Intermune Ex-CEO Harkonen Sentenced to Home Confinement in Fraud Case – Bloomberg

Intermune Ex-CEO Harkonen Sentenced to Home Confinement in Fraud Case – Bloomberg: Former InterMune CEO Scott Harkonen has been sentenced to six months of home confinement and ordered to pay a $20,000 fine for his part in disseminating a misleading press release in 2002. He also received three years’ probation.

Harkonen was at the helm when the developer distributed a press release stating its bone and immune disorder product Actimmune extended the lives of patients with a fatal lung disease known as idiopathic pulmonary fibrosis (IPF). The release maintained Actimmune reduced deaths by 70 percent in people with less severe forms of the disease. But the FDA never approved Actimmune for IPF. Even though doctors can prescribe medicines off-label, it’s illegal for drugmakers to market their products for unapproved uses. The company settled the off-label marketing case for $36.9 million in 2006; three years later Harkonen was convicted of wire fraud.

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The federal government wanted Harkonen to face a 10-year prison sentence, but his attorney told Bloomberg that prosecutors were unable to prove that anyone had been harmed by the misinformation. He added that the former exec plans to appeal the sentence.

- here’s the Bloomberg article

Read more: Ex-CEO of InterMune sentenced in fraud case – FierceBiotech http://www.fiercebiotech.com/story/ex-ceo-intermune-sentenced-fraud-case/2011-04-15?utm_medium=rss&utm_source=rss#ixzz1KYjmTfhb
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(Via bnet pharma.)

Beware of Fraudulent Weight-Loss ‘Dietary Supplements’

Beware of Fraudulent Weight-Loss ‘Dietary Supplements’: Magic diet pill!
Melt your fat away!
Diet and exercise not required!

Messages like these on weight-loss products taunt consumers looking for a quick and easy way to shed pounds.

But these products don’t live up to their claims. Even worse, they can cause serious harm, say federal regulators, who have found dozens of products being touted as dietary supplements but that actually contain hidden prescription drugs or compounds that have not been adequately studied in humans.

“These products are not legal dietary supplements,” says Michael Levy, director of the Food and Drug Administration’s (FDA’s) Division of New Drugs and Labeling Compliance. “They are actually very powerful drugs masquerading as ‘all-natural’ or ‘herbal’ supplements, and they carry significant risks to unsuspecting consumers.”

“We have seen deaths associated with these weight-loss products,” adds Levy. “Make no mistake—they can kill you.”

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Tainted Products

FDA has found weight-loss products tainted with the prescription drug ingredient sibutramine. This ingredient was in an FDA-approved drug called Meridia, which was removed from the market in October 2010 because it caused heart problems and strokes. FDA has also found other prescription drug ingredients that have been removed from the market or never approved at all.

“We’ve found other weight-loss products marketed as supplements that contain dangerous concoctions of hidden ingredients including seizure medications, blood pressure medications, and other drugs not approved in the U.S.,” says Levy.

Many of these tainted products are imported and sold through the Internet, but some can also be found on store shelves. FDA has made it a priority to seek out these dangerous products, stop them from being imported, and take legal action against firms that manufacture and distribute them.

But the problem is so big that FDA needs help. The agency is reaching out to the dietary supplement industry to help eliminate the availability and sale of these products. And FDA is enlisting the help of consumers.

“We also need consumers to be aware of these dangerous products and to learn how to identify and avoid them,” says Levy. (See FDA’s Web page7 and video on how to recognize fraudulent weight-loss products and claims.)

