Results tagged “genetics”

Peter Aldhous, San Francisco bureau chief

A controversial programme of genetic testing intended to educate students at the University of California, Berkeley, about personalized medicine is being redesigned, following the intervention of state health officials.

In July, 5500 incoming freshmen were invited to "Bring Your Genes to Cal". Each student could volunteer to give a cheek swab, which would then be analysed in a campus lab for genes that may cause lactose intolerance, heightened sensitivity to alcohol or affect the absorption of folate, a nutrient found in large quantities in green vegetables, liver and baker's yeast.

But following a hearing on the issue in the State Assembly in Sacramento on 10 August, the California Department of Public Health has now ruled that providing results to students would constitute clinical testing, and as such needs to run by a lab accredited to run such tests. "[W]hat was meant to be a group educational exercise turned into an education for the university on the politics and policy of medical testing," observes the San Francisco Chronicle.

Ewen Callaway, reporter

The sun is about to set on the Wild West that is "direct-to-consumer" genetics.

Playing the role of sheriff is the US Food and Drug Administration (FDA), which recently sent letters to several firms, including 23andMe, DeCODE genetics and Navigenics.

The letters make clear that the FDA considers their products to be medical devices that require the agency's approval before they can be sold. It says:

"You should take prompt action to respond to this letter."

These letters come on the heels of an FDA warning to one firm, Pathway Genomics, that its tests may require approval. Congressional investigators also turned up the heat on genetics testing firms, sending their own demand for answers.

Celeste Biever, physical sciences news editor

It is highly heritable, yet autism's genetic underpinnings have remained tough to pin down. Now a study in Nature, focusing on a particular type of genetic variant, has revealed a host of new, rare genes linked to the mysterious condition.

The identification of these so-called copy number variations or CNVs - in which the number of copies of a particular gene is either vastly reduced (deletions) or increased (duplications) - should allow us to piece together the complex biochemical pathways that lead to autism.

The findings also point to the development of drugs that target these pathways, and to the first biochemical diagnostic tests. Until now, such drugs have been elusive because the biochemistry of autism was unknown, while diagnosis has relied on behavioural measures.

"These genetic findings help us understand the underlying biology of autism, which can lead to the development of novel treatments," said study author Andy Shih of Autism Speaks, a US lobbying and fundraising group, in an interview with CNN.

Peter Aldhous, San Francisco bureau chief

Imagine receiving the results of a genetic test that suggests that your son is not your son. Was there a mix-up in the maternity ward? 

Fortunately, in this case it was a slip-up in the genetics lab contracted by personal genomics company 23andMe to process its customers' samples. But the news that the Californian firm has supplied 96 people with someone else's results will add to the pressure for more regulation of this emerging industry.

23andMe's announcement is available to customers logged in on its website, who are told:

Up to 96 customers may have received and viewed data that was not their own. Upon learning of the mix-ups, we immediately identified all customers potentially affected, notified them of the problem and removed the data from their accounts. The lab is now concurrently conducting an investigation and re-processing the samples of the affected customers and their accurate results will be posted early next week. We expect the investigation will be complete over the next several days and we will provide further details when we have them.

Ewen Callaway, reporter

Human evolution is looking more tangled than ever. A new genetic study of nearly two thousand people from around the world suggests that some of our ancestors bred with other species of humans, such as Neanderthals, at least twice.

"The researchers suggest the interbreeding happened about 60,000 years ago in the eastern Mediterranean and, more recently, about 45,000 years ago in eastern Asia," Nature News reports from the annual meeting of the American Society of Physical Anthropologists in Albuquerque, New Mexico.

That conclusion is based on a study of over 600 genetic markers, called microsatellites, sequenced in nearly 100 different populations.

(Image: Ökologix / Wikimedia Commons)

Andy Coghlan, reporter

A court in New York yesterday ruled that patents on two genes linked to breast cancer are invalid.

By declaring that the genes can't be patented because they are essentially products of nature rather than inventions, the US District Court for the Southern District of New York state has effectively cast doubt on whether patents on 2000 other human genes - around 20 per cent of the total - are valid, The Times of London reports.

The American Civil Liberties Union (ACLU), which brought the case together with the Public Patent Foundation, said that the victory would stop holders of gene patents from cashing in on monopolies over chemicals such as DNA that occur in nature, and so don't qualify as patentable inventions. "The human genome, like the structure of blood, air of water, was discovered, not created," said Chris Hansen, an attorney with the ACLU.

The patents that were challenged cover variants of two genes, BRCA1 and BRCA2, which raise women's chances of developing breast cancer. Myriad Genetics of Salt Lake City, Utah, developed and patented tests that enable doctors to identify women at risk by checking whether they've inherited the variants.


