Clinics Offer Expensive Whole-Genome Tests for Undiagnosed Disorders

Two university-based clinics have debuted large programs that rely on sequencing to diagnose genetic disorders, including developmental disorders such as autism

By Virginia Hughes and SFARI.org

Gene banks: Troves of sequencing data are becoming part of everyday medical care ? and may soon be filling research databases. Image: Cancer.gov

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Reprinted with permission from?SFARI.org, an editorially independent division of The Simons Foundation. (Find original story here.)

Over the past few years, teams of scientists have been finding genetic glitches related to a wide variety of disorders by sequencing exomes, the protein-coding portions of the genome. But these genetic tests are typically out of reach for people unless they enroll in research studies, and even then, they?re almost never privy to their individual results.

But that looks set to change: A few clinics are debuting large programs that rely on sequencing of exomes or even of whole genomes, and making the results directly available to individuals. For less than $10,000 each, the tests offer people with unexplained genetic disorders the chance to find the cause of their condition.

The first academic lab to offer clinical exome sequencing was the Whole Genome Laboratory at Baylor College of Medicine in Houston. Since November 2011, the lab has sequenced the exomes of some 1,700 individuals with undiagnosed conditions, including many children with developmental disorders. It now averages about 200 exomes a month.

"It's gone gangbusters," says Richard Gibbs, director of Baylor's Human Genome Sequencing Center, which helped establish the new lab. The researchers have pinpointed the genetic cause of about one-quarter of the 1,700 cases as mutations in known disease genes, he says.

Last week, the Harvard-affiliated Partners Healthcare Center in Boston launched a similar lab focused on sequencing whole genomes. And two private companies ? Ambry Genetics in Aliso Viejo, California, and GeneDx in Gaithersburg, Maryland ? have offered clinical exome sequencing since 2011.

Deciding which parts of the sequencing data should be divulged to individuals is far from straightforward. A few mutations are clearly associated with disease, but most are still tricky to interpret.

From a research perspective, however, the development is unequivocally exciting, experts say.

That's because at clinics affiliated with academic institutions, participants may choose to contribute their de-identified data into freely available databases that researchers can tap for their studies. That could prove a huge advantage for researchers funded by agencies such as the National Institutes of Health (NIH).

"A ton more samples can be screened in the clinic than can be screened in NIH-funded studies," says Jonathan Sebat, associate professor of psychiatry at the University of California, San Diego. "That's ultimately what's going to drive discovery forward."

Sharing genomes:
Many clinical tests already exist for undiagnosed developmental disorders. These tests typically screen a single gene or a panel of genes for certain rare variants, which appear only in a few people, or common variants, which crop up in at least five percent of the general population.

Source: http://rss.sciam.com/~r/ScientificAmerican-News/~3/0oBJw0UveGk/article.cfm

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FULL COMMITTEE HEARING: To explore the effects of ongoing changes in domestic oil production, refining and distribution on U.S. gasoline and fuel prices

SD-366 Senate Dirksen Building 10:00 AM

The purpose of this oversight hearing is to explore how U.S. gasoline and fuel prices are being affected by the current boom in domestic oil production and the restructuring of the U.S. refining industry and distribution system.

The hearing will be webcast live on the committee's website, and an archived video will be available shortly after the hearing is complete. Witness testimony will be available on the website at the start of the hearing.

Source: http://www.energy.senate.gov/public/index.cfm/hearings-and-business-meetings?ContentRecord_id=dc9017cc-beaa-4ea6-a7dd-9ec1f3102d27

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Brainstorm Tech Spotlight: Jennifer Dulski, President and COO of Change.org

FORTUNE -- Fortune's Brainstorm Tech Conference (July 22-24 in Aspen, Colo.) regularly brings together the best and brightest minds in tech innovation. Each week, Fortune turns the spotlight on a different conference attendee to offer his or her own personal insight into business, tech, and entrepreneurship. This week, we asked Change.org President and COO Jennifer Dulski to answer 10 questions about life outside of work, the company she admires most, and industry advice for young entrepreneurs. Her responses follow.

What is the best advice you ever received?

