Category Archives: Gene Medicine

Crowd control: Nearly 4 percent of people carry at least one genetic variant tied to a serious medical condition.

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Most adults with genetic variants tied to certain conditions, such as heart disease or cancer, go undiagnosed, according to a study of more than 50,000 people1.

The variants silence leaves these people unaware of their risk of developing the conditions later in life, says lead investigator David Carey, director of the Weis Center for Research at Geisinger Health System in Danville, Pennsylvania.

Careys team looked for genetic variants associated with 27 chronic conditions. The list of conditions does not include autism, but does include tuberous sclerosis complex. As many as half of all people with tuberous sclerosis complex have autism. Other teams are studying the same population to gauge the effects of variants linked to autism.

The value lies in the huge population, all captured within the same healthcare system. Its really fantastic, says Dan Arking, associate professor of genetic medicine at Johns Hopkins University in Baltimore, Maryland, who was not involved in the new work.

The variants in the study are clinically significant: Some increase the risk of the linked condition by up to 70 percent. But variants interact with many other genetic and environmental factors, and these interactions may cause the conditions features to be more or less severe or even absent.

People used to say anytime there is a [spontaneous] variant or something really rare, that it must cause disease, says Arking. The new study instead suggests that, on the contrary, some rare variants have weak ties to conditions such as autism, he says. The results appeared 23 December in Science2.

Carey and his team looked at data from the MyCode Community Health Initiative, launched in 2007 by Geisinger Health System in central Pennsylvania. MyCode researchers have collected DNA samples and up to 14 years worth of medical records from the participants.

The researchers probed the 50,726 participants genomes for inserted or deleted sequences, and for single nucleotide variants, called SNVs, in the code. Their analysis revealed that each individual harbors about 21,409 SNVs, consistent with findings from previous studies.

The researchers then narrowed their analysis to 76 genes known to contribute to life-threatening conditions such as cancer or cardiovascular disease. The list includes three genes tied to tumor growth and to autism: PTEN, TSC1 and TSC2. (Clinicians are obligated to counsel individuals with variants in any of these 76 genes.)

Nearly 4 percent of the general population carries variants in at least one of these genes, the researchers found. But more than one-third of these people show no symptoms and have no family history of the linked condition. For example, most of the individuals who carry a variant linked to an inherited condition that causes high cholesterol have normal cholesterol levels, according to a second study by Careys team in the same issue of Science.

The findings could mean the individual will develop the condition later in life or not, Carey says. Other variants in her genome might mitigate the risk, he says.

We generally look at one gene at a time, but we have about 20,000 genes and they all work in concert, Carey says. Were not sophisticated enough yet to be able to tease out all the genetic interactions, but we know that they exist.

Last year, another team of researchers used the MyCode data to show that genetic changes tied to autism also crop up in many people without the condition. At the 2016 American Society of Human Genetics annual meeting in Vancouver, Canada, last year, they presented results showing that about 2,000 of the MyCode participants carry large deletions or duplications of genetic material associated with autism, intellectual disability or schizophrenia. But less than 5 percent of this group has received treatment for any of the conditions.

The finding suggests that genetic variants can confer features so subtle that they go unrecognized well into adulthood. Researchers could study this group to understand the mildest end of the autism spectrum.

This cohort could help us describe the full picture of autism, the breadth of the phenotype, says Christa Lese Martin, director of the Autism and Developmental Medicine Institute at Geisinger Health System in Lewisburg, Pennsylvania. Martin was a lead investigator on the autism study but was not involved in the new work.

About 125,000 people have enrolled in MyCode so far. By early next year, researchers expect to have sequencing data for 90,000 of the individuals.

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Many people with harmful genetic variants show no ill effects - Spectrum

A newly discovered type of genetic mutation that occurs frequently in cancer cells may provide clues about the diseases origins and offer new therapeutic targets, according to new research from Weill Cornell Medicine and the New York Genome Center.

Using next-generation sequencing technology, scientists have previously traced cancers roots to mutations that disrupt the sequence of proteins. As a result, the cell either creates hyperactive or dysfunctional versions of proteins, or fails to produce them at all, leading to cancer. Now, a study published Jan. 12 in Cell illuminates a possible new type of driver of the disease: small (one-50 letter) insertions or deletions of DNA sequence, also called indels, in regions of the genome that do not code for protein.

