New cancer medicine targets rare genetic flaw, finds study – Hindustan Times

An experimental cancer medicine called larotrectinib has shown promise in treating a diverse range of cancers in people young and old, researchers said at a major cancer conference in the United States.

The treatment targets a genetic abnormality which is often found in rare cancers including salivary gland cancer, juvenile breast cancer, and a soft tissue cancer known as infantile fibrosarcoma which are particularly difficult to treat. This abnormality also occurs in about 0.5% to 1% of many common cancers.

In the study released at the American Society of Clinical Oncology conference, 76% of cancer patients both children and adults with 17 different kinds of cancer responded well to the medicine.

A total of 79% were alive after one year. The study is ongoing. And 12% went into complete remission from their cancer.

The clinical trial included 55 patients 43 adults and 12 children. All had advanced cancers in various organs, including the colon, pancreas and lung, as well as melanoma.

These findings embody the original promise of precision oncology: treating a patient based on the type of mutation, regardless of where the cancer originated, said lead study author David Hyman, chief of early drug development at Memorial Sloan Kettering Cancer Center in New York.

We believe that the dramatic response of tumours with TRK fusions to larotrectinib supports widespread genetic testing in patients with advanced cancer to see if they have this abnormality.

Researchers said 76% of cancer patients both children and adults with 17 different kinds of cancer responded well to the medicine. (Shutterstock)

Made by Loxo Oncology Inc., larotrectinib is a selective inhibitor of tropomyosin receptor kinase (TRK) fusion proteins. TRK proteins are a product of a genetic abnormality when a TRK gene in a cancer cell fuses with one of many other genes, researchers said.

The US Food and Drug Administration has not yet approved the treatment for widespread use.

The treatment was well tolerated by patients, and the most common side effects were fatigue and mild dizziness.

If approved, larotrectinib could become the first therapy of any kind to be developed and approved simultaneously in adults and children, and the first targeted therapy to be indicated for a molecular definition of cancer that spans all traditionally-defined types of tumors. said Hyman.

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New cancer medicine targets rare genetic flaw, finds study - Hindustan Times

What’s In Your Genes? – Pacific Northwest Inlander

Picture a time in the not-too-distant future when whole genome sequencing is routine. A time when, before babies even learn to talk, their parents will have the ability to learn what the future may have in store for their offspring: Is their little girl predisposed to getting breast cancer? Will their happy-go-lucky son one day develop Alzheimer's?

"There is no doubt in my mind that, in addition to going in and having blood chemistry done, you're gonna have DNA sequencing done, too. It will be there at some point," says Nicholas Schork, a quantitative geneticist at the J. Craig Venter Institute in La Jolla, California, who has studied genomic medicine for more than three decades. "We can debate about the timeline, but it'll become routine."

The hope is that genetic testing will make health care more effective by allowing doctors and patients to focus on areas that need attention the patient's genetic "vulnerabilities." At the same time, patients may learn of areas where they won't need to be quite as vigilant. And treatments could, in turn, be perfectly tailored to a patient's specific needs.

But as with any significant and broadly applicable medical advance, there are questions. For example, should patients learn that they carry markers for currently incurable genetic diseases, or that they are at high risk for developing a condition like Alzheimer's, which has no effective treatment? And just who owns all that genetic data? Who will have access to it?

Even with important questions left unanswered, health educators are moving forward to take advantage of the promises genetic testing offers. Washington State University's new Elson S. Floyd College of Medicine has announced it is partnering with Arivale, a Seattle-based company that conducts whole genome sequencing, to help complete a portrait of a person a "portrait" that can be used to promote wellness over that individual's entire lifespan. Every member of the school's inaugural class will have the opportunity to undergo testing, which will also include blood tests and a lifestyle evaluation. Then, over the next year, Arivale's team of nurses and dietitians will provide individually tailored follow-up, based on each individual's risks and goals. It's a unique partnership, made possible in large part because the medical school is new, with its first class of students starting in 2017.

Allowing the medical students to experience genetic testing firsthand is just part of the goal. "We need physicians that understand it well enough that they can make it better going forward," says John Tomkowiak, founding dean of WSU's College of Medicine. "That's where our students are going to be uniquely positioned."

WHAT GENES TELL US

Genetic testing already provides important information about a person's health or their heritage. Hospitals screen newborn babies for certain genetic disorders, and in some cases, tests can detect disorders before birth. And diagnostic testing can confirm, or rule out, many disorders in adults.

