A crackdown on firms selling gene tests direct to the consumer would come at a cost, argue Daniel MacArthur and Caroline Wright
AS WE enter the era of genomic medicine and affordable whole-genome sequencing, public understanding of genetics is becoming increasingly important. There are few better introductions to the complexities and uncertainties of modern genetics than allowing people to access their own DNA.
Unfortunately, recent attacks on direct-to-consumer (DTC) genetic testing by US regulators may signal a disproportionate crackdown that could limit this access. We believe that regulation is needed, but are worried that it will focus too heavily on "protecting" consumers from their own genomes.
Lauded as Time magazine's Invention of the Year in 2008, personal genome scans have attracted both international attention and criticism. They promise to provide consumers with information ranging from disease risk to ancestry, based on hundreds of thousands of common genetic markers.
Living up to that promise has been difficult. Despite the large amount of information contained in a genome scan, the medical value as of now is extremely limited. Scientists have uncovered only a fraction of the genes involved in complex diseases such as diabetes or rheumatoid arthritis, so risk prediction based on genetics alone is weak and subject to change.
However, the tests can provide potentially useful information including warnings of adverse drug reactions and the possibility of passing genetic diseases on to children, as well as recreational information such as ancestry. The industry has also created some innovative products, such as interfaces for explaining complex risk information and a new model for research in which customers can volunteer to participate in genetic studies.
Although making sense of the information is not straightforward, peering into your own genome can be a powerful education in modern genetics and epidemiology - just so long as the information provided is accurate and comprehensible.
Are DTC genetic testing companies delivering the goods? You certainly would not get that impression from the recent sabre-rattling of US regulators. In the past couple of months the industry has endured a brutal Congressional hearing in which its products were described as "snake oil", a report by the US Government Accountability Office blasting it for inconsistent results and unethical marketing, and threats from the Food and Drug Administration to regulate DTC genetics as "high risk" medical devices.
There are legitimate concerns about sections of the industry. Though some DTC genetics companies uphold high standards, at the bottom end of the market assorted disreputable operators offer products based on weak or non-existent science.
However, the US authorities are going over the top, conflating the two ends of the market and exaggerating the dangers of providing genetic information directly to consumers. The risk is that they translate their own hyperbole into heavy-handed legislation without any evidence that it is either wanted or needed.
In general we would argue that people should be free to access their own genetic data unless there is good reason to believe that doing so will cause them harm - and as long as the information is accurate and transparent.
What is needed is measured regulation that protects unwary consumers, punishes false claims and weeds out fraudsters without destroying the potential of DTC genetics to drive innovation and educate the public.
It is crucial that companies meet stringent standards for the accuracy of their data and use formally accredited laboratories to perform their analysis. They must also ensure that their customers are properly informed about the nature of the information they will receive and its implications and limitations. Customers should have access to expert advice if they want it, although medical supervision should not be a requirement to access your own genome. False advertising, misleading claims and unethical or illegal marketing should be punished.
Companies must also be transparent about the science underpinning their results. A central database of genetic tests being developed by the US National Institutes of Health would be a natural repository for this information, and submission of supporting evidence to such a database should be mandatory.
These needs could be met with minimal regulatory changes: standards for testing laboratories already exist in the US, and punishment for false advertising simply requires greater engagement by consumer watchdogs.
As the drama unfolds in the US, there are signs of a more measured response in the UK. On 4 August, the Human Genetics Commission published a "framework of principles" for DTC genetics that lays out guidelines in areas such as accuracy, consent and data protection. While the framework is non-binding, it is intended to serve as the basis for formal regulation.
We don't yet know what role personal genomics will play in the future of medicine. However, we do know that it has great potential for innovation and education, and we must ensure that neither excessive regulation nor medical paternalism get in the way.
Scientists have found a "genetic signature" in the blood of patients with active tuberculosis (TB) and believe their discovery could help develop better diagnostic tests for the disease, as well as better treatments.
More than 2 billion people, or a third of the world's population, are estimated to be infected with the organism Mycobacterium tuberculosis (MTB) which causes TB, but the vast majority have the infection in latent form and have no symptoms.
The British scientists said they had now found a pattern of genes in the blood which is specific to up to 10 percent of those 2 billion people who develop active TB in their lungs.
The genetic signature shows the extent of the disease in the lungs and disappears after successful treatment, they said in a study in the journal Nature on Wednesday.
"Although people have been studying TB for more than a century, there is still a desperate need for better prognostic and diagnostic tests and more information about the body's response to MTB infection, which may also help in the design of vaccines and treatments," said Anne O'Garra, of the Medical Research Council, who led the study.
TB is one of the oldest diseases known to mankind and afflicts mostly the poor in developing regions such as sub-Saharan Africa, India and China. It is among the world's top 10 leading causes of death and killed 1.8 million people worldwide in 2008, or one person every 20 seconds.
Current drugs for TB are at least four decades old and must be taken for several months. Patients often fail to take the full treatment course, which has spawned drug resistant TB and made the disease more dangerous and more difficult to treat.
Doctors say current diagnostic tests for TB have barely been improved in the last 125 years.
BLOOD TEST?
O'Garra's study was conducted in London -- which has 40 percent of all British TB cases and where 3,500 people were diagnosed last year -- and then checked on a separate group of patients in Cape Town, South Africa, where TB is often found in people whose immune systems are weakened by the AIDS virus HIV.
Results showed that around 10 percent of those with latent infection also had the genetic signature for the active disease.
The scientists said it was too early to say yet whether this 10 percent would be the same 10 percent who are estimated to go on to develop active TB, but further studies were underway.
At this stage the findings are a significant step towards developing a blood test using the genetic signature to predict which people with latent TB will get sick, they said.
Robert Wilkinson, the director of Cape Town University's clinical infectious diseases unit, who also worked on the study, said such a test would enable thousands of people at risk of active TB to be diagnosed and treated earlier, and help doctors to avoid treating large numbers of patients unnecessarily.
"It's known that treatment for latent TB is effective and can contribute to TB control -- but the doctor's dilemma...is that...you are prescribing unnecessary treatment probably to 9 out of 10 people," he said in a briefing about the work.
"If there was a way of finding out who was most at risk, then that would greatly rationalise the treatment of latent TB."
MarketResearch.com has announced the addition of MarketsandMarkets's new report "Bioinformatics Market - Advanced Technologies, Global Forecast and Winning Imperatives (2009 - 2014)" to their collection of Biotechnology market reports. For more information, visit http://www.marketresearch.com/product/display.asp?ProductID=2745333 Bioinformatics has gained high importance due to its ability to facilitate rapid clinical research, and also due to its various applications such as gene therapy and molecular science. Bioinformatics uses information technology, statistics, and algorithms to integrate biological data. Pharmaceutical companies are now adopting automated technologies to manufacture effective therapies and drugs due to increasing concerns about drug safety and the stringent regulations that govern clinical trials for drug discovery. Pharmaceutical companies have increased their focus on process improvement and quality, as the current competitive scenario offers little scope for price escalation and product differentiation. The market for bioinformatics platforms is growing at a significant pace with the increasing demand from U.S. and Europe. This trend is supported by the increasing demand for sequencing platforms with increasing life science research using techniques such as gene expression analysis, sequence analysis, and protein expression analysis. The global bioinformatics market is expected to reach $8.3 billion by 2014 at a high CAGR of 24.8% from 2009-2014. While knowledge management formed the largest submarket is 2009 at $1.3 billion, the bioinformatics platforms market is expected to have greatest market share in 2014 at an estimated $3.9 billion, due to rising demand from the U.S. and Europe.
