Matching names to genes: the end of genetic privacy?

















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Are we being too free with our genetic information? What if you started receiving targeted ads for Prozac for the depression risk revealed by your publicly accessible genome? As increasing amounts of genetic information is placed online, many researchers believe that guaranteeing donors' privacy has become an impossible task.












The first major genetic data collection began in 2002 with the International HapMap Project – a collaborative effort to sequence genomes from families around the world. Its aim was to develop a public resource that will help researchers find genes associated with human disease and drug response.












While its consent form assured participants that their data would remain confidential, it had the foresight to mention that with future scientific advances, a deliberate attempt to match a genome with its donor might succeed. "The risk was felt to be very remote," says Laura Lyman Rodriguez of the US government's National Human Genome Research Institute in Bethesda, Maryland.












Their fears proved to be founded: in a paper published in Science this week, a team led by Yaniv Erlich of the Whitehead Institute in Cambridge, Massachusetts, used publicly available genetic information and an algorithm they developed to identify some of the people who donated their DNA to HapMap's successor, the 1000 Genomes Project.











Anonymity not guaranteed












Erlich says the research was inspired by a New Scientist article in which a 15-year-old boy successfully used unique genetic markers called short tandem repeats (STRs) on his Y chromosome to track down his father, who was an anonymous sperm donor. Erlich and his team used a similar approach.













First they turned to open-access genealogy databases, which attempt to link male relatives using matching surnames and similar STRs. The team chose a few surnames from these sources, such as "Venter",and then searched for the associated STRs in the 1000 Genomes Project's collection of whole genomes. This allowed them to identify which complete genomes were likely to be from people named Venter.












Although the 1000 Genome Project's database, which at last count had 1092 genomes, does not contain surname data, it does contain demographic data such as the ages and locations of its donors. By searching online phonebooks for people named Venter and narrowing those down to the geographic regions and ages represented in the whole genomes, the researchers were able to find the specific person who had donated his data.












In total, the researchers identified 50 individuals who had donated whole genomes. Some of these were female, whose identity was given away because of having the same location and age as a known donor's wife.











Matter of time













Before publishing their findings, the team warned the US National Institutes of Health (NIH) and other institutions involved in the project about the vulnerability in their data. Rodriguez says that they had been anticipating that someone would identify donors, "although we didn't know how or when".












To prevent Erlich's method from being used successfully again, age data has been removed from the project's website. Erlich says that this makes it difficult, although not impossible, to narrow the surnames down to an individual.












"The genie's out of the bottle," says Jeffrey Kahn of Florida State University in Tallahassee. "It's a harbinger of a changing paradigm of privacy." A cultural zeitgeist led by companies such as Facebook has led to more information sharing than anyone would have thought possible back in 2002 when HapMap first began, he says.











Recurring problem













This is not the first time genome confidentiality has been compromised. When James Watson made his genome public in 2007, he blanked out a gene related to Alzheimer's. But a group of researchers successfully inferred whether he carried the risky version of this gene by examining the DNA sequences on either side of the redacted gene.












While someone is bound to find another way to identify genetic donors, says Rodriguez, the NIH believes it would be wrong to remove all of their genome data from the public domain. She says that full accessibility is "very beneficial to science", but acknowledges that the project needs to strike a careful balance between confidentiality and open access.












It is especially pertinent, says Kahn, because genetic data does not just carry information from the person from whom it was taken. It can also reveal the genetic details of family members, some of whom might not want that information to be public. A relative's genome might reveal your own disease risk, for example, which you might not want to know or have an employer learn of. While laws prohibit health insurers and employers from discriminating against people based on their genetic data, it would not be difficult to give another reason for denying you a job.












An individual's relatives could not prevent that individual from learning about themselves, says Rodriguez, but researchers should encourage would-be genome donors to discuss the risks and benefits with their families.

























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Tax cheat gets two weeks' jail






SINGAPORE: A property agent has been sentenced to two weeks' jail for using fake stamp certificates to cheat the taxman.

Koh Siew Buay, 50, pleaded guilty to three charges in December 2012 and was sentenced on Friday. Another charge was taken into consideration during sentencing.

She will serve her jail term from February 22.

Between January and June 2011, she collected the full amount of stamp duty payable from the tenants for three rental transactions she handled. But she entered shorter rental periods and lower rental amounts into the e-Stamping system of the Inland Revenue Authority of Singapore (IRAS).

