Category Archives: Gene Medicine

CAMBRIDGE, Mass.--(BUSINESS WIRE)--

Foundation Medicine, Inc., a molecular information company that brings comprehensive cancer gene analysis to routine clinical care, and Dana-Farber Cancer Institute today announced the Nature Medicine publication of results from their collaborative next-generation sequencing (NGS) study to assay cancer-relevant genes in 24 non-small cell lung cancer (NSCLC) and 40 colorectal cancer (CRC) cases. In this study, 59% of the samples were found to have genomic alterations directly associated with a clinically-available targeted therapeutic or a relevant clinical trial of a targeted therapy. Two novel gene fusions, KIF5B-RET in NSCLC and C2orf44-ALK in CRC, were discovered among the potentially druggable alterations identified in the study. Both of these findings may expand therapeutic options for a subset of cancer patients. This publication demonstrates that using targeted NGS to profile patient tumors for molecular alterations associated with therapeutic responses may have an important clinical impact in cancer treatment.

“In this collaboration, we detected clinically-relevant genomic alterations in more than half of the samples profiled, and, because Foundation Medicine’s NGS assay detects all classes of alterations with clinical-grade sensitivity, this research was able to identify both expected as well as completely novel alterations,” said Maureen Cronin, Ph.D., senior vice president, research & product development of Foundation Medicine and co-author of the study. “The discovery of novel rearrangements and fusions, such as KIF5B-RET and C2orf44-ALK, supports an important role for NGS in the clinical understanding and treatment of cancer.”

“In a common indication like NSCLC, identifying even a small subpopulation of individuals with gene fusions who may be responsive to a targeted therapy has the potential for major therapeutic impact,” said Phil Stephens, Ph.D., executive director, cancer genomics of Foundation Medicine and co-author of the study. “This joint research with Dana-Farber translates genomic research to the clinic and we expect that it may quickly have a positive impact for patients.”

Clinically-relevant alterations, which are defined here as being associated with an available clinical treatment option or ongoing clinical trial investigating a new targeted therapy, were identified in 72% of NSCLC tumor samples and 52.5% of CRC tumor samples.

The novel, recurrent KIF5B-RET fusion was identified by the NGS assay in one patient with NSCLC. In subsequent screening, 11 additional RET fusions were identified in 561 lung adenocarcinoma samples from a cohort of never or limited former smokers with NSCLC. In common with known oncogenic alterations in EGFR and EML4-ALK, the KIF5B-RET gene fusion was found more than twice as often in NSCLC samples from individuals of Asian descent (0.8% (1/212) of the Caucasian samples and 2% (9/405) of the Asian patient samples). Additionally, none of the fusion-positive tumors contained alterations in any of the other known oncogenes that drive lung cancer (EGFR, ERBB2, BRAF or KRAS or rearrangements of EML4-ALK or ROS1).Tumors with this fusion were specifically sensitive to targeted drugs that inhibit RET, suggesting that prospective clinical trials of RET-targeted therapeutics may benefit individuals with NSCLC with KIF5B-RET rearrangements.

The second novel finding in the study was a potentially clinically-relevant gene fusion between C2orf44 and ALK identified in one CRC patient. Additional assays suggest this fusion gene yields 90-fold overexpression of anaplastic lymphoma kinase (ALK), the target of crizotinib, a U.S. FDA approved therapy for NSCLC. Given the structure of the rearrangement that generated the C2orf44-ALK fusion, it is unlikely that current clinical detection methods would have detected this alteration. This research thus suggests that a previously unrecognized subset of individuals with CRC may harbor genetic alterations that may make them responsive to ALK-inhibitor treatment.

The assay used for the testing described in this Nature Medicine paper is analytically validated to have a false discovery rate of less than 1% with at least 99% sensitivity for base substitutions occurring with at least 10% frequency.

The paper, “Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies” by Lipson, D. et al. is now available online.