Genetic testing might have helped identify people who would become depressed or suicidal while taking Sanofi-Aventis' (SASY.PA) weight loss drug Acomplia, which might have helped keep the drug on the market, U.S. researchers said on Thursday.
They said partial results from a study of the drug in which five people committed suicide confirmed that it increased the risk of psychiatric side effects.
The study was halted in 2008 and the company pulled the drug from the market in Europe, but the researchers think genetic testing might have been able to identify people who were at risk of the side effects, and rescue the once-promising treatment, said Dr. Eric Topol of Scripps Translational Science Institute in La Jolla, California, whose study appears in the journal Lancet.
Acomplia, known generically as rimonabant, blocks the same reward receptors in the brain that become active during marijuana use, and for some people, it caused serious bouts of anxiety and depression that led to suicide.
"Finding the gene for severe adverse drug reactions is a lot easier than we ever thought it would be," Topol said in a telephone interview.
Topol thinks if they had thought to collect genetic information on the study's more than 18,000 participants, they might have spared the drug.
"We probably could have figured out genomically who was susceptible and that drug could be quite viable," Topol said in a telephone interview.
Hopes had been high for Acomplia, which not only helped people lose weight but helped them achieve more normal blood sugar levels and improvements in blood fats known as triglycerides and HDL cholesterol, the so-called good cholesterol.
In Topol's study, which looked at the heart benefits of the drug, four patients taking rimonabant and one person taking a placebo committed suicide.
Of the results they had, they found deaths from heart disease, heart attacks and strokes occurred at similar rates in both groups, and they did find that serious psychiatric side effects were increased in rimonabant users compared with placebo.
Due to these side effects, the European Medicines Agency recommended doctors no longer prescribe rimonabant from October 2008. Concerns about side effects prevented the drug from winning U.S. regulatory approval.
Topol says it is likely too late to revive Acomplia, but he said the study does offer insights about how to avoid similar problems with drugs in the future.
"Genomics could potentially be used to pre-empt use of the drug in individuals with risk of serious adverse events," he said in a statement.
High-risk bone marrow transplants partially cured five children with a potentially deadly genetic defect in which proteins that hold layers of skin together are absent, U.S. researchers said Wednesday.
But one other child died from side effects of a drug used to prepare for a transplant and a second died from a post-transplant infection.
People with recessive dystrophic epidermolysis bullosa, or RDEB, are plagued by painful blisters on the skin, mouth and throat, caused by the slightest trauma that can expose the body to infection and, in some cases, an aggressive form of cancer.
With the new treatment, "there was improved healing, fewer blisters, and their quality of life was positively affected. They could do things they couldn't do before, like ride a bicycle or go on a trampoline," said Dr. John Wagner of the University of Minnesota, who worked on the study.
It was published in the New England Journal of Medicine.
In addition, the patients' improvement progressed with time, he said. All five children who survived showed improvement within 100 days, although the pace varied widely, he said in a telephone interview.
Because of the high risks involved in bone marrow transplants, only the sickest patients with the rare condition -- affecting 1 in 50,000 -- have been considered candidates for a transplant, Wagner said.
Wagner reported on results of the first seven attempts, which took place at the University of Minnesota Amplatz Children's Hospital. Six other children have subsequently been treated with good results, he said.
Researchers are now trying to isolate the cells of the bone marrow best able to fix the defect and join layers of skin.
HIGH COST
The treatment, including the cost of the transplant, is between $500,000 to $1 million. But routine care for children with the collagen defect already costs about $30,000 a year and can rise due to frequent hospitalizations and complications of the disease.
"These kids have horrible pain, chronic infections of the skin, multiple hospitalizations, and systemic infections," Wagner said.
"They frequently can't eat or refuse to eat because of the pain. Often they die of chronic malnutrition and chronic blood loss."
Dr. Jakub Tolar, also of the University of Minnesota, said the treatment was unique because it showed that the effects of a bone marrow transplant can extend beyond the blood.
"What we have found is that stem cells contained in bone marrow can travel to sites of injured skin, leading to increased production of collagen, which is deficient in patients with RDEB," Tolar, who worked on the study, said in a statement.
Dr. Lenna Bruckner-Tuderman of University Medical Center in Freiburg, Germany, said in a commentary that the therapy represented a leap forward but expressed caution.
Because the disease can wax and wane, "it is difficult to determine how much of the clinical improvement in the children was due to transplantation and how much was due to a long period of careful medical attention, protection from trauma, and standardized wound care," Bruckner-Tuderman said.
ARE we witnessing the beginning of the end of "personal genomics"? After a bruising hearing in the US Congress last week, and with the Food and Drug Administration flexing its regulatory muscles, that is what some commentators predict. "There's no question that the sheer scale and ferocity of this combined inquisition from the FDA and Congress will forever change the face of the personal genomics landscape," wrote Daniel MacArthur in his Genetic Future blog, predicting "excessive, innovation-crushing regulation". But this doesn't have to be the end of the industry. If it embraces sensible regulation, then it has the chance to shift personal genomics from a minority recreational pursuit to the heart of clinical medicine. We all stand to benefit from such a shift, by being prescribed drugs that work better for our particular genetic make-up, for example. The star turn at last week's congressional hearing was a report from the US Government Accountability Office (GAO) in which investigators recounted their experience of submitting samples for DNA testing to the four leading personal genomics companies - 23andMe, DeCode Genetics, Navigenics and Pathway Genomics. Like others who have had their genomes scanned by different firms, the GAO investigators obtained varying predictions of their risks of developing common diseases. This is not surprising, given that the companies use different combinations of genetic markers and different algorithms to make predictions from these markers. More damning was a compilation of the conversations between undercover GAO investigators and representatives of genetic testing firms, including two of the personal genomics companies. Congress heard evidence that a Navigenics sales rep offered ill-informed advice on the genetics of breast cancer. And while New Scientist warned last year of the potential for genome scans to be abused by people submitting samples from others obtained without their consent, Congress heard that one of Pathway's sales team actually encouraged someone to send in a sample from her fiancé for testing for disease risks without his knowledge. Some form of regulation is clearly needed. If it is not too heavy-handed, the FDA's involvement could help move the industry into the mainstream. Genome scans could be useful in predicting a person's response to commonly used drugs, helping to determine, for example, the optimum dose they should receive. If so, then FDA involvement will be crucial as drug labels will need to indicate how prescriptions should be modified in the light of genetic information. The future for the personal genomics industry may lie in working with doctors and health insurers to test patients and help improve clinical practice. Navigenics is already working primarily through doctors. Given the limited number of people interested in having their genomes scanned for curiosity's sake - just a few tens of thousands are thought to have purchased scans so far - simple economics may send others down the same path