Dr. Marcin Imielinski Photo credit: John Abbott

Those non-coding regions are still important because they contain sequences that affect how genes are regulated, which is critical for normal cell development, said lead author Dr. Marcin Imielinski, an assistant professor of pathology and laboratory medicine at Weill Cornell Medicine and a core member at the New York Genome Center. We already know they are biologically important. The question is whether they can impact cancer development.

In the study,Dr.Imielinski and his colleagues analyzed sequencing data from several publically available databases of tumor samples, focusing on the 98 percent of the genome that does not code for protein. They initially looked at lung adenocarcinoma, the most common type of lung cancer, and found that the most frequent indel-mutated regions in their genomes landed in genes encoding surfactant proteins. Though these genes are essential for healthy lung function, they had not previously been associated with lung cancer. However, they are highly and specifically expressed by the cell type that gives rise to lung adenocarcinoma.

The researchers then looked at the genomes of 12 other cancer types and found similar patterns in liver, stomach and thyroid tumors. In each cancer, noncoding indels clustered in genes that are critical to organ function, but had not been associated with the cancer, said Dr. Imielinski, who is also an assistant professor of computational genomics in theHRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicineand a member of theSandra and Edward Meyer Cancer Centerat Weill Cornell Medicine.

This image shows genetic mutations (blue) in the context of their surrounding DNA sequence, highlighting a sequence motif (red) that Dr. Imielinski discovered.

Most strikingly, these non-coding indels are very common, occurring in 20-50 percent of the associated cancers. They occur as frequently as the most famous cancer-causing mutations, said Dr. Imielinski, who is a paid consultant for the company 10X Genomics, which sells devices and technology to analyze genetic information. Any gene or any sequence that mutated at this frequency has been shown to play a causal role in cancer. That would be an exciting outcome, if we can prove it.

Even if these mutations are not shown to cause cancer, they can be used in the future to improve cancer diagnosis and treatment. These mutations can be biomarkers that help us to diagnose a cancer early, or they could be used to pinpoint a primary cancer when there are metastases and we cant find the original cancer, Dr. Imielinski said. There are a lot of potential clinical implications from these findings.

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New Type of Genetic Mutation Identified in Cancer - Cornell Chronicle

February 23, 2017 A laboratory at UW Medicine in Seattle where DNA research is underway to better understand genetic risks of disease. Credit: Clare McLean

Gene discovery research is uncovering new information about similarities and differences underlying various neurodevelopmental disorders.

These are a wide-ranging collection of conditions that affect the brain. They include autism, intellectual impairments, developmental delays, attention deficits, tic disorders and language difficulties.

To better understand how gene-disrupting mutations contribute to the biology of neurodevelopmental disorders, researchers recently conducted a large, international, multi-institutional study.

More than 11,700 affected individuals and nearly 2,800 control subjects underwent targeted DNA sequencing of 208 suspected disease-risk genes. The candidate genes were chosen based on previously published studies.

By looking at greater numbers of cases and using a reliable yet inexpensive molecular inversion probe, the project team wanted to measure the statistical significance of individual, implicated genes.

Their results are reported in Nature Genetics. The study leaders were Holly A. F. Stessman, Bo Xiong and Bradley P. Coe, of the genome sciences laboratory of Evan Eichler at the University of Washington School of Medicine and the Howard Hughes Medical Institute. Stessman is now at Creighton University.

Their samples were collected through the Autism Spectrum/Intellectual Disability 15-center network spanning seven countries and four continents. An advantage of this collection, the researchers said, is the ability to check back on a large fraction of cases to try to relate genetic results to clinical findings.

In their study population, the researchers associated 91 genes with the risk of a neurodevelopmental disorder. These included 38 genes not previously suspected of playing a role. Based on some of the family studies, however, mutations even in two or more of the risk genes may not be necessary or sufficient to cause disease.

Of the 91 genes, 25 were linked with forms of autism without intellectual disability. The scientists also described a gene network that appeared to be related to high-functioning autism. Individuals with this form of autism have average to above average intelligence, but may struggle in learning to talk, interact socially, or manage anxiety and sensory overload.

While observing that some genes were more closely associated with autism and others with intellectual or developmental impairments, the researchers found that most of the genes implicated were mutated in both conditions. This result reinforces the substantial overlap among these conditions in their underlying genetics and observable characteristics.

