Tuesday, September 4, 2012
Early bionic eye lets patient see
| THE UNIVERSITY OF MELBOURNE |
In a major development, Bionic Vision Australia researchers have successfully performed the first implantation of an early prototype bionic eye with 24 electrodes.
Ms Dianne Ashworth has profound vision loss due to retinitis pigmentosa, an inherited condition. She has now received what she calls a ‘pre-bionic eye’ implant that enables her to experience some vision. A passionate technology fan, Ms Ashworth was motivated to make a contribution to the bionic eye research program. After years of hard work and planning, Ms Ashworth’s implant was switched on last month at the Bionics Institute, while researchers held their breaths in the next room, observing via video link. “I didn’t know what to expect, but all of a sudden, I could see a little flash...it was amazing. Every time there was stimulation there was a different shape that appeared in front of my eye,” Ms Ashworth said. Professor Emeritus David Penington AC, Chairman of Bionic Vision Australia said: “These results have fulfilled our best expectations, giving us confidence that with further development we can achieve useful vision. Much still needs to be done in using the current implant to ‘build’ images for Ms Ashworth. The next big step will be when we commence implants of the full devices.” Professor Anthony Burkitt, Director of Bionic Vision Australia and Professor of Engineering at the University of Melbourne said: “This outcome is a strong example of what a multi-disciplinary research team can achieve. Funding from the Australian Government was critical in reaching this important milestone. The Bionics Institute and the surgeons at the Centre for Eye Research Australia played a critical role in reaching this point.” Professor Rob Shepherd, Director of the Bionics Institute and a member of the Medical Bionics Department at the University of Melbourne, led the team in designing, building and testing this early prototype to ensure its safety and efficacy for human implantation. Cochlear technology supported aspects of the project. Dr Penny Allen, a specialist surgeon at the Centre for Eye Research Australia, led a surgical team to implant the prototype at the Royal Victorian Eye and Ear Hospital. “This is a world first – we implanted a device in this position behind the retina, demonstrating the viability of our approach. Every stage of the procedure was planned and tested, so I felt very confident going into theatre,” Dr Allen said. The implant is only switched on and stimulated after the eye has recovered fully from the effects of surgery. The next phase of this work involves testing various levels of electrical stimulation with Ms Ashworth. “We are working with Ms Ashworth to to determine exactly what she sees each time the retina is stimulated using a purpose built laboratory at the Bionics Institute. The team is looking for consistency of shapes, brightness, size and location of flashes to determine how the brain interprets this information. “Having this unique information will allow us to maximise our technology as it evolves through 2013 and 2014,” Professor Shepherd said. How it works This early prototype consists of a retinal implant with 24 electrodes. A small lead wire extends from the back of the eye to a connector behind the ear. An external system is connected to this unit in the laboratory, allowing researchers to stimulate the implant in a controlled manner in order to study the flashes of light. Feedback from Ms Ashworth will allow researchers to develop a vision processor so that images can be built using flashes of light. This early prototype does not incorporate an external camera – yet. This is planned for the next stage of development and testing. Researchers continue development and testing of the wide-view implant with 98 electrodes and the high- acuity implant with 1024 electrodes. Patient tests are planned for these devices in due course. About Bionic Vision Australia Bionic Vision Australia is a national consortium of researchers from the Bionics Institute, Centre for Eye Research Australia, NICTA, the University of Melbourne and the University of New South Wales. The National Vision Research Institute, the Royal Victorian Eye and Ear Hospital and the University of Western Sydney are project partners. The project brings together a cross-disciplinary group of world-leading experts in the fields of ophthalmology, biomedical engineering, electrical engineering and materials science, neuroscience, vision science, psychophysics, wireless integrated-circuit design, and surgical, preclinical and clinical practice. This research is funded by a $42 million grant over four years from the Australian Research Council (ARC) through its Special Research Initiative (SRI) in Bionic Vision Science and Technology
Editor's Note: Original news release can be found here.
|
Personal genomics: where science fiction meets reality
| EMMA HUANG, CSIRO |
While genes can tell us a lot, they still need to be considered in the context of the environment to improve prediction of disease or particular traits.