Affymetrix, Inc. (NASDAQ:AFFX) today announced that it has launched Axiom Custom Genotyping Arrays, the newest addition to the Axiom Genotyping Solution. Researchers can now leverage Affymetrix` Axiom Genomic Database, the world`s largest collection of validated common and rare SNPs, to create custom arrays containing 50,000 to as many as 2.6 million SNPs. This inherent flexibility allows researchers to conduct genome-wide association, replication, fine mapping, and candidate gene studies on a single platform. Axiom Custom Genotyping Arrays deliver unparalleled flexibility in study design and maximize researchers` ability to generate meaningful data with the most relevant SNPs for their disease or cohort. Scientists can now create extremely precise array designs leveraging Affymetrix` Genomic Database, which includes7.4 million SNPs from the 1000 Genomes Project, the International HapMap Project, and other sources. With more than 5 million validated SNPs, including more than 600,000 novel 1000 Genomes Project SNPs with a minor allele frequency (MAF) of less than 2.5 percent, the Axiom Genomic Database will enable researchers to study the role of rare variants in human disease by designing arrays with markers in specific MAF bins of their choice. Researchers can also combine SNPs from their own sequencing projects and other sources with Affymetrix` validated SNPs to design arrays with up to 2.6 million SNPs. In the near future, this capability will expand to support custom array designs containing more than 5 million SNPs. As large-scale genotyping studies begin to leverage newly discovered content, a large number of researchers are now interested in low-frequency variants and genetic diversity in a variety of populations, particularly Africans. Both of these trends signal the need for higher density arrays and the ability to customize content to maximize coverage in the population of interest. "Affymetrix` new custom offering addresses new trends in genetic research by allowing a significant amount of flexibility," said Jay Kaufman, Vice President of DNA Product Marketing at Affymetrix. "Researchers can now create arrays consisting of 50,000 SNPs for focused or replication studies, a multi-sample array plate of millions of low-frequency variants, or an array tailored to the sample cohort being studied. This new multifaceted custom option will also enable scientists to quickly leverage the most recent and novel content as SNP discovery continues." Researchers designing Axiom Custom Genotyping Arrays will receive design support and expertise from the Affymetrix team of bioinformatics scientists to ensure streamlined SNP selection and intelligently designed arrays that fulfill the objectives of their study. Customers can also screen a representative subset of their sample cohort against approximately 5 million validated SNPs to gain valuable insights into linkage disequilibrium (LD) structure, minor allele frequency information, and assay performance to assist in the design of their custom array. This one-of-a-kind selection and design process provides another valuable tool for researchers to design highly optimized genotyping arrays based on empirical data rather than speculative marker selection. This database screening service is available through the Affymetrix Research Services Laboratory. "As the needs of human disease research evolve with the rapid expansion of available markers, customization and flexibility have become increasingly important," said Kevin King, President and CEO of Affymetrix. "Researchers want to design studies to optimize their ability to answer key biological questions.Axiom Custom Genotyping Arrays enable them to do this with a wide range of formats, relevant content, and high-quality data to expedite their disease association studies." To learn more about Axiom Custom Genotyping Arrays, please visit www.affymetrix.com/axiom. About AffymetrixAffymetrix technology is used by the world`s top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government, and nonprofit research institutes. More than 1,900 systems have been shipped around the world and more than 21,000 peer-reviewed papers have been published using the technology. Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Cleveland, Ohio, and Singapore. The company has about 1,000 employees worldwide and maintains sales and distribution operations across Europe and Asia. For more information about Affymetrix, please visitwww.affymetrix.com. Forward-looking statementsAll statements in this press release that are not historical are "forward-looking statements" within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix`"expectations," "beliefs," "hopes," "intentions," "strategies," or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected. These and other risk factors are discussed in Affymetrix` Form 10-K for the year ended December 31, 2009, and other SEC reports for subsequent quarterly periods. NOTE: Affymetrix, the Affymetrix logo, and Axiom are trademarks or registered trademarks of Affymetrix, Inc.Affymetrix, Inc.Annette Summers, 408-731-5169Senior Director, Marketing CommunicationsAnnette_Summers@affymetrix.comDoug Farrell, 408-731-5285Vice President, Investor Relations
Mothers who eat a high fat diet before and during pregnancy may be putting their offspring at risk of birth defects, scientists said on Tuesday.
British researchers studying mice found that a pregnant mother's diet may interact with the genes her unborn baby inherits and influence the type or severity of birth defects such as congenital heart disease and cleft palate.
"These are very important findings as we have been able to show for the first time that gene-environment interactions can affect development of the embryo in the womb," said Jamie Bentham of the Wellcome Trust Center for Human Genetics at the Oxford University, who led the study.
"We know that poor diet and defective genes can both affect development, but here we have seen the two combine to cause a much greater risk of developing health problems and more severe problems. We are excited by this as it suggests that congenital heart defects may be preventable by measures such as altering maternal diet," he said in a statement about the findings.
Congenital heart disease is the most common form of birth defect, and previous studies have shown that children born to mothers who have diabetes or who are overweight have an increased risk of it.
It is also known that certain genetic changes -- such as deficiency in Cited2 -- can give rise to congenital heart disease, but until now scientists did not know if external factors such as a mother's diet could interact with genetic changes to affect their babies.
The British researchers, whose findings were published in the journal Human Molecular Genetics, compared healthy mice with those lacking a gene called Cited2.
Cited2 deficiency results in heart defects in mice and in humans and can also lead to a serious type of heart defect called atrial isomerism, where the left-right asymmetry of the heart is disturbed.
Researchers fed the mice a high fat diet before and during pregnancy and then studied the development of their babies using magnetic resonance imaging. The results were compared to mice from a second group who were fed a balanced diet.
Among offspring mice that were deficient in Cited2, the risk of atrial isomerism more than doubled, the researchers found, and the risk of cleft palate increased more than seven-fold when the mothers were fed a high fat diet.
The changes did not happen in the genetically normal offspring of mothers who had a high fat diet, suggesting that it is the combination of high fat diet and the genetic defect that is responsible, they said.
Jeremy Pearson, associate medical director of the British Heart Foundation charity, which part-funded the study, said the findings could shed light on human birth defects.
"This research shows that diet during pregnancy can directly affect which genes get switched on in unborn offspring. The study was with mice, but a similar link may exist in humans, leading to some cases of congenital heart disease."
He said the research reinforced the need for pregnant women to have a balanced diet and avoid eating too much fatty food.
A massive genetic study of people who lived for more than 100 years has found dozens of new clues to the biology of aging.
The findings won’t be turned overnight into longevity elixirs or lifespan tests, nor do they untangle the complex interactions between biology, lifestyle and environment that ultimately determine how long — and how well — one lives.
But they do offer much-needed toeholds for scientists studying the basic mechanisms of aging, which remain largely unexplained.
“It shows that genetics plays an extremely important role at these extreme ages. And it begins to be a not-unsolvable puzzle,” said Boston University gerontologist Thomas Perls. “If we start looking at these genes and what they do, we better understand the biology of extreme longevity.”
Published July 2 in Science, the findings come from gene tests of 801 people enrolled in the Perls-founded New England Centenarian Study, the largest study in the world of people who’ve lived past 100.
People who’ve reached that mark tend to have lives that are not only exceptionally long, but unusually healthly. Unlike most people, they rarely develop diseases of aging — such as heart disease, metabolic disease, cancer and dementia — until well into their 90s. They’re also more likely to bounce back from disease, rather than entering a spiral of declining health.
That manner of aging is a goal for most people, and a public health necessity. Modern medicine has had success in slowing individual aging diseases, but when one is postponed another soon emerges. Americans are living longer but not healthier. Nearly three-quarters of U.S. health spending now goes to treating diseases of aging. That proportion is rising.
In the last decade, scientists using animal models of disease have identified numerous genes and biological pathways implicated in aging. That animal research is valuable, but the gold standard of longevity science involves long-lived people.
Other studies suggest that whether or not someone lives to their 80s is mostly a result of common-sense lifestyle choices: moderate drinking, no smoking, plenty of exercise, a vegetable-centric diet and low stress. But beyond that, “genetics plays a stronger and stronger role,” said Perls. The concentrations of telltale gene profiles found by his group suggest “that the genetic influence is very, very strong.”
Perls’ team surveyed the genomes of 801 centenarians, focusing on “hot spots” where people are most likely to have mutations. They compared the results to genome scans of 926 random people from the general population. From this came a list of 70 gene mutations found mostly in the centenarians. After comparing those to genome scans of 867 people with Parkinson’s disease, the list was whittled down to 33 key mutations.
The researchers used these results to develop statistical models of longevity-associated gene profiles. Used to evaluate anonymized sample genomes, the model could predict whether the sample came from a centenarian with 77 percent accuracy, underscoring the importance of genetics in extreme long life.