Koh was then issued three stamp certificates.

She used them to create three counterfeit stamp "certificates" that reflected the higher stamp duty amounts payable and presented them to the tenants.

She pocketed the difference between what they had paid to her and what she had paid to IRAS, and underpaid the government S$532.

-CNA/ac



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Sony sells its Madison Ave. headquarters for $1.1 billion



Sony sells its Madison Avenue building.



(Credit:
Sony)


Sony announced today that it is selling its U.S. headquarters building located on Madison Avenue in New York City to a real estate consortium headed by The Chetrit Group. The sale price for the 37-story building is $1.1 billion.

"Given the opportunities and challenges in the current economic and real estate landscape, selling 550 Madison now is a timely and logical strategic move," Sony Corporation of America President Nicole Seligman said in the statement, according to Bloomberg.

The sale of Sony's assets is a longtime coming. The company has struggled over the past few years with increased competition and sluggish television sales. Along with getting rid of many of its assets, Sony is also cutting 10,000 jobs. The company is also reportedly looking to sell its Tokyo building for between $1 billion and $1.5 billion.

After paying back debt related to its Madison Avenue building, Sony plans to keep around $770 million from this sale.

"Sony is undertaking a range of initiatives to strengthen its financial foundation and business competitiveness and for future growth," the company said in a statement. "At the same time, Sony is balancing cash inflows and outflows while working to improve its cash flow by carefully selecting investments, selling assets and strengthening control of working capital such as inventory. This sale is made as a part of such initiatives."

While Sony is selling 550 Madison, several of its businesses -- including Sony Music Entertainment, Sony/ATV Music Publishing, Sony Pictures Entertainment, and others -- will stay in the building for the next couple of years.

The deal between Sony and The Chetrit Group is expected to close in March.

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Opinion: Lance One of Many Tour de France Cheaters


Editor's note: England-based writer and photographer Roff Smith rides around 10,000 miles a year through the lanes of Sussex and Kent and writes a cycling blog at: www.my-bicycle-and-I.co.uk

And so, the television correspondent said to the former Tour de France champion, a man who had been lionised for years, feted as the greatest cyclist of his day, did you ever use drugs in the course of your career?

"Yes," came the reply. "Whenever it was necessary."

"And how often was that?" came the follow-up question.

"Almost all the time!"

This is not a leak of a transcript from Oprah Winfrey's much anticipated tell-all with disgraced cyclist Lance Armstrong, but instead was lifted from a decades-old interview with Fausto Coppi, the great Italian road cycling champion of the 1940s and 1950s.

To this day, though, Coppi is lauded as one of the gods of cycling, an icon of a distant and mythical golden age in the sport.

So is five-time Tour winner Jacques Anquetil (1957, 1961-64) who famously remarked that it was impossible "to ride the Tour on mineral water."

"You would have to be an imbecile or a crook to imagine that a professional cyclist who races for 235 days a year can hold the pace without stimulants," Anquetil said.

And then there's British cycling champion Tommy Simpson, who died of heart failure while trying to race up Mont Ventoux during the 1967 Tour de France, a victim of heat, stress, and a heady cocktail of amphetamines.

All are heroes today. If their performance-enhancing peccadillos are not forgotten, they have at least been glossed over in the popular imagination.

As the latest chapter of the sorry Lance Armstrong saga unfolds, it is worth looking at the history of cheating in the Tour de France to get a sense of perspective. This is not an attempt at rationalisation or justification for what Lance did. Far from it.

But the simple, unpalatable fact is that cheating, drugs, and dirty tricks have been part and parcel of the Tour de France nearly from its inception in 1903.

Cheating was so rife in the 1904 event that Henri Desgrange, the founder and organiser of the Tour, declared he would never run the race again. Not only was the overall winner, Maurice Garin, disqualified for taking the train over significant stretches of the course, but so were next three cyclists who placed, along with the winner of every single stage of the course.

Of the 27 cyclists who actually finished the 1904 race, 12 were disqualified and given bans ranging from one year to life. The race's eventual official winner, 19-year-old Henri Cornet, was not determined until four months after the event.