 

Ewen Callaway, reporter

Whole-genome sequencing is touted as the tech that will finally unmask our genetic "dark matter" - as-yet unknown disease-drivers that are missed by current gene scans. It hasn't done that yet, but for the first time two separate groups of researchers have used it to uncover mutations underlying rare diseases. The breakthrough shows both the promise and challenges facing the field of personal genomics.

Right now, most personal genomics is based on gene scans that identify single-letter mutations in the genetic code known as SNPs, which can indicate that someone is at higher risk of various disorders. But complete genome sequences might tell us a lot more. This week's breakthroughs give us a taste of what that might be like.

One team identified a previously unknown mutation that almost certainly causes a neuromuscular disorder by sequencing the genome of one of its members, James Lupski, who has Charcot-Marie-Tooth syndrome. Mutations in more than two dozen genes have previously been linked to the diseases but Lupski, a medical geneticist at Baylor College of Medicine in Houston, Texas, is negative for all of them.

Whole-genome sequencing revealed that Lupski has two mutations in both copies of a gene called SH3TC2. The gene has previously been linked to neurological disease, but these specific mutations have not. "Lupski's three sick siblings also had both of these mutations, whereas his four healthy siblings and parents (who do not have the disease) carried only one mutated gene," ScienceNOW reports.

Linda Geddes, reporter

A personalised blood test that can identify tumour DNA could be the first step towards a long-promised revolution in the way cancer is treated.
 
In the short term, the test - reported by Victor Velculescu of Johns Hopkins Kimmel Cancer Center in Baltimore, Maryland, and his colleagues in Science Translational Medicine - could be used to spot cancer recurrence before tumour growth shows up on scans, meaning that treatment could be started earlier.

The test detects genetic rearrangements that distinguish cancer cells from normal cells. Eventually it might also pave the way for more personalised cancer treatments tailored to the genetic signature of individuals' tumours.

Doctors already classify cancers by some of the genes that get switched on by the disease, and use this to guide treatment in some cases. For example, breast cancers are often divided into those that express oestrogen receptors on their surface and are therefore likely to respond to the drug tamoxifen, and those that don't.

Michael Marshall, reporter

Bad news for single men: the odds of you finding an appropriate girlfriend on any given night out are 1 in 285,000.

At any rate, that's the conclusion of Peter Backus of the University of Warwick, UK, who carried out a tongue-in-cheek calculation of his odds of finding love and wrote it up as "Why I don't have a girlfriend: An application of the Drake Equation to love in the UK".

For the uninitiated, the Drake equation was set out by Frank Drake, one of the founders of the Search for Extraterrestrial Intelligence. It estimates the number of alien civilisations we should expect to find in our galaxy.

Jessica Hamzelou, reporter

African lions living over a million years ago may have carried an early form of HIV. Now, American microbiologists reckon they've found a feline genetic "pawprint" in the modern-day form of the virus.

Robert Bambara and his team at the University of Rochester in New York found a genetic sequence in the HIV genome that they think descended from an ancient gene.

The group reckon that, because the feline version of HIV - FIV - is an old virus, the newly discovered sequence might have been taken up by FIV from host lions or tigers over a million years ago.

Andy Coghlan, reporter

A pioneering Icelandic company set up 13 years ago to discover links between genes and disease by analysing the health records and DNA of Icelanders this week filed for bankruptcy.

Reykjavik-based deCODE Genetics discovered genes linked to diseases including osteoporosis, but its personalised DNA testing services failed to generate enough revenue to keep the company afloat.

In recent years, the scientific validity of individualised gene profiles aimed at foretelling someone's risk of disease have been challenged, undermining faith in the results from personalised DNA risk profiles. When a New Scientist reporter had deCODE Genetics generate his DNA profile, an error led to questions over whether the DNA was human.

But deCODE was at the forefront of efforts to unravel the links between inheritance and disease at a time when the first sequencing of the human genome promised a revolution in healthcare.

The blog Genetic Future has more on the financial fall out, and speculation on what would happen to genetic data in the result of a bankruptcy. 
 

Linda Geddes, reporter

A gene therapy that appears to bulk up muscle mass and strength in monkeys - reported today in Science Translational Medicine - will undoubtedly raise fresh concerns about the potential for gene doping in sport.

We already know that some athletes use drugs like erythropoietin to increase the amount of oxygen their blood delivers, and steroids to bulk up muscle mass.

The big advantage with gene doping is that it should be harder to detect. That's because it's difficult to test for a protein that the body already produces, especially when its levels naturally vary between individuals - which might explain why some people are inherently better at sports than others.

In the new study, Janaiah Kota and colleagues at Nationwide Children's Hospital in Columbus, Ohio, used gene therapy to add extra copies of the follistatin gene into the leg muscles of monkeys. Follistatin has been previously shown in mice to block myostatin, a protein that decreases muscle mass, resulting in bulked up "mighty mice".

Peter Aldhous, San Francisco bureau chief

When a biotech company fires its CEO and other senior staff, and announces that it is "no longer relying on...any of the previously announced test data" for its key product, you know it's in serious trouble.