Centenarians also tended to fit one of 19 different gene profiles. Some of the profiles tracked with especially low rates of cardiovascular disease, dementia and hypertension or diabetes, suggesting specific genetic pathways for those diseases.
Perls emphasized that the profiles — which came from Caucasians, and are likely different in other ethnic groups — are not intended as guides for drug cocktails or diagnostic tests.
“We’re quite a ways away still in understanding what pathways governed by these genes are involved, and how the integration of these genes, not just with themselves but with environmental factors, are all playing a role in this longevity puzzle,” he said in a press conference.
Other were excited about the findings, but echoed Perls’ restraint.
National Institutes on Aging neuroscientist Donald Ingram called the study a “very impressive genetic and statistical tour de force,” but one that leaves environmental influences unexplained.
According to Perls, one of the study’s most intriguing results is that roughly 15 percent of the general population has some of the longevity-associated genes. Yet only one in 6,000 people currently live to be centenarians — many fewer people than seems to be suggested by the genetics.
Some of the discrepancy can likely be attributed to standards of infant care and public health at the beginning of the 20th century, when these centenarians were born, said Perls. Lifestyle and genetics are also sure to play a part. There will also be genetic factors missed by the study’s narrow focus on hot spots.
According to Jackson Laboratory gerontologist David Harrison, who called the findings “very interesting,” researchers will use animals to explore the roles of genes and pathways flagged in the study.
The findings will also need to be replicated and expanded in more human studies, said National Institutes on Aging gerontologist Winifred Rossi.
“It’s groundbreaking work,” she said. “But science is not fast. It’s slow. It takes a lot of steps to get to something with an impact. We’re only at the start of exploring longevity.”
Craig Venter and his team have built the genome of a bacterium from scratch and incorporated it into a cell to make what they call the world's first synthetic life form.
Scientists have created the world's first synthetic life form in a landmark experiment that paves the way for designer organisms that are built rather than evolved.
The controversial feat, which has occupied 20 scientists for more than 10 years at an estimated cost of $40m, was described by one researcher as "a defining moment in biology".
Craig Venter, the pioneering US geneticist behind the experiment, said the achievement heralds the dawn of a new era in which new life is made to benefit humanity, starting with bacteria that churn out biofuels, soak up carbon dioxide from the atmosphere and even manufacture vaccines.
However critics, including some religious groups, condemned the work, with one organisation warning that artificial organisms could escape into the wild and cause environmental havoc or be turned into biological weapons. Others said Venter was playing God.
The new organism is based on an existing bacterium that causes mastitis in goats, but at its core is an entirely synthetic genome that was constructed from chemicals in the laboratory.
The single-celled organism has four "watermarks" written into its DNA to identify it as synthetic and help trace its descendants back to their creator, should they go astray.
"We were ecstatic when the cells booted up with all the watermarks in place," Dr Venter told the Guardian. "It's a living species now, part of our planet's inventory of life."
Dr Venter's team developed a new code based on the four letters of the genetic code, G, T, C and A, that allowed them to draw on the whole alphabet, numbers and punctuation marks to write the watermarks. Anyone who cracks the code is invited to email an address written into the DNA.
The research is reported online today in the journal Science.
"This is an important step both scientifically and philosophically," Dr Venter told the journal. "It has certainly changed my views of definitions of life and how life works."
The team now plans to use the synthetic organism to work out the minimum number of genes needed for life to exist. From this, new microorganisms could be made by bolting on additional genes to produce useful chemicals, break down pollutants, or produce proteins for use in vaccines.
Julian Savulescu, professor of practical ethics at Oxford University, said: "Venter is creaking open the most profound door in humanity's history, potentially peeking into its destiny. He is not merely copying life artificially ... or modifying it radically by genetic engineering. He is going towards the role of a god: creating artificial life that could never have existed naturally."
This is "a defining moment in the history of biology and biotechnology", Mark Bedau, a philosopher at Reed College in Portland, Oregon, told Science.
Dr Venter became a controversial figure in the 1990s when he pitted his former company, Celera Genomics, against the publicly funded effort to sequence the human genome, the Human Genome Project. Venter had already applied for patents on more than 300 genes, raising concerns that the company might claim intellectual rights to the building blocks of life.
Some lizards escape predators by "dropping" their tail, but the experience appears to leave its mark. After losing their tail, lizards end up with damaging changes to their DNA.
The parts affected are the telomeres – stretches of DNA that cap the ends of chromosomes. Telomeres naturally shorten as cells divide, and shortened telomeres are associated with the effects of ageing. In humans, shortened telomeres are linked to increased risk of heart disease and dementia.
The changes in the telomeres found in lizards that have experienced a close call adds to the evidence that environmental stress has negative effects by eroding telomere length.
To better understand this, Mats Olsson of the University of Wollongong in New South Wales, Australia, and colleagues measured the telomeres of wild sand lizards, Lacerta agilis. They found that telomere length was affected in animals that had dropped their tails to escape attack – especially in males.
Lizards that had been attacked recently were more likely to have shorter telomeres, and this effect was stronger in larger males than in both smaller males and females.
Larger males live more stressful lives than smaller males: they have more contests for female partners and are attacked by more predators. They also have higher levels of corticosteroids than smaller males. The larger lizards reap the reward for their efforts by having greater reproductive success.
Losing their tails, reduces lizards' future survival chances because the regrown tail is an inferior version of the original: it contains no bones, only cartilage, so can't be dropped again. Losing their tail also prompts a shift in behaviour, as the lizards adopt a less active lifestyle.
"Males 'in the fast lane' would be predicted to become more stressed during the mating season, and that is exactly what we see," says Olsson. Females, on the other hand, naturally live a quieter life, under relatively little pressure from predators compared with males.
"Telomere shortening is a more tangled pattern than previously thought," says Steve Donnellan, a molecular biologist at the South Australian Museum who was not involved in the work. We know the rate of telomere loss varies greatly between individuals, and that stress has a role, but we don't know specific factors, Donnellan says. "Here the researchers have identified the very specific causes of stress, seen in males as opposed to females."
A US medical diagnostics company on Tuesday promised to appeal a court ruling overturning its right to patent DNA sequences used to protect its genetic test for detecting breast and ovarian cancer.
Experts say the judgment could threaten some companies’ business models to develop new diagnostics for medical treatment.
Peter Meldrum, president and chief executive of Myriad Genetics, said he was “disappointed” at Judge Robert Sweet’s decision this week in a New York federal district court, and said he would “vigorously” defend his case in the federal appeals courts.
The action marks the latest twist in a long-running series of legal battles in the US and elsewhere over the rights of companies to seek intellectual property protection on DNA.
While some specialists argue that patents are important to persuade companies to invest large sums in genetic analysis and to stimulate innovation to improve treatment, many have criticised the tactic, including Francis Collins, the researcher who runs the US National Institutes of Health.
Richard Gold, from the Centre for Intellectual Property Policy at McGill University in Canada, said: “If this decision were to be upheld, it would lead to the invalidation of a large number of gene patents – perhaps most – as well as patents over proteins and even some chemicals.
“Myriad is not the only player here. It is clear that companies such as PGxHealth are following a similar path. In my view, the industry has nobody to blame but themselves. Neither they nor university tech transfer have taken seriously the concern by policymakers.”
The American Civil Liberties Union questioned in court 15 claims on seven patents owned or exclusively licensed to Myriad, although the company said before the appeal that 164 additional claims under these patents were not challenged. It also held that an additional 16 patents went unchallenged.