And so it went. Desgrange relented on his threat to scrub the Tour de France and the great race survived and prospered-as did the antics. Trains were hopped, taxis taken, nails scattered along the roads, partisan supporters enlisted to beat up rivals on late-night lonely stretches of the course, signposts tampered with, bicycles sabotaged, itching powder sprinkled in competitors' jerseys and shorts, food doctored, and inkwells smashed so riders yet to arrive couldn't sign the control documents to prove they'd taken the correct route.

And then of course there were the stimulants-brandy, strychnine, ether, whatever-anything to get a rider through the nightmarishly tough days and nights of racing along stages that were often over 200 miles long. In a way the race was tailor-made to encourage this sort of thing. Desgrange once famously said that his idea of a perfect Tour de France would be one that was so tough that only one rider finished.

Add to this the big prizes at a time when money was hard to come by, a Tour largely comprising young riders from impoverished backgrounds for whom bicycle racing was their one big chance to get ahead, and the passionate following cycling enjoyed, and you had the perfect recipe for a desperate, high stakes, win-at-all-costs mentality, especially given the generally tolerant views on alcohol and drugs in those days.

After World War II came the amphetamines. Devised to keep soldiers awake and aggressive through long hours of battle they were equally handy for bicycle racers competing in the world's longest and toughest race.

So what makes the Lance Armstrong story any different, his road to redemption any rougher? For one thing, none of the aforementioned riders were ever the point man for what the U.S. Anti-Doping Agency has described in a thousand-page report as the most sophisticated, cynical, and far-reaching doping program the world of sport has ever seen-one whose secrecy and efficiency was maintained by ruthlessness, bullying, fear, and intimidation.

Somewhere along the line, the casualness of cheating in the past evolved into an almost Frankenstein sort of science in which cyclists, aided by creepy doctors and trainers, were receiving blood transfusions in hotel rooms and tinkering around with their bodies at the molecular level many months before they ever lined up for a race.

To be sure, Armstrong didn't invent all of this, any more than he invented original sin-nor was he acting alone. But with his success, money, intelligence, influence, and cohort of thousand-dollar-an-hour lawyers-and the way he used all this to prop up the Lance brand and the Lance machine at any cost-he became the poster boy and lightning rod for all that went wrong with cycling, his high profile eclipsing even the heads of the Union Cycliste Internationale, the global cycling union, who richly deserve their share of the blame.

It is not his PED popping that is the hard-to-forgive part of the Lance story. Armstrong cheated better than his peers, that's all.

What I find troubling is the bullying and calculated destruction of anyone who got in his way, raised a question, or cast a doubt. By all accounts Armstrong was absolutely vicious, vindictive as hell. Former U.S. Postal team masseuse Emma O'Reilly found herself being described publicly as a "prostitute" and an "alcoholic," and had her life put through a legal grinder when she spoke out about Armstrong's use of PEDs.

Journalists were sued, intimidated, and blacklisted from events, press conferences, and interviews if they so much as questioned the Lance miracle or well-greased machine that kept winning Le Tour.

Armstrong left a lot of wreckage behind him.

If he is genuinely sorry, if he truly repents for his past "indiscretions," one would think his first act would be to try to find some way of not only seeking forgiveness from those whom he brutally put down, but to do something meaningful to repair the damage he did to their lives and livelihoods.


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Armstrong Admits to Doping, 'One Big Lie'













Lance Armstrong, formerly cycling's most decorated champion and considered one of America's greatest athletes, confessed to cheating for at least a decade, admitting on Thursday that he owed all seven of his Tour de France titles and the millions of dollars in endorsements that followed to his use of illicit performance-enhancing drugs.


After years of denying that he had taken banned drugs and received oxygen-boosting blood transfusions, and attacking his teammates and competitors who attempted to expose him, Armstrong came clean with Oprah Winfrey in an exclusive interview, admitting to using banned substances for years.


"I view this situation as one big lie that I repeated a lot of times," he said. "I know the truth. The truth isn't what was out there. The truth isn't what I said.


"I'm a flawed character, as I well know," Armstrong added. "All the fault and all the blame here falls on me."


In October, the U.S. Anti-Doping Agency issued a report in which 11 former Armstrong teammates exposed the system with which they and Armstrong received drugs with the knowledge of their coaches and help of team physicians.






