Thank you to our sponsors who went Above and Beyond

A special THANK YOU to all the sponsors of Above and Beyond: An Evening of Hope, October 24, 2010.

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A Time to Inhale

Some things our children say are indelibly etched in our memories, word for word. They make us laugh, their naive wisdom stops us dead in our tracks, or they reflect some unattractive part of ourselves we never knew they saw. For me, as I wrote about in the previous issue of this newsletter, it was Christiane’s answer when asked what made her special. She said simply “I get to learn how to read Braille, and one day I’ll get to have a Seeing Eye dog.” Not HAVE to, but GET to! I have thought of those words a thousand times, but mostly I have absorbed the concept of “have to” vs. “get to.” It has given me a fresh perspective on parenting and a summer spent every day with my children has given me the opportunity to adopt her philosophy. So swimming with the children has transformed from I’ll HAVE to wash the chlorine out of my hair, to I GET to dive to the bottom of the pool and see their faces close up when they pop up breathlessly. And, cooking has transformed from I’ll HAVE to pick egg shells out of the scorched scrambled eggs to I GET to feel her excitement and enthusiasm for success. Disciplining has morphed from I’ll HAVE to hear her whine and complain about an extra chore to I GET to see her mature as I watch her figure out how to unload the dishwasher unassisted. What a lesson she has taught me and I absolutely relish in the gift of “GETTING TO” experience my children in a way I never have before. It’s like taking a walk and slowly inhaling every fragrant flower, stopping to watch where the butterfly lands, and feeling the sun on your shoulders and breeze in your face. There is a consciousness in parenting that is often not intuitive, but so rewarding if we take the time.

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Paving the Path to Prevention: $2.5 million gift brings world famous researcher to Texas Children’s

by Sandra Bretting

published in 2010

A recent $2.5 million gift to the Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital has paved the way for noted Italian researcher Andrea Ballabio, M.D., to serve as visiting scientist at the institute for a year. Ballabio and his team conduct research into neurodegenerative disorders and lysosomal storage disorders, such as Batten disease.

The gift comes from Cherie and James C. Flores, who donated $2 million to the effort, and from the Beyond Batten Disease Foundation, which contributed $500,000. The foundation was established by Charlotte and Craig Benson, whose daughter, Christiane, was diagnosed with juvenile Batten disease in 2008.

Batten disease is a rare genetic disorder that attacks the nervous system. It was first documented nearly one hundred years ago, but research has been limited until now. There is no treatment and no cure. The earliest signs are subtle and often do not occur until a child is about 5 years old.

“It is heartbreaking to think that this disease will one day rob Christiane of her ability to see and walk and use her mind. And, eventually, it will take her from us, unless we act now,” Benson said.

“We have to believe that there’s an answer, and we are confident that there is hope for the future in terms of developing treatments for Batten disease,” he continued. “Texas Children’s Hospital is uniquely positioned to make progress against genetic disorders like Batten disease through facilitating collaborative research and recruiting world-renowned scientists like Dr. Ballabio and his associates.”

Ballabio has served on the molecular and human genetics faculty of Baylor College of Medicine. Currently, he is the scientific director of the Telethon Institute of Genetics and Medicine in Naples, Italy. He and his team recently discovered the gene that controls the body’s ability to degrade and recycle toxic molecules. The build-up of these molecules is the cause of numerous genetic disorders, including Batten disease, along with other neurodegenerative disorders such as Alzheimer’s, Parkinson’s and Huntington’s diseases.

“We have identified a ‘master’ gene that acts as a genetic switch,” Ballabio said. “By enhancing the function of this master gene, we can increase the clearance capacity of the cell and its ability to degrade toxic proteins. We believe this knowledge will help us develop better treatments and, ultimately, find a way to prevent these diseases.”

Phase one of Ballabio’s research at Texas Children’s began in July and is focused on the development of animal models for Batten disease and other disorders. Phase II, beginning next summer under the leadership of Ballabio’s research associate, Marco Sardiello, Ph.D., will investigate which drugs are able to promote activation of the master gene.

https://waystogive.texaschildrens.org/page.aspx?pid=1765

HOPE on the Green Charity Golf Tournament

Will Herndon

Dear Friends,

I would like to introduce you to our son, Will. He is an outgoing, green-eyed, 7-year old kindergartener who loves to smile and greets everyone with a hug.  He plays soccer, swims and adores his two little brothers. He loves to give “Eskimo kisses, “and say his prayers.   He collects Build-a-Bears, hunts for “waterhorse eggs” at the Beach and loves to watch the zebras at the zoo.  His future was bright, his goals limitless until a life-changing day in June, 2009:  The day our son was diagnosed with a fatal, rare, genetic neurological-degenerative disorder called Juvenile Batten Disease.  It was unimaginable to comprehend that a horrible disease we had never heard of, was planning to ruin my son’s childhood by stealing his vision, mind, mobility and ultimately, his life.