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Don’t Fall for Fraud

Look for potential warning signs of tainted products, such as

* promises of quick action, such as “lose 10 pounds in one week”
* use of the words “guaranteed” or “scientific breakthrough”
* labeled or marketed in a foreign language
* marketed through mass e-mails
* marketed as an herbal alternative to an FDA-approved drug or as having effects similar to prescription drugs

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Advice for Consumers

Generally, if you are using or considering using any product marketed as a dietary supplement, FDA suggests that you

* check with your health care professional or a registered dietitian about any nutrients you may need in addition to your regular diet
* ask your health care professional for help distinguishing between reliable and questionable information
* ask yourself if it sounds too good to be true
o Be cautious if the claims for the product seem exaggerated or unrealistic.
o Watch out for extreme claims such as “quick and effective” or “totally safe.”
o Be skeptical about anecdotal information from personal “testimonials” about incredible benefits or results obtained from using a product.

If you suspect a dietary supplement sold online may be illegal, FDA urges you to report that information online8. You or your health care professional can also report an illness or injury you believe to be related to the use of a dietary supplement by calling 1-800-FDA-1088 or visiting FDA online9.

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Dietary Supplements and FDA

Dietary supplements, in general, are not FDA-approved. Under the law (Dietary Supplement Health and Education Act of 1994), dietary supplement firms do not need FDA approval prior to marketing their products. It is the company’s responsibility to make sure its products are safe and that any claims are true.

Just because you see a supplement product on a store shelf does NOT mean it is safe or effective. When safety issues are suspected, FDA must investigate and, when warranted, take steps to have the product removed from the market. However, it is much easier for a firm to get a product on the market than it is for FDA to take a product off the market.

FDA has worked with industry to recall more than 40 products marketed for weight loss with potentially harmful ingredients, and has issued consumer alerts about dozens more. The agency also has issued warning letters, seized products, and criminally prosecuted people responsible for these illegal diet products.

FDA cannot test all products on the market to identify those that contain potentially harmful hidden ingredients. FDA has created an RSS feed10 to alert consumers more rapidly when FDA finds a tainted product.

This article appears on FDA’s Consumer Updates page11, which features the latest on all FDA-regulated products.

Posted March 15, 2011

(Via FDA Consumer Health Information Updates.)

HP speeds drug discovery research with inkjet technology

HP speeds drug discovery research with inkjet technology: HP high-performance inkjet dispensing technology is now being used to speed the evaluation of how potential drug compounds impact biologic agents like cancer cells at very low concentrations. This new capability can help researchers significantly improve accuracy when evaluating drug safety and effectiveness, testing for drug interactions and developing new drugs.

HP’s methodology also can decrease expensive labware and biological fluid waste associated with complex, conventional testing methods, reducing research costs. The process also can improve productivity by eliminating many time-consuming and tedious steps in the drug discovery process.

HP is working with several leading pharmaceutical companies to incorporate its dispensing technology into their own work flows with very promising results.

“HP is leveraging a nearly 30-year history in inkjet technology development to address non-print markets under its own brand for the first time,” said Mark Hanley, president of IT Strategies, an inkjet technology research firm. “Inkjet technology brings the same efficiencies to the drug discovery process that it brought to printing, allowing for on-demand, small-volume, high-precision production at costs significantly lower than existing analog processes.”

Bringing new value to the pharmaceutical industry

Pharmaceutical companies invest nearly $16 billion in drug discovery research each year, evaluating novel chemical compounds as potential drugs to prevent or treat diseases such as diabetes or cancer.

“Current methods for drug dosing rely on costly manual or automated processes, which are time consuming, error prone and wasteful,” said Kathy Tobin, vice president and general manager, Specialty Printing Systems, HP. “Our inkjet ‘scalable printing technology’ can precisely and rapidly dispense droplets that have one-third the width of a human hair, offering pharmaceutical companies the high-performance dispensing necessary to streamline critical R&D processes and speed drug discovery research.”

By repurposing its most advanced inkjet technology to address the needs of this important market space, HP can quickly bring new value to the biopharmaceutical industry. HP continues to evaluate other important new market spaces, such as in-vitro diagnostics, where its inkjet technology can have a positive impact.

More information: More information about HP’s digital dispensing system is available at http://www.hp.com/ … ceDispensing

(Via physorg medicines.)