About Foundation Medicine’s Comprehensive Cancer Genomic Test

Foundation Medicine’s comprehensive cancer genomic test uses next-generation sequencing to analyze routine clinical specimens (i.e., small amounts of formalin fixed, paraffin embedded tumor tissue) for all classes of genomic alterations (point mutations, copy number alterations, insertions/deletions, and select rearrangements) in approximately 200 cancer-related genes. The test is optimized for clinical-grade analysis of tumor tissues, overcoming multiple complexities (such as purity, ploidy and clonality) inherent to tumor genomes. Results are designed to serve as a helpful decision-support tool for physicians to evaluate cancer treatment approaches tailored to each patient’s molecular subtype. Each patient report is reviewed and annotated by a molecular oncologist and consists of scientific and medical literature relevant to that patient’s genomic alterations and includes information on targeted therapies and clinical trials supported by scientific and medical research.

About Foundation Medicine

Foundation Medicine is dedicated to improving cancer care through the development of comprehensive cancer diagnostics that will help physicians inform treatment decisions based on an individual patient’s molecular cancer subtype. Foundation Medicine’s first laboratory developed test, based on a next-generation sequencing platform, is designed to accommodate a broad landscape of cancer genome information and a growing repertoire of targeted treatments and clinical research opportunities. Foundation Medicine’s test will assist physicians to make prompt and informed determinations about the best cancer treatments and clinical trial options for each patient, taking into account each patient’s unique cancer-associated alterations alongside publicly available scientific and medical information. The company’s founding advisors are world leaders in genome technology, cancer biology and medical oncology; they, alongside clinicians, biotech and molecular diagnostics industry leaders, are working to harness emerging technologies to develop unparalleled tests that will identify and interpret an ever-growing set of actionable genomic alterations, truly enabling personalized cancer medicine. For more information, please visit the company’s website at http://www.foundationmedicine.com.

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Foundation Medicine and Dana-Farber Cancer Institute Identify Novel Genomic Alterations in Lung and Colorectal Cancer

News | Mind & Brain

Two doses of gene therapy restore vision to three women who were born nearly blind

By Ferris Jabr  | February 8, 2012 |

SIGHT FOR SORE EYES: A second round of gene therapy for blindness worked just as well as the first. Image: Garretttaggs55, Wikimedia Commons

Gene therapy has markedly improved vision in both eyes in three women who were born virtually blind. The patients can now avoid obstacles even in dim light, read large print and recognize people's faces. The operation, researchers predict, should work even better in children and adolescents blinded by the same condition.

The advance, reported in the February 8 issue of Science Translational Medicine, extends earlier work by the same group. Between 2008 and 2011, Jean Bennett of the University of Pennsylvania's Mahoney Institute of Neurological Sciences and her colleagues used gene therapy to treat blindness in 12 adults and children with Leber's congenital amaurosis (LCA), a rare inherited eye disease that destroys vision by killing photoreceptors—light-sensitive cells in the retina at the back of the eye. Typically, afflicted children start life with poor vision, which worsens as more and more photoreceptors die.

The treatment grew out of the understanding that people with the disorder become blind because of genetic mutations in retinal cells. One mutated gene that causes the disorder is named RPE65. An enzyme encoded by RPE65 helps break down a derivative of vitamin A called retinol into a substance that photoreceptors need to detect light and send signals to the brain. Mutant forms of RPE65 prevent the production of this enzyme in a "nursery" layer of cells called the retinal pigment epithelium, which is attached to the retina and nourishes photoreceptors by breaking down retinol, among other cellular services.

In the initial study, retina specialist and Bennett's co-author Albert Maguire of Penn Medicine injected a harmless virus carrying normal copies of RPE65 into an area of the retinal pigment epithelium, which subsequently began producing the enzyme. In each of the 12 patients, Maguire treated one eye—the one with worse vision. Six patients improved so much they no longer met the criteria for legal blindness.

In the new study, Maguire injected the functional genes into the previously untreated eye in three of the women from the first group. Bennett followed the patients for six months after their surgeries. The women's vision in their previously untreated eye improved as soon as two weeks after the operation: They could navigate an obstacle course, even in dim light, avoiding objects that had tripped them up before, as well as recognize people's faces and read large signs. Bennett showed that not only were the women's eyes much more sensitive to light, their brains were much more responsive to optical input as well. Functional magnetic imaging showed regions of their visual cortices that had remained offline before gene therapy began to light up.

