Category Archives: Genome

Our knowledge of our genomes is accelerating rapidly, associate professor Marcel Dinger

The traditional annual health check for executives is changing. While all the usual tests are still being used, for the first time there will be an option for whole genome sequencing too.

This new generation testing began in Sydney this week and, though it has the potential to add tremendous value and can already add some value it is early days and there are issues for participants to consider.

The service, called GoNavigate, is a private partnership operating from the St Vincent's campus in Sydney. It checks people from their diet to their DNA.

It combines the genomics expertise of the Garvan Institute for Medical Research and that of Executive Health Solutions, which has provided health checks for corporates in Australia for more than 30 years.

Although anyone who is curious about their health can use the service, at a cost of $6400 (excluding GST), with no Medicare rebate, it is likely to be used mostly by corporates.

It's predicted that one day whole genome sequencing will be routine and babies will have it done at birth. But getting there is complicated and costly.

A few years ago the Mayo Clinic in the US identified executives as the ideal population group to lead the rest of us into the new world of genomic medicine.

Executives were the perfect pioneers; they could afford it, they were already on health check programs and as "early adapters" they were willing to embrace the new culture of genomics.

And they would be attracted by the double benefit: the immediate benefits for their own health and the "heritage" benefits for their children and grandchildren.

While many places in Australia offer some genetic testing to patients, the Garvan is the only place that can sequence the entire genome in a clinical setting.

Now through a commercial partnership between its own company, Genome.One and Executive Health Solutions' corporate clinic, Life First, whole genome sequencing is available to the public.

Their joint service, GoNavigate, is the first attempt in Australia to embed whole genome sequencing in a comprehensive medical check. It's ambitious because genomic knowledge is still limited, although it is evolving fast.

While GoNavigate will sequence a person's whole genome and screen all 20,000 genes, presently it can only interpret 230 of them.

But the sequencing creates a lasting resource that can be mined repeatedly as knowledge grows. This means when the person returns a year or two later, more interpretations may be possible. This and subsequent checks will be far cheaper because the sequencing is already done.

From the current 230 genes this service can detect increased genetic risk for more than 49 conditions which include 31 types of cancer and 13 heart conditions where monitoring and intervention can be of benefit.

It can also predict the person's response to more than 220 medications.

While only 5 to 10 per cent of participants are expected to discover a genetic variation that increases their health risk, almost all will receive some information that can help to refine their choice of medications.

"Genetic information provides an entirely new dimension to understand your health but its value is best realised in the context of other health data," says Marcel Dinger, associate professor at the Garvan and CEO of Genome.One.

The next generation of healthcare is about prevention. He says it is about knowing what you are facing and then trying to prevent it. Genomics is a crucial part of this.

But do people want to know what is lurking in their genes? If something untoward is found, under what conditions would they be obliged to disclose it to their employer or insurance company?

These are complex issues which the service can help answer. Dinger says all information will remain strictly confidential between the service and the participant.

In addition, the service will not provide genetic information where no evidence-based lifestyle change or treatment is possible. A genetic counsellor makes this clear to participants at the outset.

While the sequencing can't diagnose cancer, it can tell if a person has a predisposition to a cancer and alert them to the value of possible precautionary action to prevent or detect it as early as possible.

A common example would involve cholesterol. A person with fluctuating high cholesterol on blood tests may be undecided about whether to try to control it with a statin. These drugs are taken over the long term and have side effects.

In recent times people have begun questioning whether they really need them. If the genetic test shows they have familial high cholesterol, then the case for taking these drugs is stronger.

"The extra genetic layer provides a more certain diagnosis of particular conditions that otherwise wouldn't be available. It allows people to have more confidence in the result," says Dinger. "And as new treatments grow for existing diseases and as we get better at identifying new diseases, so the importance of that genetic layer will increase."

Five per cent of Genome.One's revenue from this service will be dedicated to iHope, which is for families with rare and genetic conditions who can't afford genomic diagnosis.

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Health checks for executives leap into the genomic future - The Australian Financial Review

Two of the most important conferences in genome biology are coming together this year for a single event at the Earlham Institute in Norwich: Genome Science and Genome 10K. Aiming to promote cross-disciplinary communication, collaboration, and innovation, the event will help to foster relationships in the wider genomics community, increase community engagement and drive forwards research into a range of key, global issues.

We asked EI's Director of Science, Federica Di Palma, and Scientific Training Team Manager, Emily Angiolini, about the aims of this unique event, as well as the outcomes that we can most look forward to.

