farmers are clamoring for access to such strains, genetically modified wheat remains highly controversial. Indeed, it’s not clear is whether Gao’s promising strain of wheat will make it out of the greenhouses in Beijing.Gao says she has filed a global patent on the technology, suggesting it could be licensed. But there are no field trials planned yet. While China has greatly increased investments in basic biotech research, including for genetically modified crops, no new field trials of genetically engineered plants have been approved in more than a year as the government tries to mollify public concern over GMOs.Gao says gene editing can provide very efficient tools for basic research and crop improvement, including in complex organisms like wheat. “And it can be without the controversy,” she says.

Chinese Researchers Stop Wheat Disease with Gene Editing

Researchers have created wheat that is resistant to a common disease, using advanced gene editing methods. Seeds of hope : Chinese researc...

The Way of the Dodo

The dodo bird has become a metaphor for extinction. A one-meter-tall, pigeonlike, flightless bird native to the island of Mauritius, the dodo died out in the late 1600s because Dutch settlers relied on them for food and brought in alien species that killed the ground-laying bird’s young. In healthcare, what will “go the way of the dodo”? 
Will technology and the Internet decimate the healthcare industry as they have done to the music and travel industries? Will nurses be replaced by robots? Will doctors be replaced by smartphone apps? A shift is surely occurring, but we still need medical professionals, real people with real compassion giving great care. 
Three trends threaten to make much of today’s healthcare obsolete: the Internet has made patients more engaged in their own care, technology is advancing exponentially, and social media is a dominant force in daily life. Responding to these trends, the Radboud REshape & Innovation Center has initiated a range of innovations: HereIsMyData, a service that consists of a personal health record, a community aspect, and an eHealth connector; AED4US, a crowdsourced database of locations of automatic electronic defibrillators; FaceTalk, a videoconference system that allows healthcare professionals to consult securely with patients and colleagues; AYA4, an online community for young adult cancer patients; and webcasted conferences — TEDxMaastricht, TEDxNijmegen, and 360andabove — to share ideas, dreams, and examples. 
With these projects, the Radboud REshape & Innovation Center is trying to “outsmart the dodo” and avoid extinction by creating “futureproof” healthcare. 
Location and duration of stay 
Location is becoming less important in healthcare. Mobile technology and cheaper testing methods are enabling us to monitor patients in their own homes. And procedures that required up to 15 days of hospitalization a decade ago only require three days today. In the last century, technology brought healthcare out of people’s homes and into centralized hospitals, but now technology is doing the opposite, bringing healthcare back into people’s homes. 
Two-party research in a three-party world 
Until now, health research has mainly been done by the pharmaceutical industry and researchers. Now, patients are doing their own medical research. MedCrowdFund, for example, is a social platform where patients can design and find funding for innovation and research. 
Being a good doctor won’t be good enough anymore 
People are no longer choosing healthcare providers based only on the quality of medical care they or their personal acquaintances have received. Patients now routinely research their physicians online and post reviews of their healthcare experiences. Fifty percent of U.S. smartphone users use their device to look up health information. Doctors can gain a competitive edge by providing both text-based and video web content. 