FDA approves new drug for advanced melanoma

FDA approves new drug for advanced melanoma: “Ipilimumab is the first in a new class of drugs that has been shown to offer a survival benefit for metastatic melanoma, which is often a fatal disease, and hopefully, this will lead to the development of related treatments for other cancers,” said F. Stephen Hodi, MD, director of the melanoma treatment center at Dana-Farber Cancer Institute and a lead investigator of the national clinical study of ipilimumab.

The number of cases of metastatic melanoma, considered to be one the most serious form of skin cancer, has increased during the past 30 years, and its death rate is rising faster than most other cancers. The American Cancer Society estimated that the disease was diagnosed in more than 68,000 Americans and be responsible for 8,700 deaths in this country in 2010.

Ipilimumab, developed by Bristol-Myers Squibb and Medarex, is a monoclonal antibody that consists of millions of copies of a human antibody that binds to CTLA-4 protein molecule on T cells — white blood cells that patrol the body for signs of illness. CTLA-4 serves as a control switch for the immune system’s response to disease. With no antibody attached, CTLA-4 suppresses the immune response. Ipilimumab reverses that condition, unleashing the immune attack on abnormal cells, including cancer cells.

Last year, Hodi reported at the annual meeting of the American Society of Clinical Oncology and in the New England Journal of Medicine findings from a phase III trial involving 676 patients with advanced (stage III or IV), inoperable melanoma that had worsened during prior therapy for metastatic disease.

Patients were randomly assigned to receive one of three treatment regimens: ipilimumab and the gp100 vaccine (which seeks to spark an immune response by presenting the immune system with a protein fragment associated with cancer); ipilimumab alone; or gp 100 alone.

The median survival period for patients receiving ipilimumab plus gp100 was 10 months, compared with 6.4 months for those receiving gp100 alone. The median survival for participants receiving ipilimumab alone was 10.1 months.

In the ipilimumab-alone group, nine of 15 patients continued to benefit from the therapy for at least two years, as did four of 23 patients in the combination therapy group.

About 60 percent of the patients treated with ipilimumab experienced adverse side effects to the therapy, as did 32 percent of the patients treated with gp100. The complications were generally immune system-related and most often affected the skin and gastrointestinal tract. The most common included diarrhea, nausea, constipation, fatigue, decreased appetite, and rash. While the adverse effects could be severe and long-lasting, most of them were reversible with appropriate treatment.

“While ipilimumab, on average, extended the lives of patients by four months, there is also a group of patients who experienced a greater benefit and lived many months while being treated with this drug,” said Hodi. “This is a big step in the right direction because it demonstrates that this class of drugs can benefit cancer patients.”

Provided by Dana-Farber Cancer Institute

(Via physorg cancer.)

Japanese sperm cell breakthrough offers hope to infertile men

Japanese sperm cell breakthrough offers hope to infertile men: As originally reported in Nature, Takehiko Ogawa and his team from Yokohama University have discovered that by using the right mix of chemicals (which turned out to be the commercially available KnockOut Serum – a solution made to assist in stem cell growth) they could not only keep a mouse testes sample alive, but that it would, after just a few weeks, begin to produce viable sperm cells; sperm cells that when injected into a female ovum, wound up in the delivery by surrogate, of a live healthy mouse.

Scientists have been working on the problem of producing viable sperm cells for over a hundred years, with little to no success. Until now, researchers had been able to keep testes tissue alive, but when the sperm cells reached the meiosis stage, (the point during cell division when chromosomes are swapped) things simply stopped.

In the new procedure, a testes sample was taken from the testicle of a live male mouse before it was old enough to produce sperm cells. That sample was then continuously soaked in the KnockOut solution for several weeks, and then, the sample began to produce live sperm cells; complete with head, body and tails, just as they would have had they been left in their natural state. Those mice that were born as a result so far seem normal, and were even able to reproduce as well. The team also discovered the procedure would work with a previously frozen specimen as well.