Image: zmeel/iStockphoto
Imagine a future where doctors take a strand of your hair or a drop of your blood and tell you yourDNA predicts a 78% risk of developing heart disease. On the plus side, it also predicts exactly which treatments will work best for you. The genetic code is well enough understood that individual predictions and treatments based ongenomics are universal.
In science fiction, this is a “not-too-distant” future. The 1997 film GATTACA, directed by Andrew Niccol, describes a world driven by genomics. At or before birth, doctors calculate your probability of being diagnosed with heart disease, neurological and psychological disorders, and even predict how tall you will be or whether you will need glasses.
For better or worse, this decides the course of your life. In this world a genome sequence is not only cheap, fast, and readily available – it’s also easy to interpret.
Human Genome Project
So let’s compare science fiction with science reality. The Human Genome Project was started in 1990 with aims including sequencing the human genome, identifying and mapping all genes, improving tools for data analysis, and addressing potential ethical, legal and social issues associated with genomics.
It took 13 years and US$3 billion to complete. Since then, sequencing has rapidly become both cheaper and faster.
Now, sequencing a full human genome costs under US$10,000, and takes only two days. It’s cost-effective enough to be performed in large studies and, within a few years, thousands of human genome sequences will be available.
If progress continues at this pace, widespread acquisition of genetic data may indeed be “not-too-distant”. But, translating that data into knowledge through analysis and interpretation will take much longer.
Translating DNA into traits
How do we translate the 3 billion As, Cs, Ts and Gs of the human genome into a precise description of an individual’s risk for disease?
We need to identify which parts of the genome are associated with disease. More than 99.5% of the genome is identical between two humans, but that still leaves 15m positions to search through, which is akin to finding needles in a haystack.
Many different methods exist to essentially look for genetic variants which are over-represented in individuals with disease relative to those without. These work well in cases where only one variant causes disease (such as Huntington’s disease).
Indeed, more than 3,000 traits already have a causal gene characterised and annotated. This success forms the basis for a public-health funded system in Australasia to screen newborns for about 30 rare diseases, including cystic fibrosis and hypothyroidism .
The similarities with newborn testing in GATTACA are clear, but in science reality the testing won’t tell you anything about your child’s risk for heart disease.
For this and other more common diseases (such as Alzheimer’s and diabetes) there are many different genetic factors influencing risk. If these act in pairs, the size of the search problem is increased from millions to hundreds of trillions of possibilities. Further, we often need to consider networks of genetic variants, where changes in one pathway have flow-on effects to other regions of the genome.
Can we decode the DNA code?
There’s been some success in identifying individual variants affecting disease – at the end of 2011 more than 1,600 studies had reported regions of the genome associated with about 250 different traits. But these rarely account for the full spectrum of genetic effects expected for a given disease.
For human height, which, unlike many disorders, is easy to measure and highly influenced by genetic factors, the nearly 200 variants discovered account for only a small portion of the overall variation. Improving individual prediction will require researchers in biology, statistics, computational science and many other disciplines to work together for years to come.
Even if we completely understood the language of DNA sequence, it’s just the tip of the iceberg. Not only are there many effects of DNA beyond that of the sequence (such asepigenetics) – the fact that DNA is only part of the story can be seen in the fact identical twins are not identical people.
Genetics must be considered in the context of environment to improve prediction, as it plays a huge developmental role. A relatively simple example is the disease phenylketonuria, which can cause mental retardation and seizures. This is a disease with a known genetic cause, and is in fact one of the 30 screened for at birth.
The environment is critical in the course of the disease, as patients given a strict diet can lead a normal life. For diseases such diabetes and cancer, both genetic and environmental factors, as well as interactions between the two, must be considered in order to produce accurate models.
There are certainly success stories in personal genomics, and it has the potential to change medicine and society as a whole.
But even if the future is bright, we’re still a long way from making science fiction into science reality.
Editor's Note: This article was originally published by The Conversation, here, and is licenced as Public Domain under Creative Commons. See Creative Commons - Attribution Licence.
|
Explainer: what is the Human Genome Project?
| MELISSA SOUTHEY, THE UNIVERSITY OF MELBOURNE |
The Human Genome Project has already changed the way we think about our health and the world around us, but it is still in its early stages. More complex analysis of our genomes could lead to even more breakthroughs and greater understanding of our bodies and evolution.