It came from a research study by one of my favorite Cornell professors, Thomas Gilovich, focusing on regret. The research concluded, "Actions, or errors of commission, generate more regret in the short-term; but inactions, or errors of omission, produce more regret in the long run." In other words, while people in the short-term regret "bad" choices, like trying out for something and getting rejected or choosing a job and deciding they don't like it, things are different when they look back on their lives: they most often regret the things they did not try, like not accepting a certain job offer, or not asking out that person they really liked. I often think of this research when faced with a decision, and it pushes me to try new things and challenge myself.

What was the most important thing you learned in school?

The teachers who challenged me the most were also the ones I learned the most from in school. I remember a particular high school teacher of mine, Joe DiPrisco, who had impeccably high standards for strong writing and correct grammar. Even though it was uncomfortable to be corrected, I finished his class as a much stronger writer. I believe the same principle holds true in business ? understand that those who push you will make you better, and surround yourself with people who aren't afraid to challenge you. Similarly, others on your team are more likely to exhibit excellence when you expect it of them, so keep your standards high.

What has been your biggest failure?

There's one big mistake I made as a first time entrepreneur that I still laugh about. I named my startup's first product with an apostrophe. In the desire to get a name we could afford without paying through the nose for a domain, I chose "Center'd" (because "Centered" was taken and we couldn't afford to buy it). Not only is an apostrophe a "special character" that caused all kinds of issues in the code for our website, but it was also nearly impossible to speak about Center'd in the possessive, since it then had a double apostrophe! My main learning was this: pick a name that's easy to spell, helps to clearly explain what you do, and, ideally, works around the world. "Center'd" did none of those things. But "The Dealmap," the name for our second product, did all three ? and boy, was it easier to give our elevator pitch and to get people to use our product.

What do you do to live a balanced life?

I focus on being a present parent. When I look back on my childhood and young adult years, one of the things I remember clearly is that my parents were always there. They were both working parents, and yet they showed their support for me by coming to important events, even in the middle of a work day. That support helped give me confidence that I could take risks and aim big.

Now that I'm a parent myself, I want my children to feel that I'm there to support them. I leave work early to attend their dance recitals, school concerts, and other events. I even take them to nearly all of their appointments (doctors, dentists, orthodontists,

etc.) ? not because I need to, but because I want them to know I care about all the things they do, not just the big events. (Plus, I like spending time with them!)

Of course, there are times when I just can't make it, so I work hard to make sure I'm present for them whenever I possibly can be.

What would you do if you weren't working at your current job?

There's honestly nowhere I'd rather work ? I've always wanted to blend my passion for building big internet companies and my desire to drive global [and] social impact, and Change.org is the ideal place to do both. But, if I were not doing this, I could imagine going back to teaching, which I did early in my career and loved.

What do you do for fun?

My two favorite activities are spending time with my family and friends and traveling to learn about other places around the world. I look forward to taking my daughters to visit some of the 18 countries where we have Change.org offices.

What would you say to a group of young people looking to enter the tough job market?

First, believe in yourself. The first time you do anything, you've never done it before, so the best thing to do is give it your all and learn as much as you can from others. Remember that we were all there at some point ? everyone who interviews you and everyone you'll be working with as well ? so don't get intimidated. Second, look for work you believe is worthwhile. There's nothing better than working in a place where the time you invest in your job and the impact you make on the world are aligned.

What other companies do you admire? Why?

I admire what LinkedIn has created. It started as a useful tool for professionals to build their profiles and connect to each other, but it had a problem with low user engagement. But over time, new tools like "LinkedIn Today" and the influencer blog network have made the site a very engaging place to spend time. This combination of a highly useful professional tool with a diverse and strong business model really sets LinkedIn apart.

What is one characteristic that every leader should possess?

Empathy.

I believe the best leaders are excellent at listening to those around them and synthesizing their insights into great ideas. The best leaders can put themselves in others' shoes, understanding the pain points of their customers and building products that creatively solve those problems. Strong leaders also exhibit empathy for their teams, recognizing people are motivated by different things and helping them find roles and projects that leverage their strengths and bring out their best work.

Is business school necessary for entrepreneurs?

I'm a big fan of business school, both for what you learn and for the people you have the chance to meet. I still use plenty of the things I learned in business school, from negotiation tactics to financial modeling. That said, I believe it's possible to master the skills of great entrepreneurs ? primarily customer focus, creativity, and relentless persistence ? through other channels as well. In fact, I think business schools need to adapt to do a better job preparing students to become entrepreneurs. The only way to really learn what it takes is to try it, and both undergraduate and graduate schools should be helping students get more real-life entrepreneurship experience beyond classroom learning. I'm excited about some of the programs coming out in this arena.