Surprisingly, Bennett reports, the second round of gene therapy further strengthened the brain's response to the initially treated eye as well as the newly treated one. "That wasn't something we had been expecting, but it makes sense because the two eyes act in concert, and some aspects of vision rely on binocularity." In the new paper, the authors suggest that neuroplasticity plays a role: It is possible that regions of the visual cortex responding to the newly flowing channel of information from the second eye bolster activity in areas of the visual cortex responding to the initially treated eye.

An institutional review board required that Bennett work with adults in the follow-up study, but she thinks the therapy will work even better in younger patients who have not lost as many photoreceptors. She says the results "really bode well" for restoring meaningful vision to people with LCA and other forms of inherited blindness.

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Sight Seen: Gene Therapy Restores Vision in Both Eyes

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Academic Journal
Main Category: Eye Health / Blindness
Also Included In: Genetics
Article Date: 09 Feb 2012 - 0:00 PST

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Researchers from the Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia have conducted a recent study, published in Science Translational Medicine which focuses on gene therapy for congenital blindness. The scientists were able to improve sight in 3 adult patients who had previously been treated in one eye. The researchers used the same treatment on the second eye of the patients, and they were able to see in low-light situations and also find their way around. There were no conflicting effects reported.

The scientists report that the first and second treatments had no immune reactions which cancelled the genes administered. This has happened in previous studies of gene therapy on different diseases. This study in particular focused on addressing Leber congenital amaurosis (LCA), a retinal disease that results in complete loss of vision by the time the person is an adult.

Jean Bennett, M.D., Ph.D, F.M Kirby, professor of Ophthalmology at Penn., said:

"Patients have told us how their lives have changed since receiving gene therapy. They are able to walk around at night, go shopping for groceries and recognize people's faces - all things they couldn't do before. At the same time, we were able to objectively measure improvements in light sensitivity, side vision, and other visual functions."

During their research, researchers used neuroimaging to flash a dimly blinking checkerboard pattern in front of the patient's eye which had recently been treated. They found that a part of the brain responsible for vision brightened as a result of the functional magnetic resonance imaging (MRI).

Manzar Ashtari, Ph.D., of The Children's Hospital of Philadelphia, and the co-leader of the study says:

"This finding is telling us that the brain is responding to the eye's sensitivity to dim light".

The team administered patients with a vector, a genetically engineered adeno-associated virus, which was carrying a normal version of the gene named RPE65, which is mutated in one form of LCA. LCA is an accumulation of hereditary retinal diseases, in which a gene mutation challenges production of an enzyme necessary for light receptors in the retina.

Before this study, the researchers conducted a trial in Octorber of 2009, using the same gene therapy. The study involved 12 volunteers with LCA. Four of these patients were under the age of 11 when they were treated for the blindness. They only treated one eye in the patients - whichever eye was able to see better, and the study had evident results - 6 patients were able to see better, and were no longer considered "legally blind". Even though the testing on animals proved that re-administering the treatment in the second eye was safe, the researchers were skeptical that the vector in the eye which had not been treated could possibly result in inflammatory responses that could take away the benefits from the eye that wasn't treated.

The eye is somewhat separate from the body's immune system, therefore the concern was not high in terms of the inflammatory responses, however, further testing needed to be done in practice.

Bennett commented:

"Our concern was that the first treatment might cause a vaccine-like immune response that could prime the individual's immune system to react against a repeat exposure."

Like the first study, Albert M. Maguire, M.D, a study co-author, and professor of Opthalmology at Penn, administered the vector in the eye which was untreated previously, in 3 patients at The Children's Hospital of Philadelphia. These patients had received treatment 3 years prior. The authors then proceeded to observe the patients for 6 months after they had been readministered with the vector. The greatest advancements were in terms of light sensitivity, including the pupil's acknowledgments to light when it was seen in a range of different intensities. Out of the 3 patients, 2 were able to find their way through an obstacle course in very low-light situations.

The study showed no significant problems, and they actually discovered something they were not looking for. The fMRI findings demonstrated improvement in brain responses in the first treated eye, not just the newly treated one. The researchers say this is probably because the eyes were able to parallel each other in zooming in on the objects they were trying to see.

The authors say that it is important for further research to be done in order to ensure that gene therapy is an effective and safe way to treat retinal disease in humans.

Bennett concludes:

"However, the findings bode well for treating the second eye in the remaining patients from the first trial - including children, who may have better results because their retinas have not degenerated as much as those of the adults. What's more, the research holds promise for using a similar gene therapy approach for other retinal diseases."