The European patent office in late 2008 upheld Myriad’s rights over its diagnostic test established in a landmark 2001 patent, and overturned a 2004 judgment revoking its rights to the sequenced BRCA1 gene and an associated test licensed from the University of Utah.
While other diagnostic companies developing tests have since received patents and have licensed the technology to others to ensure their widespread use at low cost, Myriad has always kept tight control, insisting that all samples from patients must be sent to its own laboratories or to those of affiliated parties for testing.
Its policy triggered concerns about privacy and the unauthorised use of patient data, as well as worries about the costs of handing over the testing to Myriad’s laboratories. France has since amended legislation to give it the right to override the patent, while other European countries, including the UK, conduct testing using the techniques identified by the company but refuse to pay royalties.
RARE snippets of genetic material locked inside fragments of bone and teeth can help identify people who die at war or sea, even when little remains of their bodies. But often there simply isn't enough DNA to be sure. A new technique, recently used to identify the Titanic's "unknown child", could make it easier for bereaved families to get a positive ID.
To extract DNA, researchers mix ground-up fragments of tooth or bone with a solution containing a chemical called EDTA, which removes calcium from bone. Mike Coble of the US Armed Forces DNA Identification Laboratory in Rockville, Maryland, and his colleages increased the concentration of EDTA and added an enzyme called pro-K, which breaks down the crystallised clumps of protein that lock DNA away in bone (Forensic Science International: Genetics, in press). The net effect, says Coble, was to "liberate" more DNA, increasing the chances of identifying remains.
In the case of the unidentified child who died in the Titanic disaster, the new technique enabled Ryan Parr of Lakehead University in Ontario, Canada, to say that the remains were most probably not those of Eino Panula - as initially thought - but another child, Sidney Goodwin.
However, as with most identifications, Goodwin's relies on DNA from mitochondria, because it is more abundant than DNA from cell nuclei. Nickolas Papadopoulos of the Howard Hughes Medical Institute in Baltimore, Maryland, cautions that excluding someone on the basis of mitochondrial DNA (mtDNA) alone might be a mistake.
In a study published this week, his team shows that mtDNA can vary within different tissues of the same individual. Previously it had been assumed that mtDNA was the same in every cell (Nature, DOI: 10.1038/nature08802). "It doesn't mean that you can't use mtDNA, it just means that you have to be careful about who you exclude," says Papadopoulos.
Other evidence, like shoes found with the body, suggests that the child was indeed Goodwin. In future, though, Coble's technique should reduce the reliance on mitochondrial matching, as it will often be possible to extract sufficient amounts of nuclear DNA from badly damaged remains.
"In battlefield remains, often all you end up with is bone and teeth," says Louis Finelli, director of the US Department of Defense DNA Registry. "In most cases we weren't getting anything but mtDNA, but this technique means we can use more of the bone and as a result pull out more DNA."
That should come as welcome news to the thousands of families still waiting to find out about loved ones following conflicts like the Vietnam and second world wars. "For them, the wounds are as fresh as if it had occurred yesterday," says Finelli.
Can't lose weight on a low-fat diet? Maybe you need to cut carbs instead, and a new genetic test may point the way, maker Interleukin Genetics Inc reported on Wednesday.
The small study of about 140 overweight or obese women showed that those on diets "appropriate" for their genetic makeup lost more weight than those on less appropriate diets, researchers told an American Heart Association meeting.
"The potential of using genetic information to achieve this magnitude of weight loss without pharmaceutical intervention would be important in helping to solve the pervasive problem of excessive weight in our society," Christopher Gardner at Stanford University in California, who worked on the study, said in a statement.
Massachusetts-based Interleukin's $149 test looks for mutations in three genes, known as FABP2, PPARG and ADRB2.
The company says 39 percent of white Americans have the low-fat genotype, 45 percent have the type that responds best to a diet low in processed carbohydrates and an unlucky 16 percent have gene mutations that mean they have to watch both fat and processed carbohydrates.
The researchers randomly assigned around 140 women to one of four diets -- the low-carb Atkins diet, the ultra low-fat Ornish diet, the very low-fat LEARN diet or the more balanced Zone diet.
Interleukin went back and tested about 100 of the women for their DNA by using a cheek swab and then looked to see if the women on the "right" diets lost more weight.
MOST EFFECTIVE MATCHES
Over a year, people on diets appropriate to their genetic makeup, as determined by the test, lost 5.3 percent of body weight. People on mismatched diets lost 2.3 percent, the Stanford researchers told the meeting.
Cholesterol levels improved in line with weight loss, they said.
The company said the test looks for genes that affect metabolism.
"One of the gene variations affects absorption of fats from the intestine," Ken Kornman, chief scientific officer at Interleukin, said in a telephone interview. He said people with that particular mutation absorb more fat from their food and thus should avoid fat if they want to lose weight.
Another of the variations affects insulin response -- the body's production of insulin to metabolize sugar, he said. Simple carbohydrates such as sugar and processed flour stimulate people with that particular gene type to store more of the energy as fat.
Ten percent to 16 percent of people have both mutations, and must watch both carbs and fat, Kornman said.
"What we don't know is if they are on the right diet for their genotype whether it affects satiety or feeling full," he said. He said the company planned broader studies to ask these questions.
Interleukin markets the test under the brand name Inherent Health. It also can test who might best lose weight in response to exercise.
A personalized blood test can tell whether a patient's cancer has spread or come back, offering a better way to see if treatments are working, U.S. researchers said on Thursday.
Having a test that can detect tumors in the blood could help doctors customize cancer treatments, offering more aggressive therapy to some patients while sparing others from unneeded chemotherapy or radiation.
"We're talking about what could be a management tool for a number of patients," said Dr Bert Vogelstein of Johns Hopkins University in Baltimore and the Howard Hughes Medical Institute, who worked on the study published in the journal Science Translational Medicine.
The gene-based test takes advantage of rapid advances in the technology to sequence whole genomes -- all of a person's genetic code -- once a very costly and time-consuming task.
"This is really personalized medicine. This is not something off the shelf," Vogelstein said in a telephone interview. "This is something that has to be designed for each individual patient."
For the study, the researchers took six sets of normal and cancerous tissue from four colorectal and two breast cancer patients, and mapped out the genetic code in each.
In the cancer samples, the team looked for areas in the genetic code where there were extra DNA copies, or where sections of chromosomes had fused together.
"There are about nine or so rearrangements on average in every sample," Dr Victor Velculescu of Johns Hopkins told reporters at the American Association for the Advancement of Science meeting in San Diego. "They are not present in the normal tissue."
Once the team had identified a genetic signature of the tumor, they looked in patients' blood to see if they could find remnants of DNA that had been shed from the tumor.
They found it in two patients with colorectal cancer.
After these patients had surgery to remove their tumors, levels of the tumors' genetic signature or biomarker, fell, but later returned, suggesting that the cancer remained in the patients' bodies. After a second surgery and a round of chemotherapy, the cancer biomarker levels fell again.
The team thinks the blood tests could be used in cancer patients to detect tumors before they grow big enough to be spotted on imaging machines.
Right now, the test is too costly to be practical.
"It costs right now about $5,000 to do it," Vogelstein said. "There is no question in a couple of years that cost will come down by tenfold at least. Then, a test like this will cost less than an MRI or CT scan," he said.
Velculescu said the test could be available to a broad number of patients in as few as two years.
Meanwhile, the team plans to keep refining the technology and has filed for patents for the blood test.
Nearly every person who has had their entire genome sequenced will gather in a single room near Boston on April 27. It’s the last time this will ever happen.
Within a year, the dozen or so people in this elite group will have been joined by a thousand or more people. Soon after that, hobbyists may be roaming the streets with handheld DNA analyzers, high school athletes may experiment with gene therapy to enhance their performance and pharmacists might check our genetic records before filling prescriptions.