Source: http://tech.fortune.cnn.com/2013/07/11/brainstorm-tech-spotlight-jennifer-dulski-president-and-coo-of-change-org/

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Shadow banking bolsters China Inc. as Beijing tightens credit

Reuters

Shanghai/ Hong Kong:? Wang Zhiyong, the founder of a Shanghai-based gift card company, tried twice to get a bank loan for his business and failed both times.

So Wang turned to China's vast network of alternative lenders, opting for a so called "curb side" loan. Such a loan is just one segment of the country's shadow banking system, which includes pawn shops, credit guarantee firms, trust companies and other mechanisms as sources of funds for Chinese borrowers.

"Banks never lend a hand to start-ups like us," said Wang, 40. "They only go after big companies and state-owned firms."

The dearth of bank credit available to China's millions of small to mid-sized companies is expected to tighten as authorities seek to rebalance the world's second-biggest economy.

Source: http://news.in.msn.com/business/article.aspx?cp-documentid=253351458

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London?s Old Design Museum Building Sold to Architecture Studio

London?s Design Museum is moving to a new location from 2014, meaning its current site on the Thames is no longer needed. It?ll still be a place to hang out looking at cool things, though, as the building will be transformed into a showcase space for Zaha Hadid Architects.

The deal, which is supposedly worth around the ?10m mark, will be completed in 2015 once the Design Museum?s fully moved out, with?Zaha Hadid planning to turn the premises into a place for architecture exhibitions. So it?ll still be a place where people with elaborate facial hair can go to ponder things.

The Design Museum itself will soon be moved to Kensington?s?Commonwealth Institute (above), a rather grim 1960s concrete structure that?s currently getting a big redesign to make it a little more suitable for the task. [Dezeen]

Image credit: Fluffymark

Source: http://www.gizmodo.co.uk/2013/07/londons-old-design-museum-building-sold-to-architecture-studio/

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Greinke cools off D-Backs in dominant win

By BOB BAUM

AP Sports Writer

Associated Press Sports

updated 1:09 a.m. ET July 9, 2013

PHOENIX (AP) - The Arizona Diamondbacks had dominated opponents lately, then Zack Greinke came to town.

The Los Angeles right-hander shut down the Diamondbacks in a 6-1 Dodgers victory that snapped Arizona's five-game winning streak.

It was the opener of the first series between the teams since the one that featured the bench-clearing melee in Los Angeles last month, but any drama withered as Greinke took command and never let up. He allowed two hits in seven scoreless innings.

"That is how he won a Cy Young right there," said Arizona's Jason Kubel, who with Minnesota saw Greinke a lot when the pitcher was with Kansas City.

"He has great stuff and he swung the bat well, too. He throws hard. He throws that hard slider and it is hard to pick up until it is too late and his location is big for him. He had it going."

Diamondbacks manager Kirk Gibson said it was just one of those games when his team simply was outplayed.

"They played well all phases of the game," Gibson said. "They beat us up."

Greinke confessed to a tiny bit of added motivation.

After all, the last time he faced them, the game erupted into a bench-clearing brawl that resulted in eight suspensions.

"I might want to win a little more," he said. "That's also because they're in first place, so it's a big game because of that."

Greinke (7-2) struck out seven and walked two. He also had a career-high three hits.

He was 0-2 with an 8.71 ERA in four previous starts at Chase Field.

"I've pitched really bad here," Greinke said, "some of my worst games ever at this place, so that was nice."

Hanley Ramirez singled three times to extend his career-best hitting streak to 19 games and was one of five Dodgers with an RBI.

Los Angeles, winners of 13 of 16, tied its season high with 17 hits - 16 of them singles. Andre Ethier had three hits and A.J. Ellis drove in two runs as the Dodgers pulled within 3 1/2 games of the first-place Diamondbacks in the NL West.

"Without this little streak we've been on who knows what position we'd be in," Ellis said. "We also got a little help from the NL West coming back to the pack. Nobody ran away with it."

Randall Delgado (1-3) allowed three runs and 11 hits in six innings to take the loss.