The Children's Hospital of Philadelphia and The Center for Cellular and Molecular Therapeutics (CCMT) sponsored both trials and constructed the vector which carried the corrective gene. The director of CCMT, Katherine A. High, M.D., and pioneering gene therapy researcher, was the co-author of both studies.

CCMT, the Foundation Fighting Blindness, the National Institutes of Health, Research to Prevent Blindness, Hope for Vision, the Paul and Evanina Mackall Foundation Trust at the Scheie Eye Institute, the F.M Kirby Foundation, and anonymous donors funded this study.

Written By Christine Kearney
Copyright: Medical News Today
Not to be reproduced without permission of Medical News Today

Visit our eye health / blindness section for the latest news on this subject. AAV2 Gene Therapy Readministration in Three Adults with Congenital Blindness
Jean Bennett,, Manzar Ashtari, Jennifer Wellman, Kathleen A. Marshall, Laura L. Cyckowski, Daniel C. Chung,, Sarah McCague, Eric A. Pierce, Yifeng Chen, Jeannette L. Bennicelli, Xiaosong Zhu, Gui-shuang Ying, Junwei Sun, J. Fraser Wright, Alberto Auricchio, Francesca Simonelli,, Kenneth S. Shindler, Federico Mingozzi2, Katherine A. High, and Albert M. Maguire
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Gene Therapy Proves Effective In Treating Blindness

8 February 2012 Last updated at 14:35 ET By Helen Briggs Health editor, BBC News website

Three US citizens who lost their sight in childhood have reported a dramatic improvement in vision after having gene therapy in both eyes.

There was some improvement after the genetic fault in one eye was corrected four years ago.

Now, one woman has described her joy at seeing her children's faces, after her second eye was treated.

The research increases hopes that gene therapy can be used in a range of eye conditions, said a UK expert.

The three have Leber's Congenital Amaurosis (LCA), a rare inherited disease caused by defects in a gene encoding a protein needed for vision.

It appears at birth or in the first months of life, leading to severely impaired vision, involuntary eye movements and poor night vision.

The disorder, which can be caused by 'mistakes' in more than 10 different genes, prevents normal function of the retina; the light-sensitive layer of cells at the back of the eye.

Several teams around the world are carrying out early trials of gene therapy in blindness, including experts at the Philadelphia Children's Hospital and the University of Philadelphia, US.

Only a handful of patients worldwide have received the treatment to boost a faulty gene underlying an inherited form of blindness.

Continue reading the main story Tami Morehouse on regaining her sight

"Life's just so much easier at a level that most people take for granted. Yes, seeing my kids' faces - my son has big huge black eyes, my daughter has big beautiful blue eyes, and I have to look very carefully to see them, but I can. Everyday things were lost to me and now I have a bit of that back and I just can't tell you what that means."

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The US researchers revealed in 2008 that 12 people with LCA had recovered some vision after being injected in one eye with an engineered virus carrying the gene RPE65.

In a follow-up study they treated the other eye of three of them, and found it improved their sight even more.

The subjects could see better in dim light and two were able to find their way around obstacles.

The results were revealed in the latest edition of the journal Science Translational Medicine.

The principal investigator of the study, Dr Jean Bennett, said the patients could now do things they could never do before, such as walking around at night, going shopping for groceries and recognising people's faces.

She told the BBC: "We've shown that it is possible to safely treat both eyes of people with this particular form of retinal deficiency using a gene-based treatment and further we've demonstrated that the brain understands what the retina is seeing."

MRI scans showed the brain could "see" the newly-treated eye.

Continue reading the main story “Start Quote

I think it will be a stepping stone to treating more common forms of blindness in both eyes”

End Quote Dr Jean Bennett University of Pennsylvania

Dr Manzar Ashtari, from The Children's Hospital of Philadelphia, who carried out the brain scans, told the BBC: "We saw the brain gets activated - the brain after treatment responded to the visual stimuli."

'Incredibly valuable'

One of the three patients who took part in the clinical trial, Tami Morehouse, told the BBC how her vision gradually returned, opening up a whole new world for her.

Even though she can't see well enough to read or drive a car, she can now make-out her children's faces, watch them play baseball and see the light change over Lake Erie, where she lives.