George Burns/Courtesy of Harpo Studios, Inc./AP Photo













Lance Armstrong Admits Using Performance-Enhancing Drugs Watch Video









Lance Armstrong's Oprah Confession: The Consequences Watch Video





The U.S. Postal Service Cycling Team "ran the most sophisticated, professionalized and successful doping program that sport has ever seen," USADA said in its report.


As a result of USADA's findings, Armstrong was stripped of his Tour de France titles. Soon, longtime sponsors including Nike began to abandon him, too.


READ MORE: Did Doping Cause Armstrong's Cancer?


Armstrong said he was driven to cheat by a "ruthless desire to win."


He told Winfrey that his competition "cocktail" consisted of EPO, blood transfusions and testosterone, and that he had previously used cortisone. He would not, however, give Winfrey the details of when, where and with whom he doped during seven winning Tours de France between 1999 and 2005.


He said he stopped doping following his 2005 Tour de France victory and did not use banned substances when he placed third in 2009 and entered the tour again in 2010.


"It was a mythic perfect story and it wasn't true," Armstrong said of his fairytale story of overcoming testicular cancer to become the most celebrated cyclist in history.


READ MORE: 10 Scandalous Public Confessions


PHOTOS: Olympic Doping Scandals: Past and Present


PHOTOS: Tour de France 2012


Armstrong would not name other members of his team who doped, but admitted that as the team's captain he set an example. He admitted he was "a bully" but said there "there was a never a directive" from him that his teammates had to use banned substances.


"At the time it did not feel wrong?" Winfrey asked.


"No," Armstrong said. "Scary."


"Did you feel bad about it?" she asked again.


"No," he said.


Armstrong said he thought taking the drugs was similar to filling his tires with air and bottle with water. He never thought of his actions as cheating, but "leveling the playing field" in a sport rife with doping.






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Drought, fire, ice: world is gripped by extreme weather


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New wave of Rohingya migrants arrive in Thailand






BANGKOK: More than 130 Rohingya migrants have landed on Thai soil in less than 24 hours, a local official said Thursday, as the kingdom grapples with a flurry of arrivals from the Myanmar minority group.

Some 88 Rohingya came ashore at Phra Thong island in the south of the country on Wednesday in full view of television cameras, according to Kuraburi district chief for Manit Pienthong.

Another 48 landed on the Andaman sea island on Thursday morning claiming they were Royingya, Manit said, adding they were sent to immigration officials in the provincial capital of Phangnga to start the process of returning them to Myanmar.

Over the last week hundreds of Myanmar migrants have been arrested in police sweeps of remote areas in rubber plantations near the border with Malaysia, leading the UNHCR to try to confirm whether any of them plan to seek asylum.

The UN's refugee agency said Wednesday it had received permission from Thailand to visit about 850 people, many thought to be Rohingya, held after raids on camps in the Thai south.

Thousands of Rohingya, a minority group not recognised as citizens in Myanmar, have fled communal unrest in the country's western Rakhine state, heading to Thailand and other countries.

Many take to makeshift boats and drift south to the Thai coast.

Rights groups have criticised Thailand for failing to help Rohingya who reach its territory, instead pushing them back to Myanmar or into neighbouring countries including Malaysia, which offers sanctuary to the minority group.

-AFP/ac



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Otherworldly Craigslist ad seeks 'Star Trek' role-players



The author of the Craigslist ad will most likely be wearing a Captain Picard uniform similar to this one auctioned by Christie's in 2006.



(Credit:
Christie's Images Ltd. 2006)


Those ladies who are fluent in Klingon but just can't seem to find a boyfriend are now in luck. Apparently, a certain someone is seeking women for "Star Trek" role-playing -- strictly "The Next Generation."

A recent Craigslist ad titled "Make It So" is making the joke rounds on Twitter today. The ad promises "no nudity, no touching" but asks for two to three women to get in character with the ad's author as he plays the "honorable" and "intellectual" Captain Picard.



Apparently Make It So has some serious issues with Captain Kirk, who he says "isn't half the Captain that Picard is" and is also a "fat chauvinist ladies man." He says that last time he tried to role-play "The Original Series," it was a "disaster." "There will be no mixing of eras," he proclaims.

Once he finds some suitable women that "know a lot about the show," the roleplaying can commence in his mom's garage where he has built a bridge and a small shuttlecraft. He will provide the scripts. The women have to have their own costumes and a phaser or VISOR would also be helpful.