What aims have you set out for this years meeting?

The concept behind bringing together these two conferences is two-fold. Firstly, to engage the wider research community in important community projects, such as the Genome 10K project. The second aim is to facilitate cross-talk between research disciplines related to genomics. Including Genome Science assists us with this goal, as a primary mission of the meeting is to explore, develop and communicate recent developments in genomic technologies. Furthermore, bringing the event to Norwich allows us to engage with a greater delegation of European researchers involved in biodiversity genomics efforts.

Why are events like this important for fostering partnerships and advancing research in genomics and computational biology?

Conferences such as this are important as they provide a platform to share, discuss and review ideas, which will lead to novel developments and applications. They provide a mechanism for networking, identifying common interests and potential collaborations to help move projects forward. The Genome 10K Community of Scientists (G10KCOS) has used this model to great success to deliver significant milestones and inspire new initiatives.

Which element of the Genome 10K and Genome Science event are you most excited about this year?

Bringing together these two previously separate communities is the most exciting element of this conference. The inspiration, guidance and sheer power that can be gleaned by joining new thoughts together has massive potential to advance genomics research and address key, global issues such as conservation, food security and health.

What is the Genome 10K Community of Scientists and what are they trying to achieve?

The Genome 10K Community of Scientists (G10KCOS) is working to achieve a unified approach to systematically sequence the genomes of 10,000 living vertebrates (at least one from each genus). This information will provide a unique resource to understand the complexity of genomes, their resilience to environmental changes, how populations adapt to bottlenecks and why some species undergo massive expansion, essentially to help conserve the rich diversity that we enjoy today.

Register for the event here -http://www.earlham.ac.uk/genome-10k-and-genome-science-conference

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Genome Biology: Fostering Partnerships and Advancing Research - Technology Networks (blog)

A scientist from Vista was part of the team that unlocked the genome for the threatened desert tortoise, a feat that could guide conservation of the animal and advance understanding of reptile genetics.

Brian Henen, the base ecologist for the U.S. Marine Corps at Twentynine Palms and a graduate of Vista High School, worked with a team of researchers from California, Arizona and Canada to unravel the DNA of the long-lived animal. They published their findings in the online science journal PLOS One on May 31.

Its the first time scientists have sequenced the entire genome of a tortoise, and one of only about eight projects in which they have deciphered the genome of a reptile. A genome is the complete set of genes in an organism, and guides its development and function. It also makes up a library of information about the organisms evolution, physiology and relationship to other species.

The genome is a tremendous resource to identify the ability of the tortoise to persist, Henen said. The species have both preexisting traits and things from other species that help it survive in the Mojave Desert, such as disease resistance or the ability to survive the arid climate.... Almost all of those have a genetic basis.

Plodding through the desert with a rounded shell and stumpy legs, a desert tortoise can live an estimated 50 to 80 years. Its native to parts of California, Arizona , Nevada , Utah and Baja, Mexico, and specializes in digging long burrows where it spends most of its time.

The species has existed for 15 to 20 million years, according to the National Park Service. But loss of habitat and disease have wiped out parts of its population, and the desert tortoise is now listed as threatened under the Endangered Species Act, and ranked as vulnerable by the International Union for Conservation of Nature. Genetic analysis has become an increasingly important resource in scientists toolkit for studying and reversing that decline.

To sequence the tortoise genome, researchers took tissue samples of muscle, lung, brain and blood, the paper reported. They processed them in a machine that matches a complete set of base pairs, the chemical building blocks of DNA, Henen said, and then placed those in sequence. Then they compared that to genomes of other species to identify specific genes that control particular traits. Some of those are similar to humans, he said, and some may be found among tortoises, crocodiles and birds.

By tracing common genes, they can better map out the lineage of desert tortoises in relation to other species, he said. And they can investigate genes that control key traits such as the tortoises heat tolerance or immune response. An infection called upper respiratory tract disease syndrome has been linked to the species decline and was a factor in its threatened listing, Henen said. Other conditions such as metabolic bone disease and shell disease, which cause deterioration of the skeleton and shell, are also threats.

Researchers will mine the genome to see how some of the animals ward off those conditions, and why others dont.

The formation of those tissues has genetic basis, Henen said. Those things may help us understand if there are some individuals or populations that are more susceptible because they dont have the best genetic makeup.

That could help researchers develop treatments for disease among the animals, and enable them to focus conservation efforts on tortoise populations that are most at risk, he said.