The reason this breakthrough is so important is because it might help infertile men, particularly those who as young boys lost their ability to reproduce due to cancer treatment, have children. It’s also important because it will help researches better understand how cells work; which might eventually lead to more breakthroughs in other areas.

More information: In vitro production of functional sperm in cultured neonatal mouse testes, Takuya Sato, Kumiko Katagiri, Ayako Gohbara, Kimiko Inoue, Narumi Ogonuki, Atsuo Ogura, Yoshinobu Kubota & Takehiko Ogawa, Nature 471, 504–507 (24 March 2011) doi:10.1038/nature09850

(Via physorg biotech.)

Research Vital to Economic Growth

Research Vital to Economic Growth

1. Raymond L. Orbach

+ Author Affiliations

1.
Raymond L. Orbach is Director of the Energy Institute at the University of Texas at Austin. He served as the Under Secretary for Science at the Department of Energy for President George W. Bush. He is a member of the AAAS Board of Directors.

1. E-mail: orbach@energy.utexas.edu.

Figure
“CREDIT: MARSHA MILLER/THE UNIVERSITY OF TEXAS AT AUSTIN”

It was with a mixture of astonishment and dismay that I watched as the U.S. House of Representatives approved H.R. 1, a bill to fund the federal government for the rest of the 2011 fiscal year. Left intact, the massive cuts in research contained in the bill passed on 19 February would effectively end America’s legendary status as the leader of the worldwide scientific community, putting the United States at a distinct disadvantage when competing with other nations in the global marketplace. Other countries, such as China and India, are increasing their funding of scientific research because they understand its critical role in spurring technological advances and other innovations. If the United States is to compete in the global economy, it too must continue to invest in research programs.

As the Under Secretary for Science at the Department of Energy (DOE) in the administration of George W. Bush, I can personally attest that funding for scientific research is not a partisan issue—or at least it shouldn’t be. The cuts proposed in H.R. 1 would reverse a bipartisan commitment to double the science research budgets of the National Science Foundation, the DOE Office of Science, and the National Institute for Science and Technology over 10 years. These are national goals supported by both Presidents Bush and Obama, and they were affirmed as recently as last December in the America COMPETES Act.
Figure
“CREDIT: THINKSTOCK”

The spending cuts included in the bill would have a devastating effect on an array of critical scientific research. For example, H.R. 1 removes $900 million from the budget for the Office of Science, the basic research arm of the DOE—a reduction of some 20%. The bill specifically targets the Office of Biology and Environmental Research, slicing its budget by 50%; reductions that would all but eliminate funding for the office’s three Biological Research Centers, the hope for developing transportation fuels derived from plant cellulose. The hugely successful Energy Frontier Research Centers, which support activities based at 28 universities and 16 national laboratories, would be cut in midstream. The university centers support 1300 students working on the conversion of sunlight and heat into electricity, improved efficiency of photosynthesis in plants for the production of fuels, and enhanced combustion efficiency to increase mileage for automobiles. The work now at risk at the national laboratories includes projects to improve solid-state lighting and the conversion of coal into chemicals and fuels. This research is vitally important if the United States is to be a leader in transforming how humans get and use energy globally, in a way that maintains societal and economic viability.

To make matters worse, the bill would also destabilize the large-scale scientific facilities operated by the DOE’s Office of Science. These research projects include the country’s work with powerful light sources (which other countries are copying en masse), so vitally important to the U.S. biological, medical, and materials communities. Also included are the nation’s remaining accelerators, responsible for advances in the high-energy and nuclear science communities; its spallation neutron source and nanotechnology centers, critically important to both university and industrial communities; and the quest for environmentally benign unlimited energy through investment in the International Thermonuclear Experimental Reactor.

The budget deficit is serious. But escaping from its clutches requires economic growth as well as budget reductions. Well over half of U.S. economic growth in the past century can be traced to investments in science and technology. To compete in the global economy, the United States must remain a leader in science and technology. For that to happen, the Senate must restore funding for science in the fiscal year 2011 budget. Failure to do so would relegate the United States to second-class status in the scientific community and threaten economic growth and prosperity for future generations of Americans.