She said: "Life is so much easier at a level that most people take for granted. Any amount of vision that you can get when you have almost nothing is incredibly valuable."

The researchers now hope to treat the second eye of the remaining nine patients, and extend the clinical trial.

Dr Bennett said: "I think it will be a stepping stone to treating more common forms of blindness in both eyes."

Commenting on the study, Clara Eaglen, policy and campaigns manager at the Royal National Institute of Blind People (RNIB), UK, said: "The early results of this small scale trial are encouraging, but clearly, a lot more research is needed to maximise the benefits of gene therapy techniques and understand how they can then be turned into effective treatments for a variety of more common degenerative eye conditions."

Professor Robin Ali of the Institute of Ophthalmology at University College London leads a UK team carrying out a similar trial of gene therapy.

He said: "This is confirmation that it is possible to administer gene therapy safely to the second eye of patients.

"This is reassuring and increases the prospect of this type of therapy for treatment of a wide range of eye conditions."

Link:
Gene therapy 'gave me sight back'

WEDNESDAY, Feb. 8 (HealthDay News) -- As a child, Tami Morehouse had vision problems. She struggled to read the blackboard at school, and homework took hours.

Yet, she made it through high school and college, and became a social worker. Although she was never able to drive, she learned to ride a bike.

But in her 30s, with three young children, her vision took a turn for the worse. "I'd be reading a book and the words faded away," she said.

Morehouse was going blind, the result of Leber congenital amaurosis (LCA), a rare inherited eye disease that causes a progressive loss of vision. "As my kids needed me more and more, I was able to do less and less," Morehouse said.

That changed in 2009, when she was one of 12 people to undergo an experimental treatment using gene therapy in one eye. Now, scientists report even more progress, having successfully treated the second eye of three patients, including Morehouse. The new results are published Feb. 8 in Science Translational Medicine.

LCA is caused by a faulty gene, RPE65, that fails to produce an enzyme needed by the retina, the tissue in the back of the eye that converts light images into nerve signals that get sent to the brain.

Lack of the enzyme causes toxic byproducts to build up in the retinal cells, gradually killing them.

"It's inevitable and progressive, and people watch as they are losing more and more of their vision," said Dr. Jean Bennett, an ophthalmology professor at University of Pennsylvania Perelman School of Medicine and co-leader of the research team that pioneered the treatment. "By the time they're teenagers or young adults, they are severely impaired."

The treatment involved injecting a virus genetically engineered to carry a normal version of gene RPE65 into the retinal cells.

About two weeks later, with the eyes now producing the enzyme, the patients -- adults and children -- saw a marked improvement in their vision.

"They all gained vision in a very meaningful way," said Bennett, also a scientist at Children's Hospital of Philadelphia. "Children can read books, ride their bikes to their friends' houses -- things which they never could do before."

Initially, researchers only injected one eye because of safety concerns, Bennett explained. The fear was that the first injection would prime the immune system to recognize the virus and attack it when it was injected into the second eye. That would cause inflammation in the eye, potentially leading to more vision loss.

But animal studies showed that didn't happen, and so they decided it was safe to try the second eye in adults.

"It's amazing," Morehouse said. "I just feel so different. I used to wake up in the morning, so afraid and so anxious, that I would look over at the alarm clock and see nothing."

Prior to the treatments, she could see light and dark, but most of the world was hazy and gray. By night time, when her eyes were tired, she could see very little.

Today, her vision is still significantly impaired. She needs help finding her way to a table in a restaurant, for example, and reading isn't really possible. Yet, she can tell when someone is approaching, and she can make out a smile.

"Seeing my daughter walk across the basketball court. Seeing my son step up to the plate when he's playing ball -- it's phenomenal," Morehouse said.

Researchers verified that patients could see more by performing functional MRI scans before and after the second eye treatment. The brain imaging showed much more response to visual stimuli after their second eye was done.

At 47, Morehouse was the oldest patient. The prior study taught researchers that children improved the most, probably because their retinal cells had suffered less damage.

Now that researchers have established the procedure is safe in adults, they've started using gene therapy on the second eyes of children with the condition, Bennett said.

Though more research needs to be done and there are "technical" issues to be overcome, "we want to be able to use this approach in developing similar treatments for other more common blinding diseases," she said.