Collaboration 
Healthcare providers need to stop assuming they know what patients need, or, from an industry perspective, what healthcare professionals need. Listening is asking. The Radboud REshape & Innovation Center appointed a chief listening officer in 2009 to interview patients, family members, and caregivers about how the Center could help them. Feedback from these target groups has significantly benefited the Center’s healthcare projects. The Center also teams with innovators nationally and internationally, finding these likeminded collaborators through the Internet and particularly through social media. 
Rules and regulations 
Time-to-market for medical devices is much shorter today than it used to be, and many more devices are being released, leaving regulatory agencies to play catch-up. In addition to implementing regulatory requirements for digital healthcare innovations, policymakers should make open technical standards mandatory for information exchange and the reuse of existing and proven applications. And the financial system must be improved to ensure that the talented developers and producers of digital healthcare innovations are well compensated for their contributions. 
Information systems 
Huge amounts of data are being generated by information systems, medical records, tracking devices, lab results, and imaging resources. But all of this data currently resides in inaccessible silos where patients can’t make use of it. We need a central repository where individuals can access their own data in a comprehensive way, mine all of the different types of data, and understand their meanings, interrelationships, and interactions. We need open, transparent, user-friendly, and cooperative systems based on open technology standards that actively promote interoperability. 
To speed the evolution of personal health data systems, the Radboud REshape & Innovation Center started a noncommercial service to set up these systems, validate them scientifically, and make them widely available. The Center recently introduced HereIsMyData, a service that provides a personal health record, as well as a platform for patients, caregivers, and families to talk about a specific disease, and connectivity tools for personal health devices, data visualization tools, and the Center’s own FaceTalk™ and MedCrowdFund™. 
This initiative has made the Center a clearinghouse for developing, implementing, and evaluating medical innovations. Last summer, upon discovering that the viewing angle of Google Glass prevents surgeons from using it optimally, the Center provided the Google Glass team with valuable feedback — and continued receiving and implementing ideas from inspired medical professionals worldwide on how to use Google Glass to improve quality of care. This approach will enable the Radboud REshape & Innovation Center to beat the dodo. 
Read the full  article here. 
Lucien Engelen is the Director of the Regional Acute Healthcare Network at Radboud University Nijmegen Medical Center in the Netherlands, as well as an advisor to the executive board on questions relating to changes in healthcare, enhancing patient participation, and working toward participatory healthcare. He is the founding director of the Radboud REshape & Innovation Center, an institution that creates, develops, and implements healthcare innovations. 
Tagged: Computing, Biomedicine, Web, healthcare, innovation, healthcare IT, information security, digital healthcare Reprints and Permissions | Send feedback to the editor <img alt="close" height="10" id="vftm-tooltip-close" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgpdlG8IyUdR-c1Gwv8h9JCO6V_DK-xtLP2EXjt-Dcr3z0BAV7tLe85E6F1P2SdvXgc9nFJEJDqi8a8dSQGBpILUcLNMVSrsp8pah2tOIzHPvXUZyil3ngqLXOfcJdVEsuRKeGeh8h3n6el//" width="10" /> 
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The Way of the Dodo