Scientists discover first breast cancer ‘oncogene’ in five years

Scientists discover first breast cancer ‘oncogene’ in five years: This is the first time in over five years that scientists have discovered a new breast cancer ‘oncogene’ – cancer-causing genes that when overactive upset the normal checks and balances that control when and how often a cell divides.

The researchers, based at Cancer Research UK’s Cambridge Research Institute at the University of Cambridge and at the British Columbia Cancer Agency in Vancouver, Canada, believe testing patients tumours to see if the gene – called ‘ZNF703′ – is overactive could help identify patients with more aggressive tumours, so their treatment can be tailored accordingly.

The research is published in the journal EMBO Molecular Medicine today (Friday, 18 February) alongside a study from an independent research group identifying the same gene, providing definitive evidence that ZNF703 is a genuine breast cancer oncogene.

It’s thought that up to a third of more aggressive oestrogen positive breast cancers could have multiple copies of the ZNF703 gene.

If this is confirmed in larger studies it could pave the way for the development of cancer treatments specifically targeting ZNF703.

Testing for ZNF703 activity in the tumour could help reveal if patients are likely to respond to such drugs, in the same way that testing for Her2 activity is used to reveal if a patient may benefit from Herceptin.

To make the discovery the researchers used ‘microarray technology’, which allows large numbers of tissue samples to be tested simultaneously, picking up subtle differences in gene activity between normal cells and cancer cells.

Lead author Professor Carlos Caldas, from the Cancer Research UK’s Cambridge Research Institute and the Department of Oncology where he is Professor of Cancer Medicine, said: “Using this state-of-the-art technology we’ve been able to pinpoint the precise gene behind this more aggressive type of breast cancer.

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“Scientists first discovered this region of DNA may be harbouring genes linked to the development of breast cancer twenty years ago. But it’s only with the technology we have today that we’ve been able to narrow down the search sufficiently to pinpoint the gene responsible.

“Crucially, testing whether this gene is overactive in a patient’s tumour could help highlight those more likely to be resistant to standard hormone therapies, such as tamoxifen or aromatase inhibitors, helping to make sure the right drugs are matched to the right patient.”

Dr Samuel Aparicio, who co-led the study and is based at the University of British Columbia and British Columbia Cancer Agency in Vancouver, Canada, said: “The discovery of ZNF703, as a new ‘driver gene’ in oestrogen receptor positive breast cancer, is another product of the very fruitful and long standing collaboration with our colleagues in the UK, emphasising that the fight against breast cancer takes place at the international level, with all partners bringing their unique skills and resources.”

The researchers had already identified a region on human chromosome eight likely to harbour genes linked to the development of a more aggressive form of oestrogen positive breast cancer, because multiple copies of it are commonly found in tumours but not in healthy tissue.

Focusing on this region, they studied the patterns of gene activity in 1172 breast tumours, as well as breast cancer cells grown in the lab. This allowed them to eliminate one gene at a time until there was only one gene left within that region that was overactive in all the samples tested.

Crucially there were two patients in which ZNF703 was the only gene shown to be overactive, providing further evidence that it was the driving force in the development of the cancer.

Dr Lesley Walker, director of cancer information at Cancer Research UK, said: “This is the first gene of its kind to be discovered in breast cancer for five years. This is exciting because it’s a prime candidate for the development of new breast cancer drugs designed specifically to target tumours in which this gene is overactive. Hopefully this will lead to more effective cancer treatments in the future.”

Provided by University of Cambridge (news : web)

(Via physorg cancer.)