"He didn't throw the ball bad at all," Gibson said. " ... He held us in the game, but Greinke was good tonight. He had everything working, it was the most talented we have seen him in a while."

Arizona averted the shutout on Eric Chavez's RBI single in the ninth.

Greinke was a major player in the events leading up to that June 11 brawl. Ian Kennedy, who hit Yasiel Puig and Greinke with high pitches to trigger the melee and served a 10-game suspension, starts for Arizona in the second game of the series on Tuesday night.

Puig and Greinke were booed roundly when they came to the plate. Not that it had any impact.

Greinke struck out four of the first five and didn't allow a hit until Paul Goldschmidt's leadoff single in the fourth. The only other hit off the Los Angeles right-hander was Martin Prado's two-out double in the seventh. Goldschmidt also had an infield single in the ninth and scored Arizona's run.

Ramirez and Ethier singled with one out in the fourth. A.J. Ellis flew out to center, then Juan Uribe singled Ramirez home from second to put Los Angeles up 1-0. Ethier was stranded at third when Mark Ellis flew out to center.

Greinke's single started a two-run fifth that put the Dodgers up 3-0. After one out, Puig singled, then Adrian Gonzalez and Ramirez each got an RBI hit to right. Kubel mishandled Ramirez's hit but threw the runner out trying to take second on the play.

The Dodgers scored two off reliever Charles Brewer with two outs in the sixth on Ethier's RBI double and Ellis' run-scoring single.

Arizona center fielder Gerardo Parra got a big ovation after chasing down Ellis' fly with a lunging grab as he fell to the warning track to start the sixth.

Before the game, the Dodgers placed Matt Kemp on the 15-day disabled list, retroactive to Saturday, with joint inflammation in his left shoulder. Kemp is to see the team doctor in Los Angeles on Tuesday.

Notes: Ricky Nolasco, acquired from Miami on Saturday, makes his first start for the Dodgers on Tuesday night. He took the roster spot of RH Stephen Fife, who was placed on the 15-day DL for the second time this season with right shoulder bursitis. ... Ramirez's hitting streak is the longest active one in the majors and longest by a Dodger since Ethier's 30-game streak from April 2 to May 6, 2011. ... Outfielder Scott Van Slyke was recalled from Triple-A Albuquerque to take Kemp's roster spot. ... The Diamondbacks announced the signing of six international players, including 16-year-old Venezuelan catching prospect Jose Herrera. The other five signees also are 16. ... Greinke had allowed a combined nine earned runs and 18 hits in his previous two starts, although he won both.

? 2012 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

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HBT: The All-Star Game will be ruined if another player wins MVP, then is banned for PEDs, a columnist says. But that's just silly.

HBT Daily: Phillies face critical juncture

??HBT Daily: Craig Calcaterra predicts strong numbers from Phillies Triple-A call-up Darin Ruf upon replacing the injured Ryan Howard. Also, after winning five of their last seven games, will management in Philadelphia look to buy or sell at the upcoming trade deadline?

Source: http://nbcsports.msnbc.com/id/52427180/ns/sports-baseball/

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Lebanon: Bombing wounds 53 in Hezbollah stronghold

BEIRUT (AP) ? A car bomb rocked a stronghold of the Shiite militant Hezbollah group south of the Lebanese capital on Tuesday, wounding at least 53 people and setting several cars ablaze in the most serious knock-on effect from Syria's civil war on its smaller neighbor since the crisis began, officials said.

The powerful blast struck a bustling commercial and residential neighborhood as many Lebanese Shiites began observing the holy month of Ramadan. It was the worst explosion to hit Beirut's southern suburbs in years. While there was no immediate claim of responsibility, there have been growing fears in Lebanon that Hezbollah could face retaliation for its now overt role fighting alongside President Bashar Assad's troops inside Syria, including, activists say, in the embattled city of Homs near the Lebanese border.

The bombing also is likely to inflame already simmering tensions in Lebanon itself, where deadly clashes between Shiites and Sunnis have grown increasingly common as the civil war in Syria has taken on ever darker sectarian overtones. Some Sunnis in Lebanon, many of whom support Syria's rebels, have expressed growing resentment over what they see as Hezbollah's unchecked power in the country.

Tuesday's blast struck the area of Beir el-Abed, and was most likely caused by a car bomb, officials said, speaking on condition of anonymity in line with regulations. They said it went off in the parking lot near the Islamic Coop, a supermarket usually packed with shoppers, and a petrol station.