Juvenile Batten is a fatal, inherited disorder of the nervous system affecting 2 to 4 of every 100,000 births in the U.S.  Early symptoms of this disorder usually appear between the ages of 5 and 10, when a previously normal child begins to develop vision problems or seizures. Over time, affected children suffer mental impairment, worsening seizures, and progressive loss of vision and motor skills. Eventually, they become blind, bedridden, and physically and mentally incapacitated, requiring 24-hour care. Batten disease is fatal, often by the late teens or early twenties. Over the past year, Will has gone legally blind, suffers short-term memory loss, occasional stuttering and extreme anxiety.  With no current treatments or cure, this is our Will’s prognosis, and at the moment it is grim.  We are in a literal race against time.

But, there is HOPE.  Our family has partnered with the Beyond Batten Disease Foundation.  Beyond Batten was started in August of 2008 by the Benson Family of Austin, TX who also have an affected daughter, similar in age and symptoms to Will. The foundation is currently funding a group of Italian researchers at Texas Children’s Hospital who are working on a developing a potential treatment for Batten disease.   Together, we will work to accomplish our shared mission:

TO ERADICATE JUVENILE BATTEN DISEASE.

HOPE has been the theme of our journey, which began with our first major, local fundraiser “HOPE Under the Stars” for the Will Herndon Fund for Juvenile Batten Research and the Beyond Batten Disease Foundation that took place in November, 2009. At this event, we were able to share Will’s story and our mission to more than 600 guests and raise nearly $220,000 for research.  Our hope is to continue this momentum with the 2nd Annual Brake Specialists Plus “HOPE on the Green” Charity Golf Tournament and Dinner to take place on Thursday, September 16, 2010 at Grey Rock Golf Club in Austin, Texas.

Monies raised will be donated to fund researchers working to find a treatment and/or cure for Juvenile Batten disease right now.  With no current treatment or cure, our HOPE rests heavily with the privately funded researchers dedicated to fight this disease.    The more researchers dedicated to this rare disease, the higher the chance of a development within our children’s lifetime.  Our goal is to save Will and the hundreds like him.  Failure is not an option; our son’s life depends on it.

On behalf of our family, thank you for your interest, prayers and continued support of The Beyond Batten Disease Foundation.

Kindest regards,

Wayne and Missy Herndon

For more information regarding the 2nd Annual Brake Specialists Plus HOPE on the Green Charity Golf Tournament click here.

Rainbows

This summer, I spent some time hiking alone early in the morning while our family was on vacation visiting a remote island. It rained briefly almost every day and the weather changed quickly.

One morning, I climbed a ridge with a path of rocks that led me almost straight up like a staircase winding through a jungle where there were swarms of black butterflies, exotic birds with melodic whistling voices, and an occasional iguana perched on a rock. The ground was blanketed with wet leaves and shaded by bright green tropical trees and every so often, there was a break in the canopy, revealing spectacular glimpses of the view below.

When I reached the top, I was welcomed by an absolutely breathtaking view of a blue sky full of white puffy clouds, a turquoise colored sea below and other islands that reached into the distance. I had arrived at the highest point on the island and had a 360 degree view of utter paradise. I stopped to take it all in, and enjoy the peaceful surroundings and pray.

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A Mother’s Story

A Mother’s Story, by Charlotte Benson

As Christiane and I sat doing her homework one afternoon, hopelessness mounted inside of me as her strong will, independence and defiance reduced me to complete frustration. While fully rejecting my input on a first time attempt, she proclaimed “I already know how to do this, Mom. I’m going to do it like I like to do it.” I retreated to my room in defeat and I didn’t know if I’d ever be able to cope with her strong character. Only a few days later, I found myself praising God for her strength.