Scientists bioengineer a protein to fight leukemia

Scientists bioengineer a protein to fight leukemia: “Scientists at the Children’s Center for Cancer and Blood Diseases and The Saban Research Institute of Children’s Hospital Los Angeles today announced a breakthrough discovery in understanding how the body fights leukemia. They have identified a protein called CD19-ligand (CD19-L) located on the surface of certain white blood cells that facilitates the recognition and destruction of leukemia cells by the immune system. This work represents the first report of a bioengineered version of CD19-L, a recombinant human biotherapeutic agent, targeting CD19-positive leukemic stem cells.”

(Via physorg cancer.)

Sanofi-Aventis to buy Genzyme for $20.1 bln cash

Sanofi-Aventis to buy Genzyme for $20.1 bln cash: Sanofi-Aventis, the world’s fourth-largest drug maker, overcame Genzyme’s reluctance to a takeover by raising its previous offer and agreeing to make additional cash payments contingent on the success of several drugs.

The announcement comes after nearly nine months of back-and-forth between the two companies, with Sanofi-Aventis finally deciding Genzyme’s portfolio of rare disease treatments was worth stumping up an extra five dollars a share to its original $69 per share offer.

The boards of both companies unanimously approved the deal, which is expected to close early in the second quarter, Sanofi-Aventis said in a statement.

Sanofi-Aventis chief Chris Viehbacher launched a hostile takeover bid for Cambridge, Massachusetts-based Genzyme last October, only to meet stiff resistance from Genzyme’s founder and CEO Henri Termeer. The two sides have since softened their positions, with Genzyme opening its books to share confidential data with Sanofi-Aventis earlier this month, signaling a deal was near.

The agreement “will create a meaningful new growth platform for Sanofi-Aventis while expanding our footprint in biotechnology,” Viehbacher said in a statement.

Sanofi-Aventis shares rose on the announcement, and in mid-afternoon trading Paris time were up 3.5 percent at euro51.56. In U.S. premarket trading, Genzyme stock rose $1.22 to $75.52.

Termeer will step down as chairman and CEO of Genzyme following completion of the deal, but will keep a consulting role as co-chairman with Viehbacher of an integration steering committee.

Genzyme would give Sanofi a new platform for growing its biotech business, let it expand into the growing – and lucrative – market for drugs for rare diseases, increase its U.S. presence and give it more experimental drugs in mid- and late-stage testing. Those include three for high cholesterol, a huge global market. And Genzyme has said it is close to resolving manufacturing problems that have limited sales of two key drugs for genetic disorders.

Genzyme’s drugs for rare genetic disorders are in a hot niche for big pharmaceutical companies trying to diversify beyond blockbuster pills that get slammed by cheaper generic rivals after a decade or so. Genzyme won U.S. approval last May for a new drug for Pompe disease, an often fatal disorder in which limb and respiratory muscles steadily weaken. Its experimental drug for multiple sclerosis is getting an expedited U.S. review.

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Genzyme’s best-seller Cerezyme treats Gaucher disease, an enzyme disorder that can result in liver and neurological problems. Its second-best seller, Fabrazyme, treats an inherited disorder known as Fabry disease, which is caused by the buildup of a particular type of fat in the body’s cells.

The deal gives Genzyme shareholders one “contingent value right” for each share owned. These CVRs give holders the right to cash payments based on Genzyme meeting certain goals, including raising production levels for Cerezyme and Fabrazyme, getting final FDA approval for multiple sclerosis treatment Lemtrada, and higher sales targets.

Genzyme says it expects three new product approvals by the end of 2013. Those are Lemtrada, a new Gaucher’s disease treatment called eliglustat, and mipomersen, which is a treatment familial hypercholesterolemia, a genetic disorder that causes high cholesterol levels.

Genzyme also reported its fourth-quarter results Wednesday. The company said its profit climbed to $471.9 million, or $1.76 per share, from $23.2 million, or 9 cents per share a year ago. Excluding items like divestiture and acquisition costs and stock based compensation expenses, its profit rose to 82 cents per share from 29 cents per share. Its revenue climbed 23 percent, to $1.15 billion from $938.3 million.