Dr. Richard Lewis, a clinical correspondent for the American Academy of Ophthalmology, called the results "exciting." Not only did the results show that treating the second eye is safe and effective, but that vision in the first eye also appears to improve as well.

"This is setting us up for the next step, which is to take the 5-year-old, the 8-year-old, or even the 6-month-old who has the mutation in this particular gene, and replace the enzyme using gene replacement therapy before permanent damage is done," said Lewis, who is a professor of ophthalmology at Baylor College of Medicine's Cullen Eye Institute in Houston.

More information

The Foundation Fighting Blindness has more on LCA.

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More Success With Gene Therapy for Blindness

Treating Two Eyes Safe and Effective, New Study Confirms

By Salynn Boyles
WebMD Health News

Reviewed by Laura J. Martin, MD

Feb. 8, 2012 -- Functionally blind for many years, Tami Morehouse calls the gene therapy that partially restored her sight nothing short of a miracle.

Morehouse was the first of 12 patients with a rare congenital retinal disease to receive the experimental treatment in one eye three years ago, and she is one of just three who has now had the gene therapy in both eyes.

The 47-year-old Ohio social worker and mother of three says before having the treatment she worried everyday that she would lose what little sight she had left.

"This treatment literally gave me a much brighter future," she says. "My world just lit up and I saw things much more clearly. Soon after the second treatment I went out to dinner with my husband and I looked down and thought, 'Oh my gosh, I can see the glass sitting in front of me.'"

Gene Therapy Targets Eye Mutation

The study Morehouse took part in was among the first to show that gene therapy can improve vision in people with inherited blindness.

The updated findings prove that treating both eyes is safe and beneficial, says researcher Jean Bennett, MD, PhD, of the University of Pennsylvania.

Patients received injections of healthy copies of a dysfunctional gene into their eyes in an effort to get the cells to work better.

The injections worked so well that Bennett and colleagues plan to treat the second eyes of the remaining five children and four adults who took part in the original study.

"There was some concern that the first injection would set up an immune response, causing the body to reject the second injection," Bennett says. "If that happened, the benefits to the first [treated] eye could be threatened."

But that is not what happened.

After having the injections in their second eye, the three patients were better able to see in dim light, and two of the three were able to navigate obstacles in low-light situations.

Half of Patients No Longer Legally Blind

All of the patients had an inherited, degenerative retinal disease called Leber congenital amaurosis (LCA), which is caused by a mutation in the RPE65 gene and generally progresses to blindness by mid-adulthood.

Morehouse says her vision became worse with each of her three pregnancies.

By the time she reached her early 40s, she saw little light or color, and most objects looked like "dark, hazy, blurry blobs," she says.

The treatment involved injections of a genetically engineered virus that carried a normal version of the RPE65 gene.

After the first injections, the vision of six of the 12 study participants improved to the point that they were no longer classified as legally blind.

"One of the children who took part in the original study was riding a bicycle within a year," says study co-author Manzar Ashtari, PhD, of the Children's Hospital of Philadelphia. "This is a child who used a cane and held on to adults to guide him before having the treatment."

Gene Therapy Might Prevent Blindness

The hope is that similar therapies targeting other mutations can be used to treat a large number of inherited diseases that cause blindness.

Katherine A. High, MD, of Children's Hospital of Philadelphia, who also worked on the study, says there are now 200 known genetic mutations that cause vision loss.

Because LCA is a degenerative disease, there is also hope that the treatment may one day be used in very young children, or even babies, before vision loss has occurred.

"For many genetic diseases -- not just this one -- early intervention will hold the key to optimal outcomes," High says.

Morehouse is most excited by this promise.

"If this treatment or treatments like this one can keep children from losing their vision in the first place and spare them the struggles that I had growing up, that is truly a miracle," she says.

SOURCES: Bennett, J. Science Translational Medicine, Feb. 8, 2012.Jean Bennett, MD, PhD, F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania at Philadelphia.Manzar Ashtari, PhD, department of radiology, Children's Hospital of Philadelphia.Katherine A. High, MD, Children's Hospital of Philadelphia.News release, Science Translational Medicine.News release, Children's Hospital of Philadelphia.

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Gene Therapy Helps People With Inherited Blindness See