We will be able to direct our efforts to areas to protect genetic diversity, Henen said. If there are certain populations that are small and vulnerable we may need to protect them more. We may have to spend more effort to protect that population from predators or invasive plant species, or climate change.

About 100,000 of the tortoises remain including 5,000 to 10,000 on the Marine base at Twentynine Palms, said Henen, who supervises efforts to protect and restore the species.

The (desert tortoise) species continues to decline, and because of that we need to understand what are the critical factors, that affect its survival, he said. And having this as a reference is a tremendous step in that direction.

deborah.brennan@sduniontribune.com Twitter@deborahsbrennan

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Vista scientist helps unlock genome for threatened tortoise - The San Diego Union-Tribune

Nature.com

Diving into the genome of papillary RCC unearths therapeutic pearls Nature.com A recent paper published in European Urology has characterized the genomic profile of papillary renal cell carcinoma (pRCC), and could help to inform future personalized therapy options for patients with this rare subtype of kidney cancer. Although ...

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Diving into the genome of papillary RCC unearths therapeutic pearls - Nature.com

An Australia-first service that combines whole genome sequencing and a comprehensive health assessment couldofferindividuals anunprecedented glimpse into their future health.

People with a niggling curiosity and $6400 can now find out if their genetics and lifestyle has left themprone todevelopinga suite of life-threatening conditionsincluding 31 types of cancer and 13 heart conditionsacross 230 genes.

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Patients with rare genetic disease will have access to whole genome testing at Australia's first clinic in Sydney's Garvan Institute.

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Eight months after the family died in a murder-suicide at their home in Davidson, mother of two Maria Lutz is recognised at the 2017 NSW Parents Council Awards.

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Accused bomber Roberto Saenz de Heredia told a jury he doesn't know how his DNA traces got on the parcel's stamp and card.

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Police arrest a 39-year-old man on the Central Coast in relation to the death of Carly McBride who disappeared in September 2014.

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Following a 5-year legal battle, David Cottrell has lost his job after he was accused of sending tip offs about car crashes to a tow truck driver in Sydney.

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Ginger Gorman sits down with a troll who is part of an international network that relentlessly bullies online victims.

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A man has died after he was struck by a bus on the corner of Bathurst and Elizabeth streets in Sydney's CBD. Vision: Seven News.

Patients with rare genetic disease will have access to whole genome testing at Australia's first clinic in Sydney's Garvan Institute.

Launched on Tuesday by Sydney'sGarvan Institute's Genome.One lab and corporate clinic Life First, the service also offers individualsthe ability to predict how they would likely reactto more than 220 medications, allowing clinicians to better tailor treatment to their patients.

CEO of Genome.One Dr Marcel Dinger said the service marked the start of a new era in precision medicine that balanced an individual's genetic predisposition to disease with lifestyle factors.

"Today's launch is a major milestone towards transforming our health system into one based on truly individualised information and one that focuses on prevention rather than treating disease," Dr Dinger said.

"Genetic information provides an entirely new dimension to understand your health, but its value is best realised in the context of other health data.

"Personal and family medical history and lifestyle are key components for consideration in this service," he said.

With its hefty price tag and government subsidies, the service is geared towards those who can afford to pay for it and took a highly proactive approach to their health.

"Others are simply curious about what their genome holds, and if they have any predispositions they want to know about them," Dr Dinger said.

Blood samples provide the raw material needed to sequence a patient's genome. Individuals also undergo a physical examination as well as pathology testing and a review of lifestyle risks like smoking, diet and alcohol intake.

Genetic counsellors guidepatients through the process, explaining how the testing works, managing expectations and interpreting the results.

Roughly 5 per cent to 10per cent of people would discover they carried a genetic variation in their genes that put them at increased risk of one of the conditions the service tests for, Genone.One genetic counsellor Mary-Anne Young said.

"It's not about giving people good news or bad news. It's about explaining 'you have a variation in your genes that causes an increased risk or say, heart disease or cancer or another treatable condition'," Ms Young said.

"Some people are taken aback at first. But the counterbalance is that it doesn't necessarily mean they are going to develop the condition.

"It means they have a higher risk than the average person and they can take steps to reducing their risk," she said.

The service can refer patientsfor further testing, treatment and prevention programs via First Lifeprograms attached to St Vincent's outpatient clinicsin Sydney and Melbourne.

The service only offers testing for conditions with known treatments and effective evidence-based prevention strategies.

Medical ethicists have previously raised concerned about the potential of genetic testing for predispositions leading to over-testing and inappropriate treatment, and creating a cohort of "worried well".