“There was a time that only guys in white labcoats had the credentials and training to operate computers,” said Jason Bobe, co-organizer of the GET conference, where the fully sequenced group will meet. ”Nowadays, we’re all experts to some degree. This is happening in genetics too.”
Bobe hopes to recruit 100,000 people to donate their genetic information to create a public database for medical research.
The next five years will bring massive genetics experiments and breakthroughs in personalized cancer treatment, according to Harvard University geneticist George Church. Doctors will test medications on stem cells derived from their patients to check whether they will work.
The first human genome sequence, finished in 2003, cost an estimated $2.7 billion. Today, the price has dropped below $1,500 for a complete sequence, and it’s on the way to becoming so inexpensive that most everyone will be able to afford it.
But it’s not clear how we will use all of that information. Personalized medicine may be the most important use of DNA analysis, but many industries will be affected by the plummeting costs of gene reading equipment.
“Lets not overlook the ways that genomics will be incorporated into other aspects of our lives,” Bobe said, “like our foods, our households, our backyards, consumer goods, our identities and social interactions.”
The shelves of most big grocery stores are already lined with products that contain genetically modified vegetables. Students have used DNA bar code analysis to identify fake tuna in fancy sushi restaurants. And anyone can sign up for a dating website that matches people based on their genetic traits.
“Genetics know-how will have spread even faster than the rise of computers from obscurity in 1980 to access for everyone today, even in developing nations,” Church said.
Access to the event, however, will be limited. Only two-hundred people can attend, and tickets will cost $999. But anyone will be able to watch video clips of the best discussions for free.
Genetic abnormalities -- missing DNA or duplicate DNA -- that fuel the growth of one type of cancer may actually be at work in several others, U.S. researchers said on Wednesday.
The finding, based on a large-scale study of the genetic make-up of 26 different types of cancers, suggests cancer has less to do with where in the body it occurs, and more to do with the genetic changes that cause it to grow.
"A lot of the events that cause cancer are common between cancers of different tissue types," said Matthew Meyerson of the Dana-Farber Cancer Institute and the Broad Institute of Harvard and the Massachusetts Institute of Technology in Boston, whose study appears in the journal Nature.
"You have breast cancer, lung cancer, cancer of the kidney -- many of the events that cause these cancers are going to be the same," Meyerson said in a telephone interview.
"What that means for treatment is that many treatments may be used across many different kinds of cancers."
The finding is based on an effort started in 2004 to systematically map the genetic changes across different types of cancers.
The team focused on specific aberrations in the genetic code known as somatic copy-number alterations, in which segments of a tumor's genome contain extra copies of a piece of DNA or lack the segment altogether.
For the study, the team collected more than 2,500 cancer specimens representing more than 24 cancer types, including lung, prostate, breast, ovarian, colon, esophageal, liver, brain and blood cancers.
They combined this with publicly available data from another 600 tumor samples.
"What we're seeing here is that the copy number events that are happening in some of one cancer type are happening in some of another cancer type," Meyerson said.
Out of 17 different types of cancer, they found that most copy number changes -- either extra or missing DNA -- were present in more than one type.
For drug companies, Meyerson said the finding suggests that rather than developing drugs to treat a specific type of cancer, companies may need to focus on drugs that target genetic changes that drive cancer growth.
"In principle, there could be broader drugs that could be effective against many cancers," he said.
Gene tests that combined over 100 genetic mutations proved ineffective at predicting a woman's risk of a heart attack or stroke, U.S. researchers said on Tuesday.
They said high cholesterol, high blood pressure and a family history of heart disease were the strongest predictors of a woman's heart disease risk.
Many variations of genes have been identified that are associated with a higher risk of heart disease, but combining them into a risk prediction score did not help researchers find which women in a study of 19,000 participants would eventually develop the disease.
They found that after adjusting for traditional heart risk factors, a genetic risk score that combined 101 so-called single nucleotide polymorphisms or SNPs -- a single-letter change in the genetic code -- was not useful in predicting heart disease risk.
For years, teams have been using a tool called a genome-wide association study, in which researchers compare the genomes of people with a disease to those of healthy people, to look for common genetic differences that could help predict disease.
"While multiple genetic markers associated with cardiovascular disease have been identified by genome-wide association studies, their aggregate effect on risk beyond traditional factors is uncertain, particularly among women," Nina Paynter of Brigham and Women's Hospital in Boston, and colleagues wrote in the Journal of the American Medical Association.
The team developed two genetic risk scores based on genetic markers known to be associated with either heart disease or factors that cause heart disease, such as high cholesterol.
During follow-up, women in the study had 199 heart attacks, 203 strokes, 63 deaths from heart disease and 312 procedures to open blocked arteries.
After adjusting for traditional heart disease factors, such as blood pressure and total cholesterol, the genetic risk score was not associated with heart disease risk.
Instead, they found that family history of an early heart attack was one of the biggest independent risk factors.
"Our findings confirm the importance of family history of cardiovascular disease, which integrates shared genetics, shared behaviors, and environmental factors," Paynter and colleagues wrote.
"While the importance of genetic data in understanding biology and etiology is unchallenged, we did not find evidence in this study of more than 19,000 women to incorporate the current body of known genetic markers into formal clinical tools for cardiovascular risk assessment," they wrote.
British scientists say they have developed a way of pinpointing variations in a person's genetic code using a chemical test on saliva, meaning quick, cheap DNA tests for risks of certain diseases may be around the corner.
Researchers at Edinburgh University said their technique, based on chemical analysis, can deliver reliable results without the need for expensive enzymes used in conventional DNA testing.
Juan Diaz-Mochon of the university's School of Chemistry, who led the research, said the chemical method was able to detect genes linked to cystic fibrosis in laboratory experiments using synthetic DNA.
With funding from commercial partners and the Scottish Enterprise fund, he said his team planned to market a cystic fibrosis test very soon and then run further research to see if the same method could be used to decode entire human genomes.
"We're hoping to bring the first test for cystic fibrosis to the market within five months," he told Reuters. "With the scientific data we already have, we believe we can develop this test further and in different ways."
Tests which identify tiny variations or omissions in DNA code are increasingly being developed and marketed as ways of determining whether or not a person is healthy, susceptible to disease, or has a disease or serious risks of developing one.
Cystic fibrosis, a life-threatening inherited disease in which internal organs such as the lungs and digestive system become clogged with thick sticky mucus, is one of a small number of diseases caused by a single, identifiable faulty gene.
Companies around the world are racing to develop ever faster and cheaper gene sequencing techniques to offer scientists and drug developers swifter routes mapping whole genomes.
U.S. firm Illumina launched its latest genome sequencing tool, HiSeq 2000, in January and challenges rivals at Life Technologies, Roche, Affymetrix, Agilent Technologies and Helicos BioSciences.
Experts say the "holy grail" for such firms is to be able to decode a person's entire genetic sequence for $1,000.
Diaz-Mochon said the his chemical method would offer a "speedy, cost-efficient alternative" to existing DNA analysis.
"The market for DNA testing is quickly expanding as it becomes more affordable. Our method could help reach the goal of complete genome analysis in a few hours for less than $1,000," he said in a commentary about the study, which was published in the journal Angewandte Chemie and funded by Scottish Enterprise.
Mark Bradley, who also worked on the study, said the team planned to extend their collaborations with researchers and companies working in DNA "and establish our first commercial operations within the next six months."
Brain cells can be switched on and off like light bulbs using newly identified microbial proteins that are sensitive to the colour of laser light.
The discovery is the latest in the fast-moving field of optogenetics, which has already given researchers unparalleled control over brain circuits in laboratory animals. The technology may lead to treatments for conditions such as epilepsy, Parkinson's disease and blindness. New Scientist explains the science and its promise.