The dodo bird has become a metaphor for extinction. A one-meter-tall, pigeonlike, flightless bird native to the island of Mauritius, the dod...

Mathematicians Explain Why Social Epidemics Spread Faster in Some Countries Than Others

Psychologists have always puzzled over why people in Sweden were slower to start smoking and slower to stop. Now a group of mathematicians have worked out why. <img alt="" height="565" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeIliddqSecYK-XRClJdOE0mbQBQg15v5aAcEOzyLlBrt3rD8A2j0TNMEYUFTab93mLpgbxpZv5OLWzevqxi1VikJXOMasv4Y-GxCYmRuY8ly6JjlQRpPLyaMMhZwy6wOFgWiYiQnBpQfx//" width="616" /> 
 
In January 1964, the U.S. Surgeon General’s Advisory Committee on Smoking and Health published a landmark report warning of the serious health effects of tobacco. It was not the first such report but it is probably the most famous because it kick-started a global campaign to reduce the levels of smoking and the deaths it causes. 
In the 50 years since then, the patterns of smoking all over the world have changed dramatically. In the U.S., the numbers of smokers peaked in 1965 and have fallen precipitously since then. Similar patterns have occurred in all industrialized countries. 
But here’s a curious thing. While the general pattern of smoking has been similar—an increase in numbers followed by a decrease—the rate of change has been dramatically different from one country to another. In other words, some countries adopted smoking more quickly and stopped smoking more quickly than others. 
That raises an important question. How is smoking behavior transmitted through a population and why does it differ from one country to another? 
Today, we get an answer thanks to the work of John Lang at the University of Waterloo in Canada and a couple of pals. These guys have gathered the largest historical data set on smoking ever compiled and study how its prevalence is correlated with the types of societies involved. Finally, they create a mathematical model of how smoking behavior is transmitted through a society. 
Treating smoking like an epidemic in this way finally reveals what’s going on. They say their results can explain the rate of change of smoking in various industrialized countries. And they say the crucial difference is the level of individualism in each society. 
Perhaps the most extreme difference in smoking patterns come from the U.S. and Sweden (see graphic above). In 1920, a relatively small portion of both populations smoked, less than 10 percent. In the U.S. this proportion rose dramatically to just under 40 percent of the population in 1965 and then fell to just under 20 percent in 2010. 
By contrast, in Sweden the number of smokers peaked at around 30 percent in the early ’70s and then declined to around 20 percent in 2010. So the Swedes adopted smoking more slowly, peaked later, and then stopped smoking at a slower rate than people in America. And yet the Swedes had access to the same data about the dangers of smoking at more or less the same time. 
One crucial difference between Swedish and American society is the level of individualism. This is essentially the emphasis on the worth of the individual as opposed to the emphasis on the interdependence of individuals: individualism versus collectivism. 
This measure of society was promoted in the 1960s by Geert Hofstede, a Dutch social psychologist who developed ways to measure a set of cultural dimensions for comparing cultures. These include things like uncertainty avoidance; the strength of the social hierarchy; masculinity versus femininity and so on. 
In the 1960s and 1970s, Hofstede surveyed more than 100,000 IBM employees to measure how these dimensions varied in different countries around the world. And since then, his ideas have become increasingly influential. 
Hofstede found that societies in countries such as the U.S., the U.K., and Australia tend to emphasize individualism while societies in countries such as Sweden, France, and Japan place much greater emphasis on collectivism. In other words, in these countries there is greater social pressure to conform. 
Psychologists have always assumed that patterns of behavior change more quickly in countries that emphasize collectivism. Once an idea has taken hold, the pressure to conform means it spreads rapidly. “It has previously been argued that social support mechanisms in collectivistic societies make it more likely that a person will stop smoking,” say Lang and co. 
And conversely, in countries that emphasize individualism, patterns of behavior must change more slowly because there is less social pressure to conform. 
The puzzle is that the data on smoking shows exactly the reverse. Sweden was much slower to adopt smoking and much slower to stop. 
Now Lang and co think they know why. They’ve created a mathematical model that includes the effects of social pressure allowing them to simulate the way behavior spreads through societies with different levels of individualism. 
The model reveals why Sweden stopped smoking more slowly. “Our model suggests that … social inertia will inhibit decisions to stop smoking more strongly in collectivistic societies than in individualistic societies,” say Lang and co. 
Conversely, the social freedoms in individualistic societies allow anybody to make a decision to stop smoking more easily. 
That’s an interesting result with significant implications for government health policies. It shows that differences in culture affect the dynamics of social spreading processes in a measurable way. 
That will be crucial for the way that governments design strategies to help people stop smoking. “Interventions designed to discourage smoking should be tailored diferently in societies or social groups whose cultures differ in how they value individualism versus collectivism,” say Lang and co. 
What’s more, smoking behavior is just one example of a socially contagious phenomenon. Lang and co’s approach should also apply to other forms of cultural transmission. In general, this kind of transmission should lead to slower change in societies that value collectivism versus individualism. 
And that’s an idea that could influence everything from drugs policy to social network studies to the marketing of beef burgers. 
Ref: arxiv.org/abs/1407.2188 : The Influence of Societal Individualism on a Century of Tobacco Use: Modelling the Prevalence of Smoking

Mathematicians Explain Why Social Epidemics Spread Faster in Some Countries Than Others

Psychologists have always puzzled over why people in Sweden were slower to start smoking and slower to stop. Now a group of mathematicians ...