"If people have those concerns we should be addressing them," Ms Young said.

"But I think this is less likely creating a society of worried well and more likely creating a preventative, personalised health system instead of waiting for people to develop the condition then doing something about it."

A total of 47,753 Australians will die of cancer, and 134,174 new cancers will be diagnosed in 2017, government estimatespredict

In 2015, heart disease was responsible for 45,392 deaths and 480,392 largely preventable hospitalisations,according to the Heart Foundation.

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Australian-first whole genome sequencing and health testing open to public - The Sydney Morning Herald

Abaddon1337/CC BY-SA 4.0

The 'Napoleon' oak has few single-letter mutations in its genome.

The towering 234-year-old 'Napoleon' oak on the campus of the University of Lausanne in Switzerland has weathered storms both meteorological and political. The tree was young when Napoleons troops passed through town in 1800, and has grown into a majestic city landmark. But through it all, its genome has remained largely and surprisingly unchanged.

Researchers at the university discovered this unexpected stability after sequencing the genome in different branches of the tree. Their work posted on 13 June as a bioRxiv preprint, which has not been peer reviewed meshes with a growing body of evidence that plants are able to shield their stem cells from mutations1. The practice may be valuable for sustaining their health over a lifespan that can reach hundreds of years.

If you just accumulate more and more mutations, you would eventually die of mutational meltdown, says Cris Kuhlemeier, a developmental biologist at the University of Bern in Switzerland.

Each time a cell divides, mutations can arise because of errors made while copying the genome. Animals shield their reproductive cells from these mutations by isolating them early in development. These cells, called the germline, then follow a different developmental path, and typically have a low rate of cell division.

But plants do not have a dedicated germline: the cluster of stem cells that gives rise to the reproductive parts of flowers also generates plant stems and leaves. Because of this, scientists thought that the stem cells would accumulate many mutations, and that newer branches at the top of a long-lived tree would be remarkably different from the lower branches.

Plant biologist Philippe Reymond and his team at the University of Lausanne decided to test this hypothesis using the universitys prized oak tree. They sequenced the genome from leaves on lower, older branches and upper, younger ones, and tallied the number of single-letter changes they found in the tree's DNA. (Reymond declined to be interviewed by Nature because the paper is currently under review at a scientific journal.)

The team found that the number of mutations was much lower than would be expected based on calculations of the number of cell divisions that occurred between the lower branch and the higher one.

Its a tantalizing study, says Daniel Schoen, a plant evolutionary biologist at McGill University in Montreal, Canada. It touches on something that was simmering always, in the back of the minds of plant biologists.

It is too soon to say how general this phenomenon will be in plants, cautions Karel ha, a plant geneticist at the Central European Institute of Technology in Brno, Czech Republic. The researchers also looked only at one kind of genetic change single-letter changes to the sequence and did not evaluate other kinds of mutations, such as deleted DNA.

Mao-Lun Weng, a plant evolutionary biologist at South Dakota State University in Brookings, notes that the team used a stringent filter to weed out background noise in the sequencing data, and may have inadvertently missed some mutations as a result.

This could mean that some mutations were left out of the analysis. But ha and Weng are quick to note that the results are in line with two studies published last year. In the first2, led by Kuhlemeier, researchers tracked individual stem-cell divisions in the growth region of plants called the meristem. They found that in tomato and thale cress (Arabidopsis), the meristem contains a set of three or four cells that are set aside and divide much less often than the other cells in the region. The other study3, led by ha, also found few mutations between old and new leaves in thale cress.

For Kuhlemeier, the results provide an answer to a question that has troubled him ever since a trip to Oregon 20 years ago. As he looked up at a soaring, 400-year-old Douglas fir, Kuhlemeier wondered how the branches towards the top of the tree would differ from those at the bottom. I had always thought of a tree not as an organism, but as a collection of organisms with different genomes more like a colony, he says. Many ecologists shared his view, but now he has begun to question his earlier idea.

A clearer picture of plant development could help breeders as they increasingly focus on long-lived, perennial plants, says Schoen. If, as plants age, there is this mutation accumulation that could impact vigour, we would want to know about it, he says. We need more information of this type.

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Ancient oak's youthful genome surprises biologists : Nature News ... - Nature.com

BBC News

Genome pioneer John Sulston enters elite club - BBC News BBC News Sir John Sulston is elevated to the Companion of Honour in the Queen's birthday list. Birthday Honours: gongs for Cambridge genome scientist John ...Cambridge News Cambridge scientists among those honoured by Queen | Anglia ...ITV News all 3 news articles »

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Genome pioneer John Sulston enters elite club - BBC News - BBC News

The more data, the better, right? When it comes to genetics, it turns out that might not be the case.