How do scientists control brain cells with lasers?
Neurons fire when electrically charged atoms – ions – flood in and out of them, creating a tiny electric potential across their membranes. In 2005, a team at Stanford University in California reported that light-sensitive microbial proteins that also move ions can cause the same changes when they are genetically engineered into neurons.
One algal protein, channelrhodopsin-2, turns neurons on when bathed in blue light, while its foil, halorhodopsin, silences neurons under yellow light.
If these proteins are already around, what's new?
Channelrhodopsin-2 works swimmingly: it recently helped identify a brain circuit that, when activated, may ease symptoms of Parkinson's.
However, halorhodopsin has fallen short of hopes. The protein fails to fully silence neurons and grows sluggish after repeated cycles of light, says Ed Boyden, a neuroscientist who worked on both proteins at Stanford with his colleague Karl Deisseroth: "It didn't work very well and it hasn't found much of an application."
Now, Boyden's team at the Massachusetts Institute of Technology has discovered two new light-sensitive proteins that are up to the task, at last offering an on/off switch for brain cells. "We can do digital shutdown of neurons," he says.
Why is that useful?
For one, the new proteins give researchers the power to tease out how specific brain circuits underlie behaviour, Boyden says. They can be genetically engineered into specific kinds of neuron, such those involved in forming certain kinds of memories. These cells could then be turned off in laboratory animals to see how their behaviour changes.
Furthermore, one of the newly discovered proteins, called Mac, shuts off neurons under blue light instead of yellow. By expressing Mac in one cell type and a yellow-sensitive "off switch" protein in another, it would be possible to independently silence two sets of neurons that originate in a single area, such as the prefrontal cortex, but dart off to different parts of the brain.
Will optogenetics ever be used to treat diseases in humans?
It's hard to say. However, clinical trials may begin in the next decade, says Boyden, who is involved in a company, Eos, that aims to use optogenetics to treat blindness. Another fledgling firm is hoping to apply the technology to spinal cord injuries.
The success of these efforts will depend on the ability to safely and effectively send genes and light to neurons – no easy feat.
Even if human brains never come under the control of lasers – as those of flies, mice and even monkeys now have – optogenetics will almost certainly lead to medical breakthroughs, Boyden contends.
If optogenetic research can establish the brain circuits disturbed in neurological and psychiatric illnesses, these cells could be targeted with drugs or more established technologies such as deep brain stimulation. "We can use these tools for real principles of treatment," he says.
Rogue genetic elements previously dismissed as "junk" DNA may play a role in the development of some cancers, or at least act as a marker of the disease's progression.
That's the conclusion of a study that found that some recurrent DNA sequences previously thought to be nothing more than molecular parasites appear to be active, but only in breast and colon cancer cells.
"If this 'junk' DNA does turn out to play a role in cancer then we could be at the tip of the iceberg in understanding a completely new mechanism behind the disease," says Cristina Tufarelli at the University of Nottingham in the UK.
Only about 3 per cent of the human genome actually encodes instructions into RNA for making proteins. Much of the rest has no apparent role and is often dismissed as junk. Sometimes, however, what seems like junk later turns out to have a function after all.
About 17 per cent of our DNA is made up of recurrent sequences called L1 elements that have colonised the genome by making copies of themselves and inserting these into new locations. Many geneticists had dismissed L1 elements as molecular parasites that do nothing but further their own survival, but recent studies have hinted that they are sometimes transcribed into RNA too.
To investigate if there might be differences in the transcription of L1 elements in cancerous cells, Tufarelli and her colleagues compared RNA transcripts in human breast cancer cell lines with those found in normal breast cells.
They found two L1 RNA transcripts that were present in both cell lines and five that were present only in the breast cancer cells.
A similar analysis on colon cancer cell lines and normal colon cells also revealed some L1 elements that were only transcribed in the cancerous cells.
What's more, three of the L1 RNA transcripts found in the colon cancer cells were only found in the most aggressive cancers, suggesting that they may be linked to the progression to a more invasive type of tumour.
Since L1 elements have previously been found on DNA next to or even within some tumour-suppressor genes, Tufarelli suggests that they might influence the progression of cancer by reducing, or down-regulating, the expression of these genes.
The next step is to confirm whether L1 elements are driving cancer, or whether the L1 transcripts found in tumours are simply the result of the cancer itself.
If they are driving it, drugs could be developed that target specific L1 elements, potentially slowing cancer progression. Even if they are innocent by-products, they might be useful in diagnosing or monitoring the disease.
"We are learning more about the genes involved in cancer but these so-called 'junk' regions receive relatively little attention," says Lesley Walker, director of cancer information at Cancer Research UK, which funded the research. "We are beginning to see that they could play a really important role."
Enticed by millions of dollars in tax breaks and a location close to universities and federal agencies, officials with the Ignite Institute for Individualized Health, a nonprofit organization specializing in DNA research, announced that the center's facility would be in a 300,000-square-foot campus in the Northern Virginia suburb. A location has not been selected.
The institute's founder, California geneticist Dietrich Stephan, said the institute would create 415 jobs in the region over the next five years and would partner with Fairfax-based Inova Health System, the community hospital company where Stephan will serve as an executive director.
"This is the place where personalized medicine will take root and flourish," Stephan said.
Virginia Gov. Timothy M. Kaine (D) was on hand for Monday's announcement, along with Gov.-elect Robert F. McDonnell (R). Kaine called the Ignite center "not just a catalyst but an accelerator of biotechnical expertise in Virginia."
San Francisco and Boston were also considered as potential sites for the lab, but Stephan said the Washington area was a "perfect fit," with its educated workforce and proximity to the nation's capital.
Research at the Ignite Institute will focus on personalized medicine using patients' molecular blueprints -- a rapidly developing industry in which therapies can be "made to order" for diseases such as Alzheimer's, autism, cancer and diabetes. Drugs can be chosen based on their interaction with specific genes, and gene analysis, or genotyping, can screen for congenital conditions years before symptoms crop up. At Ignite, doctors and researchers will work side by side in an attempt to create drugs and medical devices, said J. Knox Singleton, Inova's president and chief executive.
Ignite will differ from similar facilities in that it will focus more on the practical applications of its DNA research, said Timothy A. McCaffrey, professor and vice chairman of the Department of Biochemistry and Molecular Biology at George Washington University's School of Medicine and Health Sciences.
"While this DNA research has matured, many doctors have been slow to integrate it," McCaffrey said. "You have to remember, there's a lot of physicians out there that were trained when Watson and Crick first discovered the DNA sequence in the 1950s. So to actually incorporate this technology with patients, to me, is a game-changer."
Fairfax beat out neighboring Loudoun County in snagging the facility; Loudoun had been pursuing the project but didn't offer the financial advantages Fairfax proposed, officials said.
Fairfax County Board of Supervisors Chairman Sharon Bulova (D) touted the move as a sign the county had become a "major player" in the national biotechnology industry. She also said the institute would provide a boost to the county's commercial tax base, as did moves by Hilton Hotels and Science Applications International Corp. to Fairfax this year.
Emma Riccobena presents something of an under-informed, alarmist take on issues surrounding the UK's National DNA Database (3 October, p 29). As one of the "experts" to whom she refers, I would be delighted to respond.
Riccobena's contention that a DNA database would lead to corrupt experts framing celebrities for money applies to any other evidence type, including eyewitness testimony and CCTV, and disregards the excellent work done by scientific experts - working for the defence, in many cases - who enforce the rigorous application of science.