What's in it for those lady callers? Maybe a lunch made by Make It So's mom and some blank doctor's prescriptions.

"Nothing weird is going to happen," he promises.


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6 Ways Climate Change Will Affect You

Photograph by AP Photo/Marcio Jose Sanchez

The planet keeps getting hotter, new data showed this week. Especially in America, where 2012 was the warmest year ever recorded, by far. Every few years, the U.S. federal government engages hundreds of experts to assess the impacts of climate change, now and in the future.

From agriculture (pictured) to infrastructure to how humans consume energy, the National Climate Assessment Development Advisory Committee spotlights how a warming world may bring widespread disruption.

Farmers will see declines in some crops, while others will reap increased yields.

Won't more atmospheric carbon mean longer growing seasons? Not quite. Over the next several decades, the yield of virtually every crop in California's fertile Central Valley, from corn to wheat to rice and cotton, will drop by up to 30 percent, researchers expect. (Read about "The Carbon Bathtub" in National Geographic magazine.)

Lackluster pollination, driven by declines in bees due partly to the changing climate, is one reason. Government scientists also expect the warmer climate to shorten the length of the frosting season necessary for many crops to grow in the spring.

Aside from yields, climate change will also affect food processing, storage, and transportation—industries that require an increasing amount of expensive water and energy as global demand rises—leading to higher food prices.

Daniel Stone

Published January 16, 2013

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Notre Dame: Football Star Was 'Catfished' in Hoax













Notre Dame's athletic director and the star of its near-championship football team said the widely-reported death of the star's girlfriend from leukemia during the 2012 football season was apparently a hoax, and the player said he was duped by it as well.


Manti Te'o, who led the Fighting Irish to the BCS championship game this year and finished second for the Heisman Trophy, said in a statement today that he fell in love with a girl online last year who turned out not to be real.


The university's athletic director, Jack Swarbrick, said it has been investigating the "cruel hoax" since Te'o approached officials in late December to say he believed he had been tricked.


Private investigators hired by the university subsequently monitored online chatter by the alleged perpetrators, Swarbrick said, adding that he was shocked by the "casual cruelty" it revealed.


"They enjoyed the joke," Swarbrick said, comparing the ruse to the popular film "Catfish," in which filmmakers revealed a person at the other end of an online relationship was not who they said they were.


"While we still don't know all of the dimensions of this ... there are certain things that I feel confident we do know," Swarbrick said. "The first is that this was a very elaborate, very sophisticated hoax, perpetrated for reasons we don't understand."






Mike Ehrmann/Getty Images











Notre Dame's Athletic Director Discusses Manti Te'o Girlfriend Hoax Watch Video









Notre Dame Football Star Victim of 'Girlfriend Hoax' Watch Video









Eddie Lacy, Barrett Jones Discuss 'Bama Win Watch Video





Te'o said during the season that his girlfriend, Lennay Kekua, died of leukemia in September on the same day Te'o's grandmother died, triggering an outpouring of support for Te'o at Notre Dame and in the media.


"While my grandma passed away and you take, you know, the love of my life [Kekua]. The last thing she said to me was, 'I love you,'" Te'o said at the time, noting that he had talked to Kekua on the phone and by text message until her death.


Now, responding to a story first reported by the sports website Deadspin, Te'o has acknowledged that Kekua never existed. The website reported today that there were no records of a woman named Lennay Kekua anywhere.


Te'o denied that he was in on the hoax.


"This is incredibly embarrassing to talk about, but over an extended period of time, I developed an emotional relationship with a woman I met online," Te'o said in a statement released this afternoon. "We maintained what I thought to be an authentic relationship by communicating frequently online and on the phone, and I grew to care deeply about her."


Swarbrick said he expected Te'o to give his version of events at a public event soon, perhaps Thursday, and that he believed Te'o's representatives were planning to disclose the truth next week until today's story broke.


Deadspin reported that the image attached to Kekua's social media profiles, through which the pair interacted, was of another woman who has said she did not even know Te'o or know that her picture was being used. The website reported that it traced the profiles to a California man who is an acquaintance of Te'o and of the woman whose photo was stolen.


"To realize that I was the victim of what was apparently someone's sick joke and constant lies was, and is, painful and humiliating," Te'o said.






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