Image: mevans/iStockphoto
For many decades humans have pursued work to characterise the human genome. Today,publicly available references to genome sequences are available and have been instrumental in effecting recent advances in medicine, genetics and technology.
But interpretation of the human genome is in its early stages and large initiatives are now embarking on more complex pursuits to characterise the human genome that include understanding individual genome variation.
What is the human genome sequence?
The human genome sequence is contained in our DNA and is made up of long chains of “base pairs” that form our 23 chromosomes. Along our chromosomes are the base pair sequences that form our 30,000 genes.
All humans share a great degree of similarity in their genome sequences – the same genes are ordered in the same manner across the same chromosomes, yet each of us is unique (except for identical twins) in terms of the exact base pair sequence that makes up our genes and thus our DNA/chromosomes.
It is this similarity that, in a genetic sense, defines us as “human” and the specific variation that defines us as individuals.
Launching the Human Genome Project
As early as the 1980s, momentum was gathering behind activities that supported, and would eventually define, the Human Genome Project.
Conversations had turned into workshops that likened characterisation of the human genome to characterisation of the human anatomy that had centuries earlier revolutionised the practice of medicine.
In 1990, with continued support from the United States Department of Energy, the United States National Institutes of Health (NIH) and widespread international collaboration and cooperation, the $3 billion dollar Human Genome Project was launched.
The project aimed to determine the sequence of the human genome within 15 years. By 2000 (well ahead of schedule) a working draft of the human genome was announced. This was followed by regular updates and refinements and today we all have access to a human “reference genome sequence”.
This sequence does not represent the exact sequence of the base pairs in every human, it is the combined genome sequence of a few individuals and represents the broad architecture of all human genomes that scaffolds current and future work aiming to characterise individual sequence variation.
The detail and stories behind the Human Genome Project are themselves extraordinarily human. This project benefited from our human drive for discovery and advancement and our human response to competition.
It forced us as individuals and communities to consider our personal, ethical and social attitudes towards the availability of human genome information, intellectual property protection (especially gene patenting) and public versus private/commercial enterprise in a broad sense.
Advancing the project's success
In the years after the initiation of the Human Genome Project there were constant and significant advances in key areas that facilitated the enormous DNA sequencing effort.
These advances were achieved in all areas key to the efficient processing of DNA into electronic DNA sequence information. They included:
The then state-of-the-art DNA sequencing chemistry used in the Human Genome Project wasSanger sequencing – capable of sequencing single stretches of several hundred base pairs at a time.
Advances in analytical methods of putting these pieces back together into the 3.3 billion base pair human genome was fundamental to the progress of the project.
The Human Genome Project was also advanced by competition. In 1998 a privately funded project with similar aims was launched in the United States by Celera Genomics.
Using a modification of the DNA sequencing technique and a smaller budget it was partly responsible for the accelerated progress of the Human Genome Project.
This competition brought forward other aspects of the project for ethical and legal scrutiny and discussion.
Patent wars
The issue of patenting genes formed a background to the Human Genome Project and many other similarly focused projects for some time. In the early 1990s it had been a serious issue of contention between James Watson and Bernadine Healy (then Director of NIH).
Competition between Celera Genomics and The Human Genome Project now brought the discussion into a different dimension.
The publicly-funded Human Genome Project released new data freely and in 2000 released the first working draft of the genome on the web.
In contrast, Celera filed preliminary patent applications on more than 6,000 genes and also benefited from the data provided by the publicly-funded project.
In March 2000, the US president Bill Clinton announced that the genome could not be patented and should be made freely available.
The stock market dipped transiently because this announcement did not reflect the tangible benefits for biological research scientists.
Within 24 hours of the release of the first draft of the human genome, the scientific community downloaded half a trillion bytes of information from the University of California, Santa Cruz’sgenome server – a strong indication of the relevance of this information to the biological, biotechnological and medical research communities.
Interpretation of the genome sequence is in its early stages but has already improved our ability to offer genetic testing and clinical management of many diseases.
We are now embarking on more complex pursuits to characterise the human genome so as to understand individual genome variation. This work is supported by projects related to, and of the same magnitude as, the Human Genome Project, including projects characterising the genomes of other species, among them mice and yeast, the International HapMap Project,The Personal Genome Project and the 1000 Genomes Project.
These projects are greatly enhanced by the next generation of sequencing methodologies, which will expedite the characterisation of the human genome at an individual level in coming years.