That weekend, Christiane was a first grade princess presented in the Helping Hands luncheon, a fundraiser for a children’s foster home in Austin. While each girl was presented on a stage, a bio was read of questions they had answered in their own words. I watched Christiane walk to the center of the stage in her organza white dress and rhinestone tiara, and was moved to hear her answers booming across the loud speaker.

She was asked, if you could invite any famous person to your birthday party, who would it be? She answered, “Monet, the famous artist, because he had low vision too.”

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A Legacy For and Beyond Batten Disease

by Kevin Davies in Bio-IT World

published March 16, 2010

‘The day we got Christiane’s diagnosis was a horrible, obviously very painful day. Disbelief. Despair. Sorrow. Agony. Fear. And unbearable pain. It forever changed our path.” – Charlotte Benson

Christiane Benson started to lose her vision two years ago, at just five years of age. She is legally blind, suffering primarily from a loss of visual acuity. “We’d never heard of Batten disease, but it completely changes your life forever,” says her father Craig Benson, CEO of Rules Based Medicine, a biomarker testing laboratory and diagnostic company in Austin, Texas.

As Benson and his wife Charlotte researched their daughter’s incurable neurodegenerative disease, they found many family foundations dedicated to raising money for similarly rare genetic disorders. “With a disease that affects so few people, it’s hard to get attention when there’s so many other good causes,” says Benson. He wanted to make his own foundation—the Beyond Batten Disease Foundation (BBDF)—relevant for an audience outside Batten disease. “Fortunately, I work with people who are a lot smarter than me,” he says. Among them were his business partner, a serially successful scientific entrepreneur named Mark Chandler, who was founder/chairman of Luminex, and his chief medical officer, Mike Spain.

“We thought, treatment and cures are great, but how do we prevent a disease like this? We were familiar with the Tay Sachs model in the Ashkenazi Jewish population that took pretty aggressive carrier screening and family counseling to virtually eliminate that disease in that population over about 15 years,” recalls Benson. “It appeared the only hindrance to taking that exact same proven strategy to a much broader perspective was technology and cost.”

Chandler happened to serve on the board of directors of the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico. Benson called NCGR director Stephen Kingsmore, who has a background in orphan diseases. Kingsmore supported Benson’s ideas about a universal carrier screening strategy using next-generation sequencing to offer, as Benson says, “not just a handful of diseases like CF or Tay Sachs or Pompe’s or adrenoleukodystrophy, but actually try to take every medically devastating autosomal recessive or X-linked condition and multiplex it and put it on a sequencing platform… It’s perhaps the first and initially the best utilization of the sequencing application. You get meaningful, actionable information out of it.

“They decided to be quite audacious about it,” says NCGR’s Callum Bell, formerly of Genzyme. “Rather than just look at a single disease, study the long tail of diseases that are individually very rare, but if you add them up they become quite common. A few percent of live births have some kind of genetically related problem.”

Time and Money

Benson says his goal is “to put 500 diseases we’ve selected, what we consider the most medically devastating diseases, onto a single panel. Our hope is to offer that test for less than $500.”

The current Beyond Batten list is actually 437 disorders. “In OMIM [Online Mendelian Inheritance in Man], there are about 1000 recessive diseases with a known gene. Our panel is aiming to address about 450 of those,” says Bell, who is leading the Beyond Batten project.

The criteria were recessive disorders that caused childhood fatality or extreme childhood disease. Some disease foundations worked with Benson to have their own gene(s) of interest included in the test. “We didn’t want any controversy that these were traits or not life threatening,” says Kingsmore. “We didn’t want to get into any stigma with doing carrier testing. [It had to be] morally unequivocal.” One issue is that there are still some diseases where patent holders are unwilling to share their exclusive rights, a plight Kingsmore calls “tragic, because these tests are not economically viable unless on a panel.”

The NCGR will use a next-generation sequencing platform to sequence the coding regions of all 437 disease genes (see “Technology Target”). The plan is to set up a new CLIA-compliant entity to perform the test. Kingsmore anticipates a limited launch later this year that won’t yet be a billable carrier screening test.

Benson is searching for a permanent location for the DNA analysis lab, with the choice narrowed down to four (unnamed) sites. In addition to target enrichment, compute facilities and sequencing, the partners need economic development resources to raise money to get the program off the ground.