The current woes of Sequenom of San Diego, which has just completed an investigation of "mishandled" research results, surround a new test for Down's syndrome, intended to avoid the risk of miscarriage associated with the leading current method - which involves inserting a needle through a pregnant woman's belly to extract amniotic fluid.

Sequenom is developing a test based on a simple blood sample from the expectant mother. Invented by Dennis Lo of the Chinese University in Hong Kong, the test examines RNA from part of chromosome 21 that is expressed only in fetuses. By looking at genetic markers called SNPs, it determines whether the fetus carries an extra copy of chromosome 21 from the mother or father.

Linda Geddes, reporter

A project to use DNA and isotope analysis to help evaluate the claims of asylum seekers, and decide who can enter the United Kingdom, is underway.

So says Science magazine, which obtained UK Border Agency documents showing that isotope analyses of hair and nail samples will be conducted "to help identify a person's true country of origin". A DNA-based program to identify nationality was also recently revealed by the UK newspaper The Observer.

It's not clear just what stage the project has reached, but scientists have understandably reacted with concern.

Ewen Callaway, reporter

Efforts to uncover genetic mutations that predispose people to schizophrenia have previously progressed at a snail's pace.

Common variations weakly linked to the disease in one group were rarely confirmed in others, while more potent mutations - such as those found in a gene called DISC1 - explained a paucity of schizophrenia cases.

Now, a trio of genetic studies of tens of thousands of people have identified a bevy of DNA variations that are associated with the debilitating mental illness, thought to affect about 1 per cent of the general population.

"Individually, these common variants' effects do not all rise to statistical significance," Harvard University's Shaun Purcell, says in a press release. "But cumulatively, they play a major role, accounting for at least one third - and probably much more - of disease risk."

Debora MacKenzie, consultant

With the WHO announcement that it has moved its alert to level 5, we are on the brink of a full-scale flu pandemic.

It is clear that the virus came from pigs. As we report this week, the virus comes from a tribe of flu viruses that emerged in US pigs in 1998 and became the dominant pig flu in North America. Scientists have repeatedly warned that these viruses, especially the ones with the same surface proteins as the flu that is spreading from Mexico, posed a real risk of making a species jump and becoming a human pandemic.

So what are the world's top human and animal health organisations doing? Battling to keep this from harming the pork industry.

Ewen Callaway, online reporter

Labradoodles, golden doodles and other designer dogs may be relatively new to the kennel, but dog breeders produce these animals through a decidedly old school approach: Introduce a golden retriever to a poodle and let nature take its course.

But new discoveries in dog genetics could provide dog breeders with far more control in selecting for traits such as size, colour, perhaps even temperament.

Thanks to a fully sequenced dog genome and genetic tools that allow researchers to rapidly scan hundreds of thousands of gene mutations at once, geneticists have uncovered a handful of genes that determine coat colour, variations in size, as well as some congenital diseases.

The first UK baby genetically selected to be free of a form of breast cancer - caused by a gene called BRCA1 - has been born in London.

Doctors said three generations of women in the baby girl's family had suffered from breast and ovarian cancer in their 20s, and this child will be free of that risk.

"The lasting legacy is the eradication of the transmission of this form of cancer that has blighted these families for generations," said Paul Serhal, of the Assisted Conception Unit at University College Hospital.

"We have discovered the secret of life," Francis Crick declared when he helped work out the structure of DNA. Well, not quite.

The secret of life is not so much DNA itself as the information stored in it. Much of this information - but not all of it - comes in the form of genes: the recipes for making proteins.

Where does this information come from? Put another way, how do genes evolve? How did simple cells acquire the blueprints need to make more complex animals, from the collagen that holds us together to the haemoglobin that carries oxygen in our blood to the crystallin proteins bending the light passing through your eyes as you read this?

It might all seem so unlikely at first glance, but thanks to the explosion in genome sequencing, we are increasingly able to trace the history of genes and uncover how they evolved.

As Barack Obama starts receiving briefings from the CIA ahead of his inauguration, he has some big decisions to make and promises to fulfill. As far as his daughters are concerned, chief among them will be the appointment of the new First Dog.

What breed should it be? Malia 10, wants a "Goldendoodle", a hybrid Golden Retriever and Poodle. Goldendoodles are hypoallergenic, apparently, so are popular among allergy sufferers such as Malia.

However, according to an American Kennel Club survey reported in the Chicago Tribune, voters said they would like the Obamas to adopt a purebred poodle.

Why do we care? Well, purebred dogs are notorious for suffering from genetic diseases so it might be better to break from tradition and go for a non-purebred animal. 

Incidentally, the two current First Dogs (Barney and Miss Beazley) are Scottish terriers, and have their own government website. The pedigree of the current First Cat (Willie), was not available at the time of writing.

Rowan Hooper, online news editor