Editor's Note: This article was originally published by The Conversation, here, and is licenced as Public Domain under Creative Commons. See Creative Commons - Attribution Licence.
|
Glaucoma genes discovered
| AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH |
Singapore scientists have identified three new genes associated with Primary Angle Closure Glaucoma (PACG), a leading cause of blindness in Chinese people. PACG affects 15 million people worldwide, 80% of whom live in Asia. The discovery, published in the prestigious scientific journal, Nature Genetics, on 26 August 2012, was conducted collaboratively by scientists from the Singapore Eye Research Institute (SERI)/Singapore National Eye Centre (SNEC), Genome Institute of Singapore (GIS), National University of Singapore (NUS), National University Hospital's Department of Ophthalmology and Tan Tock Seng Hospital. The team of scientists led an international consortium that carried out a genome-wide association study (GWAS) of 1,854 PACG cases and 9,608 controls of over five sample collections in Asia. They performed validation experiments in another 1,917 PACG cases and 8,943 controls collected from a further six sample collections from around the world. A total of 1,293 Singaporeans with PACG and 8,025 Singaporean controls were enrolled in this study. This work is the first to study PACG genetics using a genome-wide perspective. This finding confirms the long-standing suspicion of Professor Aung Tin, the lead Principal Investigator of this project, who is Senior Consultant and Head of Glaucoma Service at SNEC, Deputy Executive Director at SERI, and Professor of Ophthalmology at NUS. Aung has worked on PACG for over 10 years and believes from clinical observations that the disease is strongly hereditary. "This provides further evidence that genetic factors play a role in development of PACG," said Aung. "It is a major achievement for our Singapore team leading the largest international consortium of doctors and scientists involved in glaucoma research. The results may lead to new insights into disease understanding and open the possibility of novel treatments in the future as well as the potential of early identification of people at risk of the disease." The study showcases one of many exciting scientific collaborations between GIS and SERI, and highlights the importance and significant advantages of inter-disciplinary collaborations between the two institutes under such joint efforts. The study was funded primarily by the Translational Clinical Research (TCR) program grant from the National Research Foundation that was awarded to SERI in 2008, as well as other grants from the National Medical Research Council (NMRC), Biomedical Research Council (BMRC), and funding from GIS. GIS Acting Executive Director Professor Ng Huck Hui congratulated the team on the success of the project. "This is an exemplary demonstration of the potential power in genomics being used to dissect complex human diseases with hereditable predispositions. The collaboration between SERI and GIS is synergistic in many broad aspects, and it marries core strengths from both institutions." Professor Wong Tien Yin, Executive Director at SERI and Provost's Chair Professor and Head, Department of Ophthalmology, NUHS, said, "This is a landmark finding, and may potentially change how we view PACG as a disease with genetic links. It highlights how a collective effort from scientists and clinicians and clinician-scientists can unravel diseases of major importance to Singapore. Because this disease is more common in Asians than in the Western populations, such studies will not be done in the US/Europe. This study has to be done in Asia as it is a disease with more implication for Asians. As such, Singapore has led the way forward." Dr Khor Chiea Chuen, Principal Investigator, Human Genetics, at GIS added, "Modern genomics is a very powerful tool in dissecting the hereditable basis of common human diseases. It gives all of us a ray of hope, however far-fetched it may be, that one day we will be able to tailor treatments based on individual genetic profile." "The information on genes involved in PACG has also opened up new and exciting research areas for us that we hope will culminate in new treatment modalities for angle closure glaucoma in the future," Said Dr Eranga Vithana, Associate Director, Basic and Experimental Sciences at SERI, and lead author of the paper. Professor Janey Wiggs, Paul Austin Chandler Assoc. Professor of Ophthalmology, Harvard Medical School added, "This is a landmark study identifying three genes that contribute to angle-closure glaucoma, a form of glaucoma that is particularly common in Asians. These data are the first critical steps toward a better understanding of the underlying molecular events responsible for this blinding disease." SERI is the national body for ophthalmic and vision research in Singapore based at SNEC and NUS. The GIS is a research institute under the umbrella of the Agency for Science, Technology and Research (A*STAR), Singapore.
Editor's Note: Original news release can be found here.
|
Subscribe to:
Posts (Atom)