"Most of these genes are clearly risk factors for neurodevelopmental disorders in a broad sense," the researchers explained. "But analysis of both the genetic and subsequent patient follow-up data did single out some genes with a statistical bias towards autism spectrum disorder, rather than an intellectual disability or developmental delay."

Additional findings suggest that less severe mutations may be behind autism that is not accompanied by intellectual disability.

By following up with patients, the researchers could start to assess the newly discovered mutations. Such clinical information is important in determining how the genes might function, and how their disruption might lead to specific traits or symptoms.

In addition to looking at the overall severity of each neurodevelopmental disorder present, the scientists also summarized other features such as seizures, head size, and congenital abnormalities.

The researchers did in fact observe patterns from combining clinical and genetic data. They partitioned those genes most strongly associated with autism, and those more related to developmental disabilities.

Although the overall numbers were low, several autism risk genes appeared predominantly in males, including some detected exclusively in males who had autism without intellectual impairment.

To obtain additional evidence for how risk genes might affect behavior and nervous system function, the researchers investigated 21 genes in fruit fly models. They wanted to see if any of the mutations disrupted a fundamental form of learninggrowing accustomed to harmless stimuli.

Problems with the neuronal mechanisms behind habituation are thought to account for some autism features, such as inability to filter sensory input. The fruit fly studies showed habituation deficits from several of the gene mutations under review, thereby providing additional evidence that they may have a role in cognitive function.

Numerous grants and other funding from government agencies and private foundations in several countries supported this research.

"The scientists are continuing this project and are eager to work with interested families," said Raphael Bernier, associate professor of psychiatry and behavioral sciences and clinical director of the Seattle Children's Autism Center and associate director of the UW Center on Human Development and Disability.

Explore further: Genetic cause identified for previously unrecognized developmental disorder

More information: Holly A F Stessman et al, Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases, Nature Genetics (2017). DOI: 10.1038/ng.3792

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A research team from the United States and Canada has developed and successfully tested new computational software that determines whether a human DNA sample includes an epigenetic add-on linked to cancer and other adverse ...

Gene discovery research is uncovering new information about similarities and differences underlying various neurodevelopmental disorders.

A University of Toronto (U of T) study on fruit flies has uncovered a gene that could play a key role in obesity in humans.

Our genes play a significant role in how anxious we feel when faced with spatial and mathematical tasks, such as reading a map or solving a geometry problem, according to a new study by researchers from King's College London.

Gene editing techniques developed in the last five years could help in the battle against cancer and inherited diseases, a University of Exeter scientist says.

(Medical Xpress)A team of researchers with New England Biolabs Inc. (NEB) has found that sequenced DNA samples held in public databases had higher than expected low-frequency mutation error rates. In their paper published ...

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Sorting out risk genes for brain development disorders - Medical Xpress

February 20, 2017 Credit: CC0 Public Domain

Gene editing techniques developed in the last five years could help in the battle against cancer and inherited diseases, a University of Exeter scientist says.

Dr Edze Westra said the ability to splice selected DNA into cells with great precision would become "super important" in the next two decades. There could be benefits for generations of people affected by cancer, failing vision and the diseases of old age or bad genes.

"There is always a risk with this kind of technology and fears about designer babies and we have started having discussions about that so we can understand the consequences and long-term risks," said Dr Westra, of the Environment and Sustainability Institute on the University of Exeter's Penryn Campus in Cornwall. "I think in the coming decades gene editing will become super important, and I think we will see it being used to cure some inherited diseases, to cure cancers, to restore sight to people by transplanting genes. I think it will definitely have massive importance."

On Tuesday, two highly influential academic bodies in the US shook up the scientific world with a report that, for the first time, acknowledged the medical potential of editing inherited genes. The National Academy of Sciences and National Academy of Medicine ruled that gene editing of the human "germline"eggs, sperm and embryosshould not be seen as a red line in medical research.

Many critics insist that powerful new gene editing techniques should never be used to alter inherited DNA. They argue that such a move would be the start of a slippery slope leading to "designer" babies with selected features such as blue eyes, high intelligence or sporting prowess.

But the two pillars of the American scientific establishment said that with necessary safeguards, future use of germline gene editing to treat or prevent disease and disability was a "realistic possibility that deserves serious consideration".