"The explosion was so strong I thought it was an Israeli air raid," said Mohammad al-Zein, who lives near the blast site. "My wife was sleeping in bed and all the glass fell on her, injuring her in the mouth, arms and legs."

Another resident said that he was fasting on the first day of Ramadan and was on his way to shop for the evening meal that would break his daylong fast. Some Shiites began observing Ramadan on Tuesday while other Shiites and Sunnis across the Muslim world will start on Wednesday.

"I was riding my motorcycle on my way to a sweets shop and then there was this massive explosion that knocked me off and I fell on the ground," said a 52-year-old employee of a private company. He declined to be named out of security concerns.

Health Minister Ali Hassan Khalil said 53 people were wounded. He said most of injuries were light, and that many of them were caused by breaking glass.

The parking lot where the bomb went off is a few hundred meters (yards) away from what is known as Hezbollah's "security square," where many of the party's officials live and have offices. Hezbollah leader Hassan Nasrallah received dignitaries there before the 2006 war. The area was bombed by Israel in that conflict and Nasrallah has gone underground since then, only rarely appearing in public and never for more than few minutes, fearing Israeli assassination.

"This (blast) is a message, but we will not bow," said Ziad Waked, a municipal official speaking to Hezbollah's Al-Manar television.

With smoke still hanging in the air after the bombing, a group of about 100 outraged Hezbollah supporters stormed through the area, carrying pictures of Nasrallah, shouting in support of their leader and chanting sectarian slogans.

Hezbollah operatives fired in the air to disperse people who attacked the interior minister with stones after he inspected the scene of the blast, trapping him for 45 minutes in a building before he was escorted through a backdoor.

"The Shiite blood is boiling," the Hezbollah supporters shouted.

Interior Minister Marwan Charbel is seen by some Shiites as sympathetic to hardline Sunni cleric Ahmad al-Assir, who was agitating against Hezbollah for months and is now on the run.

Tuesday's explosion is one of the biggest in the capital's southern suburbs since the end Lebanon's 15-year civil war in 1990, and a major breach of a tightly controlled, high security area.

"It is a large area heavily populated. No force in the world can protect every area and every street," Hezbollah lawmaker Ali Moqdad said.

President Michel Suleiman said "such acts are a reminder of darker days, which the Lebanese would like to erase from their memories."

Syria-based militant Islamic groups and rebels have vowed to target Hezbollah areas in Lebanon in retaliation for the group's role in Syria's conflict. At least one Islamist brigade claimed responsibility for Tuesday's attack on its Facebook page, but its authenticity could not be verified.

The Syrian National Coalition, the main Western-backed Syrian opposition group, denounced "in the strongest terms the terrorist explosion."

"Targeting civilians is a criminal act that goes against the aims of the (Syrian) revolution and its principles," it said in a statement.

Television footage from the scene revived memories of that conflict, when car bombs set by sectarian groups were common. There have been numerous car bombs targeting politicians and journalists since then, but random car bombings have been rare.

Hezbollah operatives in civilian clothes, some of them carrying Kalashnikov rifles, cordoned off the site of the explosion with yellow ribbons. They and Lebanese security officials barred journalists from approaching the site itself.

Ambulances and fire engines raced to the area, and witnesses said casualties were rushed to two nearby hospitals.

The power of the explosion shattered windows and damaged several buildings in the busy area. A security official said the bomb was placed in a car and that it weighed 35 kilograms (70 pounds).

In May, two rockets slammed into a Hezbollah stronghold in south Beirut, wounding four people. The rockets struck hours after Nasrallah vowed in a speech to help propel Assad to victory in Syria's civil war. In June, a rocket slammed into the same area, causing no casualties.

Hezbollah has openly joined the fight in Syria, and the group's fighters were instrumental in a recent regime victory when government forces regained control of the strategic town of Qusair near the Lebanese border.

Lebanon's Sunni Muslims mostly back the overwhelmingly Sunni rebels in Syria, while many Shiites support Assad, who is a member of Syria's minority Alawite sect, an offshoot of Shiite Islam.

___

Associated Press writer Zeina Karam contributed to this report.

Source: http://news.yahoo.com/lebanon-bombing-wounds-53-hezbollah-stronghold-134426001.html

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