One way to prevent the planting of genetic material that has been stolen from a DNA database is a comprehensive national database in which only the profile - not the genetic material itself - is stored. The use of new, more advanced profiling tests can future-proof such a database, eliminating the need for tissue retention for future re-sampling. Such profiles do not include information specific to race, appearance or any genetic conditions that could be abused by any hypothetical, future, dystopian government, eliminating many of the privacy concerns such proposals often attract.
Lastly, the trustworthiness of forensic experts of all kinds is one of the hot topics in the UK forensic science community. The Forensic Science Society works to ensure that people giving evidence in our courts are qualified and competent to do so.
Gene therapy is coming in from the cold. Two boys treated three years ago with a gene therapy for X-linked ALD, the brain disease featured in the film Lorenzo's Oil, fared so well that doctors have treated a third and are now looking for adult volunteers.
"They have normal, family lives," says Nathalie Cartier of the Descartes University in Paris, France, a member of the team that pioneered the ALD gene therapy. "We want to treat more children in France and the US, and adults with the disease."
ALD is caused by a faulty gene that prompts the myelin sheath coating nerves in the brain to wear away, causing impaired speech, movement and eventually death.
Cartier and her colleagues took blood stem cells from two 7-year-old boys with ALD, infected the cells with a virus carrying a correct copy of the defective gene, then re-injected the stem cells. The boys' symptoms stabilised within 14 months and have not worsened since.
Early gene therapy trials were stopped after triggering cancer. Previously, the only treatment for ALD was an oil developed by the parents of Lorenzo Odone who died in 2008 aged 30.
Journal Reference: Science, DOI: 10.1126/science.1171242
CONTAMINATED crime-scene DNA samples that would normally be written off as forensically useless can now be rescued, thanks to amplification enzymes that tolerate pollution.
Before a profile can be obtained from a DNA sample recovered from a crime scene, it must be amplified using enzymes called polymerases. Pollutants such as tobacco or aluminium from drink cans can stop the enzyme working, but now Johannes Hedman and colleagues at the Swedish National Laboratory of Forensic Science have come up with some alternatives to the AmpliTaqGold enzyme, which is preferred by forensic labs.
The team amplified 32 polluted samples of saliva using three other polymerases regularly used to process non-forensic samples. Of these samples, 20 showed statistically significant improvements in the quality of the profile compared with using AmpliTaqGold (Biotechniques, vol 47, p 351).
Hedman suggests that employing these enzymes could be useful for samples that till now would not yield a complete DNA profile.
Nanoparticles can damage the DNA of cells some distance away, even when the cells seem safe behind an impassable barrier of tissue, new research has found.
But what does this curious finding, revealed yesterday by researchers at the University of Bristol, UK, mean about the safety of nanoparticles and medical treatments based on them? New Scientist puts the news in context.
Did the experiment represent something that could happen in my body?
The experimental set-up was entirely artificial, and nothing like it occurs naturally in humans or animals. Nor are the nanoparticles in question used in any current treatments, experimental or otherwise.
The tissue barrier, about four cells deep, was made from "BeWo" human cancer cells. They are a standard cell line that has become well adapted to lab work, making them very different to any cells found in the body.
The nanoparticles were 30-nanometre-wide beads of surgical cobalt-chromium alloy, a material used in much larger pieces to make surgical implants such as hip prostheses.
The "target" cells on the other side of the BeWo barrier to the nanoparticles were human fibroblast cells, found in skin and connective tissue.
What exactly were the results?
After a day in a lab dish, DNA damage was discovered in the fibroblasts. It wasn't extensive, but included single and double-strand breaks in DNA, and abnormal chromosome doubling in some cells. Careful checking found no leaks in the barrier, and no cobalt-chromium beads on the wrong side of it.
How could that happen?
The nanoparticles directly influenced the nearest layer of barrier cells and disrupted their mitochondria – chambers where energy is generated and stored.
That released signalling molecules – mainly the energy-transport molecule adenosine triphosphate (ATP) – which in turn triggered a cascade of biochemical messages inside the cell. That signalling storm eventually reached the other side of the barrier cell, opening channels that spread the message to the next layer of barrier cells.
This Chinese-whispers process continued until signalling molecules reached the fibroblasts, somehow damaging their DNA – the researchers don't yet know how this happened.
How do we know that's what happened?
When compounds that block the "message" channels in cell membranes were added to the dish, there was no damage to fibroblasts.
What is special about these nanoparticles that lets them do this?
Nothing, really. Further experiments showed that there are ways to transmit the ghostly messages without using nanoparticles.
Solutions containing cobalt or chromium ions caused the same damage to fibroblasts. So did using much larger particles of cobalt-chromium in place of the nanoparticles.
Might other kinds of chemicals, drugs and nanoparticles perform this trick too?
Possibly, but the only way of finding out is to test a wider range of substances using the same experimental set-up.
Hundreds of thousands of people receive cobalt-chromium implants every year, and there has been no evidence of ill effects reported.
Could the same effect occur naturally?
Possibly, but we don't know yet. "Maybe small particles like viruses or prions act through these processes too," says Patrick Case, who led the research.
Does this suggest that all nanoparticles may be unsafe?
No. There are hundreds of nanostructures under development and being tested as possible medical treatments and for other uses. It would be ridiculous to suppose that they would or could all cause this phenomenon.
What about skin creams like sunblocks that contain nanoparticles? Might they cause unknown effects below the skin?
Possibly. But again, this is such a newly discovered phenomenon that it's too soon to say. The researchers are adamant that their set-up can't and shouldn't be extrapolated to any structures in the human body.
Is more research into the new phenomenon planned?
Yes. Experiments are planned to see if other nanoparticles or chemicals can perform the same trick.
It will also be fascinating to see if signalling is possible across the body's natural barriers, such as the skin, placenta or blood brain barrier.
Much research is trying to design drug molecules able to cross such barriers, which can act as very specific filters. But it may be possible to exploit this newly discovered effect to avoid having to cross them altogether.
WASHINGTON - Want to know your entire DNA sequence? A California company has done it for as little as $1,700.
Privately held Complete Genomics says it can do a better quality, usable genome map for about $4,400 -- compared with the $100 million the Human Genome Project spent to complete the first sequencing of the human genome in 2000.
"Whole-genome sequencing costs have dropped from the more than $100 million cost of the first human genomes to the point where individual labs have generated genome sequences in a matter of months for material costs of as low as $48,000," the company's Radoje Drmanac and colleagues reported in the journal Science.
"This high-quality, cost-effective approach to genome sequencing will allow researchers to study complete genomes from hundreds of patients with a disease to advance the understanding of the genetic causes of that disease, with an end to preventing and treating common human ailments," said Cliff Reid, chief executive officer of Complete Genomics.
Two of the people whose DNA was mapped had taken part in an international sequencing project called the International HapMap project -- a man of European descent and a Yoruban female.
The third came from a white man taking part in the Personal Genome Project, an online registry in which people are asked to donate both their DNA and a little money.
Genome sequencing is still early stage science. While researchers can get the code, figuring out what it means is a different matter.
Genomics pioneer Craig Venter had his own genome sequenced -- at a cost of "several million" dollars -- and found the analysis could only show he was likely to have blue eyes, for instance. Venter does have blue eyes.
Last month Pauline Ng of the J. Craig Venter Institute in San Diego and Sarah Murray of Scripps Translational Science Institute in La Jolla, California, tested kits provided by California-based firms Navigenics Inc, a private company, and 23andMe, backed by Google Inc.
They found they varied in predicting disease risk.
Complete Genomics and The Institute for Systems Biology said earlier this week they plan to sequence the genomes of 100 people to try and find insights into Huntington's disease.
Scientists also use a technique called genome-wide association to try to find genes that no one suspected were involved in various diseases.