Dr Westra is taking part in a discussion on gene editing and its potential implications for society at the American Association for the Advancement of Science (AAAS) annual meeting in Boston, Massachusetts. He said gene editing technology not only held out the promise of fixing genetic faults, but could be used to turn cells into miniature factories that churned out therapeutic chemicals or antibodies.

One application was the use of "gene drives" that increase the prevalence of a certain trait in a population. For instance, gene editing machinery placed inside the cells of large numbers of malaria transmitting mosquitoes could prevent them spreading the organism that causes the disease to humans.

The most promising form of gene editing, known as CRISPR/Cas9, was first demonstrated in 2012. It employs a defence system bacteria use to protect themselves against viruses. A carefully targeted enzyme is used as chemical "scissors" that cut through specific sections of double stranded DNA. Then the cell's own DNA repair machinery can be exploited to insert the "pasted" genetic material.

Dr Westra said: "Gene editing is causing a true revolution in science and medicine because it allows for very precise DNA surgery. "A mutation in a gene that causes disease can now be repaired using CRISPR."

Explore further: No designer babies, but gene editing to avoid disease? Maybe

A research team from the United States and Canada has developed and successfully tested new computational software that determines whether a human DNA sample includes an epigenetic add-on linked to cancer and other adverse ...

Gene discovery research is uncovering new information about similarities and differences underlying various neurodevelopmental disorders.

A University of Toronto (U of T) study on fruit flies has uncovered a gene that could play a key role in obesity in humans.

Our genes play a significant role in how anxious we feel when faced with spatial and mathematical tasks, such as reading a map or solving a geometry problem, according to a new study by researchers from King's College London.

Gene editing techniques developed in the last five years could help in the battle against cancer and inherited diseases, a University of Exeter scientist says.

(Medical Xpress)A team of researchers with New England Biolabs Inc. (NEB) has found that sequenced DNA samples held in public databases had higher than expected low-frequency mutation error rates. In their paper published ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

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Gene editing could help tackle cancer and inherited diseases - Medical Xpress

THE 1997 FILM Gattaca predicted a near future in which cities are powered by vast solar thermal arrays, humans launch manned missions to Saturns moons, and doctors design super smart and strong babies. A generation later, it is the gene editing that is proving most prescient.

Over the past decade, huge advances in gene-editing techniques have enabled researchers to slice up and rewrite DNA with incredible precision. At the forefront of the ensuing revolution is the CRISPR-Cas9, a technology derived from bacteria that enables scientists to snip and repair DNA, nucleotide by nucleotide, quickly and cheaply. The potential uses are vast. And so are the ethical quandaries.

The National Academies of Sciences and the National Academy of Medicine convened a panel to recommend guidelines for the use of powerful gene-editing tools. The results, released this week, are thoughtful and should for the moment, anyway channel research and testing in unambiguously positive directions.

CRISPR can be used in basic laboratory research, revealing how disease works on the molecular level. This is similar enough to other types of lab research that it requires no novel scientific or ethical standards. Researchers can also treat live humans with gene editing technologies, for example by taking immune cells out of the body, altering them and re-inserting them to fight an advanced cancer. Therapies such as these are already under development, and although researchers have to be cautious about off-target gene slicing, existing rules governing the development of medical treatments should suffice.

The ethics get much trickier when researchers want to change the DNA in reproductive cells, which would alter the genes that parents pass to children, forever. Doing so could prevent vast amounts of human suffering. But there is a problem of consent: Future generations have no say in their alteration. Disability communities would no doubt feel threatened and stigmatized, because gene editing could be used to essentially remove their type from the gene pool. Changes made to enhance human offspring, rather than simply to combat disease and disability, could redefine what it means to be human, while those to whom these techniques are unavailable would risk becoming a genetic underclass. A line would have to be drawn between heritable changes that are clearly valuable and those that risk unnecessarily humiliating people, destabilizing society and changing the nature of humanity.

The panel attempted to draw a preliminary line and put it in the right place. Heritable changes should be attempted only when scientists are convinced that specific genes cause or strongly predispose people to getting a serious disease or a condition, and when they know what normal genetic code should look like. They should only intervene when there are no reasonable alternatives available to families, and when real-world evidence shows that the benefits outweigh the risks.

The debate will not and should not end there. But before society has a full chance to process these questions, the panels approach is the right one. The goal should be to stop crippling diseases, not to build designer babies.

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A way forward in gene editing - Washington Post

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Gene therapy treats muscle-wasting disease in dogs - Science Daily