As both genetic sequencing has gotten cheaper and computerized data analysis has gotten better, more and more researchers have turned to what are known as genome-wide association studies in hopes of sussing out which individual genes are associated with particular disorders. The logic here is simple: If you have a whole lot of people with a disease, you should be able to tell what genetic traits those people have in common that might be responsible. This thinking has resulted in an entire catalogue of hundreds of research studies that has shed light on the genetic origins of diseases such as type 2 diabetes, Parkinsons disease, Crohns disease, and prostate cancer, while helping fuel the rise of personalized medicine.

Now, though, a new analysis calls the entire approach into question.

Writing in the journal Cell, a group of Stanford University geneticists write that such large studies are likely to produce genetic variants with little bearing on the disease in questionessentially false positives that confuse the results.

Intuitively, one might expect disease-causing variants to cluster into key pathways that drive disease etiology [the causes of disease], they write. But for complex traits, association signals tend to be spread across most of the genomeincluding near many genes without an obvious connection to disease.

Their analysis suggests an intriguing new way of viewing the genome in which nearly every gene impacts every other gene. Instead of a system in which you can plug and play different variables to affect different results, its a complex, inter-related network. They call this the omnigenic model.

Their work has broad, sweeping implications for the entire field of genetics. First off, that all those big, expensive genome-wide association studies may wind up being little more than a waste of time because they turn up genetic variants that, while perhaps interconnected to the disease, may not actually point to a viable target for things like drug therapy.

Indeed, genes that often seem related to diseases have stumped researchers in terms of the role they actually play in the condition. In the paper, for example, the Stanford researchers re-analysed a 2014 study of 250,000 people which found nearly 700 DNA variants linked to heightbut only 16 percent of these variants had anything to do with a persons height. In the paper, the Stanford researchers suggest that the impact of each variant has a teeny impact on height.

Far from solving a problem though, this new research merely opens up an entirely new line of questioningand shows us once again, that we may not know nearly as much as we thought we did.

[Cell]

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This Study is Forcing Scientists to Rethink the Human Genome - Gizmodo

MedCity News

Are genome-wide association studies fundamentally flawed? MedCity News From 5,000 to 10,000 to one million and beyond. The scale of so-called genome-wide association studies (GWAS) has grown at a voracious pace over the last decade. And there's no sign the initiatives are slowing down. As sequencing and data analysis ...

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Are genome-wide association studies fundamentally flawed? - MedCity News

Thermo Fisher Scientific has launched a program of four-day lecture-based and hands-on CRISPR (clustered regulatory interspaced short palindromic repeats) and TALEN (transcription activator-like effector nuclease) genome-editing workshops at its global training facilities.

The workshops will provide an overview of CRISPR/Cas9 and TALEN technologies through both lecture-based sessions and laboratory practice. The focus will be on topics spanning experimental design strategies, methods for delivering guide RNAs (gRNAs) and Cas9 mRNA/Cas9 proteins into cells for generating gene knockouts, the use of TALs as genome-editing tools for gene knockins, and approaches to analyzing editing efficiency. The workshops will highlight the use of TALEN genome-editing technology for genome-editing applications, including single-nucleotide polymorphism (SNP) repair.

Workshop participants will have the opportunity to design a genome-editing experiment with experts in the field. "Our workshops are designed to equip researchers with the instruction and hands-on training they need to comfortably utilize the leading genome-editing technologies in their own labs," said Helge Bastian, Ph.D., vp and general manager of synthetic biology at Thermo Fisher Scientific. "As the practice of engineering nucleic acids in silico, in vitro, and in living cells evolves at a high-speed pace, it is increasingly important for life science professionals to learn about the basics and the newest formats of these high-precision molecular technologies. This will enable them to unravel the underlying mechanisms of normal cellular processes and disease onset or progression, support the discovery and development of new drugs, and enhance biomanufacturing and therapy solutions."

Thermo Fisher says that as a result of strong demand following workshops in the U.S., Germany, and the U.K., it has now more than doubled the number of workshops offered, and plans to hold courses throughout North America, Europe, the Middle East, and Asia.

Last month, the firm reported a deal to acquire contract development and manufacturing organization (CDMO) Patheon, for $7.2 billion.

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Thermo Fisher Launches CRISPR and TALEN Genome-Editing Workshops - Genetic Engineering & Biotechnology News (press release)