Analysts expected a profit of 85 cents per share and $1.16 billion in revenue, according to FactSet. Analyst estimates generally exclude one-time items.

The company said sales of treatments for genetic disorders rose 45 percent to $505.6 million as it rebuilt its supplies of Cerezyme and Fabrazyme, and began selling its Pompe disease treatment Lumizyme in the U.S.

©2010 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

(Via physorg biotech.)

Contamination found in nearly a quarter of genome databases

Contamination found in nearly a quarter of genome databases: A new genomics study by molecular biologists at the University of Connecticut has shown that at least 22 percent of non-human genome databases are contaminated with human DNA. Their results imply that this level of contamination could also exist in records of the human genome, which could produce major problems in identifying human diseases.

Associate professor Rachel O’Neill, graduate student Mark Longo, and associate professor Michael O’Neill of the molecular and cell biology department in the College of Liberal Arts and Sciences published their findings today in an online edition of the journal PLOS One.

Longo says that he had originally been scanning the genome of zebrafish and comparing it with the human genome to find what are called ultraconserved regions, or bits of DNA that are so ancient they are similar among species that are distantly related, like humans and fish.

But, to Longo’s surprise, he found a region of DNA that was identical to one in humans and couldn’t be a part of the fish genome. That’s when he knew that the fish genome database he was using was contaminated.

“Contamination in these databases could be from people’s skin or hair, or it could be DNA from other sequence libraries kept in the same facility,” says Longo. “We knew we needed to quantify this to see how many of the databases contained human contamination.”

The researchers gathered sequences from all the major global DNA repositories, including the archives at the National Center for Biotechnology Information, the University of California Santa Cruz, the Joint Genome Databases, and the Ensembl genome browser. Any sequencing project funded by federal funds is required to be deposited in one of these archives.

Using a section of DNA that is specific to primates and abundant in the human genome, the researchers identified 454 non-primate genomes out of the 2,027 they sampled as contaminated with human DNA.

Rachel O’Neill says this result led them to reason that if these non-human genome databases were contaminated with human DNA, then it’s just as likely that many human databases would be contaminated as well. But, she says, the catch is that it’s virtually impossible to identify a foreign bit of human DNA in a human genome database.

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“In sequencing, you have to put all the pieces of the genome together like a big jigsaw puzzle. The pieces that don’t fit stand out,” Longo says. “But if you’re working on a human puzzle, it’s like working on a three-billion piece puzzle, and it’s all black.

“It’s virtually impossible to find human contamination in human genome databases,” she adds, because they simply don’t stand out as anything unusual in a human genome. This, she says, could lead to some terrible mistakes.

A portion of the National Center for Biotechnology Information includes a Cancer Genome Atlas: a library documenting mutations that occur in cancer cells. O’Neill says there’s no room for error in these databases.

“It would be very upsetting to be told you have a mutation for breast cancer, when in fact you don’t, and it was just a contamination from another sample,” she says.

O’Neill emphasizes that scientists need to exercise extreme caution when performing their sequencing, and that they should validate results through tests in their own laboratories before submitting them to databases. Longo points out that the UConn researchers found contaminations in some sequences that they had produced in their own laboratories, which they then discarded. O’Neill says these practices should be the norm.

“We’re compounding this problem in our rush to move forward with genomics,” she says. “Millions of dollars are invested each year in these sequence databases, but we’re plowing ahead with less caution than we should. The result is that we might have a harder time recognizing the etiology of something like cancer.”

Longo notes that in his analysis, there was one type of DNA database that showed no contamination at all: that of influenza. Because viruses are so dangerous, great care is taken in their preparation, he says – much more than is usually taken with a commonplace and harmless genome. This kind of caution should be extended to all sequencing, says O’Neill.

“The sequencing world has moved in leaps and bounds,” she says. “It’s time for validation to catch up.”

Provided by University of Connecticut (news : web)

(Via physorg biotech.)