As for when it would be offered, Benson says: “Ultimately we’d like it to become standard-of-care for a young woman at the ob/gyn.” Another likely market will be in vitro fertilization clinics, where Benson says families are already undergoing an extensive out-of-pocket procedure. He sees the Beyond Batten test as providing more information.

“It’s intended to prevent the disease,” says Bell. “It will be for couples considering pregnancy… We’re hoping it’s adopted in same way as Tay Sachs testing. Or for girls at their first ob/gyn appointment, when they get a vaccination for HPV—that would be an optimal point to have them tested. They could later make informed family planning choices based on the test results.”

Benson and Kingsmore were hoping to launch the test this May, but various issues may push that out a little.

Eradicate and Cure

The launch of a test that could encourage some to seek abortions for affected fetuses could provoke controversy, but Benson doesn’t see it that way. “My personal faith would make me concerned about that anyway,” he says. “We were not oblivious to it. Our intention for this test and the market we plan to sell into is not for someone who is 2-3 months pregnant. We’re planning to offer this testing very early, before anyone’s even thinking about a family. We think it will provide useful information for families to make decisions because there are so many choices. IVF, adoption, there are alternatives families can choose that will not lead them down that path.” Benson quotes a saying: “It’s always good to stay on the side of the angels.” That way, he says, “you can always sleep well at night.”

“Our drive is to get the cost of this down to a level that is going to be affordable without insurance,” says Benson. BBDF will get some proceeds from test sales. “We view this test and its commercialization as the means of sustainability and a permanent funding source for our treatment and cure efforts… This is not really a commercial venture,” he concludes. “This is, for us, a legacy.”

Technology Target

The NCGR will sequence the coding regions of a total of 437 selected disease genes—about 2 megabases in all. While the Illumina platform remains the NCGR benchmark, Kingsmore says the Life Technologies SOLiD system is improving, and NCGR is also one of the early-access partners for Pacific Biosciences.

Kingsmore’s original assumption was that he would screen the disease genes using a custom DNA chip, similar to those in use in clinical labs for copy number variant detection. But issues of allelic heterogeneity and the error-filled cataloguing of variants prompted him to reconsider. Taking a longer view, needing a platform that could adapt to the discovery of new mutations or genes, the choice was either redesigning the chip every six months or taking the sequencing route. “I do believe sequencing will become cheaper than chips eventually,” says Kingsmore.

Bell and colleagues have been evaluating four enrichment technologies, including Agilent, febit, and RainDance. The favorites are currently Agilent and RainDance. “Agilent is very cost effective, but there are concerns that there are some targets we can’t design for. RainDance works very nicely, but cost is an issue,” says Kingsmore.

The NCGR team is also facing unexpected challenges in validating variations and improving software. Some of the interpretation challenges Kingsmore’s group has encountered means his team needs to validate its assays to a much higher degree than he’d envisioned just six months ago. “There isn’t a gold standard database of reference material, which surprised me,” says Kingsmore. He’s finding both deleterious mutations that cause devastating childhood diseases that the literature has mis-annotated, as well as variants called deleterious mutations that are sometimes just common SNPs. “It means we’re going to have to fold into this a whole level of discovery effort I hadn’t anticipated. We want something clinically useful and actionable.”

“Everyone’s going to be a carrier for about five disease mutations,” adds Bell. “Plus, how do you deal with those for which you haven’t got a confirmed phenotype—so called Variants of Unknown Significance (VUS)? If you find a nonsense mutation or a frameshift VUS, you may think there’s an obligation to do some kind of reporting around that. A weak link will be the physician that orders the test. I don’t know that the average doctor is equipped to counsel patients based on that number of genes. If you start introducing probability of disease based on an algorithmic approach to VUSs, it gets even more difficult.”

One priority at NCGR is to upgrade the Grindstone Laboratory Information Management System (LIMS) to handle different security levels, since it will be handling clinical data and needs to be CLIA compatible. It also needs to be able to handle multiplexing. Then there’s the Alpheus variant detection pipeline (see, “Jumping on Next-Gen Sequence Data Analysis,” Bio•IT World, July 2009), which Kingsmore says is “designed to do on-the-fly query of datasets. For a diagnostic or carrier screening, we want to lock that down, giving a standard well annotated report. We’ve got to do a lot of code hardening there as well.”

http://www.bio-itworld.com/BioIT_Article.aspx?id=97662&terms=+legacy++beyond+batten+disease

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