Testing doesn't have to be ordered by a physician. For $200, you can provide a saliva sample, mail it back to 23andMe.com and find out not only your ancestry, but also your risks for a number of diseases, including Alzheimer's and Parkinson's. Ancestry.com offers a glimpse into your heritage for $99. Color.com claims to reveal your risk for the most common hereditary cancers, and even offers "complimentary genetic counseling" for a $249 fee.

But if genetic testing is to revolutionize the health care industry, as many have promised, there's still a ways to go. "The technology is at the beginning stages," says Thomas May, a faculty researcher for the HudsonAlpha Institute for Biotechnology.

Companies like 23andMe offer genetic tests that may provide information about some genetic disorders from currently known genetic variants. But whole genome sequencing is different; it will reveal all your individual genetic variants.

How valuable is that information? There are a relatively small number of conditions that researchers are confident result from a specific genetic variant, May says. For example, there is one variant that researchers have found is associated with an increased risk of developing breast or ovarian cancer. A genetic test that shows an increased risk for breast cancer is considered an "actionable" outcome, meaning there are things you can do to prevent the outcome, like beginning mammograms earlier. Though there are more than 50 actionable outcomes like that, it's still a relatively small number.

Adding to the confusion is the fact that not everyone who develops breast cancer actually has the genetic variant in fact, May says only about 10 percent do. So even if testing shows that you don't have the "breast cancer gene," that doesn't mean it's OK to stop getting mammograms.

"Most variants and correlations are of that type: We can't say for certain if you're gonna get a disease," May says.

Doctors are mixed about whether genetic testing is currently having a real impact on patients. In a May survey conducted by the Medscape Physician Oncology Report on Genomics Testing, 71 percent of oncologists surveyed felt that genetic testing was either "very" or "extremely" important to the oncology field. At the same time, 61 percent said that, currently, fewer than a quarter of their patients would actually benefit from genetic testing.

The number of diseases with "actionable" outcomes will inevitably grow, as more people are tested and more data becomes available. But this leaves deeper questions, says Schork, the quantitative geneticist. A company or health care provider would likely give patients information about diseases that can be prevented or cured. If someone is predisposed to obesity, for instance, then he or she can elect to receive targeted care to reduce that risk.

But what about diseases that, right now, are incurable?

Take Huntington's disease, a genetic disorder that breaks down nerve cells in the brain. It's rare, but it's a "hideous way to die," Schork says. A person can be screened at the age of 25 and be found to carry the Huntington's gene, but there's debate about whether or not that information should be shared with a client or not. The same goes for genetic variants related to Alzheimer's disease.

"If there's nothing they can do about it, then there's a concern about whether or not that information should be imparted," Schork says.

When the Food and Drug Administration ordered 23andMe to stop telling customers their odds of contracting diseases in 2013, Harvard Medical School genetics professor Robert Green and Laura Beskow, a professor at Duke University's Institute for Genome Sciences and Policy, argued against the FDA. They cited a number of studies showing that direct-to-consumer genetic testing does not cause a large percentage of customers despair. In an interview with the New York Times in April, Green said the potential for distress based on results of a genetic test for Alzheimer's was "much smaller than anticipated."

Another question: Who really owns the DNA data that is being collected from willing users of genetic testing? Consider Myriad, a company that offers genetic testing both to help determine cancer risk and design better treatment plans for patients who already have cancer. The company has something that "others do not," Schork says: insight into which genetic variants predispose women to breast cancer.

What Myriad is really selling, then, is not the genetic test itself, but access to insights it has gained through mining its database, insights that can be leveraged into whatever level of payment the company decides to charge.

It's potentially critical information that could help save a life, and some argue that the data should be in the public domain not held by a private company.

"There have been huge debates about whether the community should challenge the monopoly that Myriad has," Schork says. "There are many groups out there that would like to counteract the monopoly Myriad has, by building public domain data sets."

JUST ONE TOOL

"Genetic testing is not a blueprint. It's really not," says Jennifer Lovejoy, chief translational science officer for Arivale. "Genes are really just one factor the environment, diet, exercise, pollutants and even emotional state have a big impact on genes."

That's why Arivale not only collects genetic information on each client, but also evaluates various blood tests and lifestyle factors to create a "dense data cloud" of information about a patient.

"That is the grand vision: that everybody would have these dense, dynamic data clouds, and understand the choices that will be optimal to optimize wellness and avoid disease," says Lovejoy.

Arivale touts the success stories among its nearly 2,000 clients. One client found out he had a gene associated with high sensitivity to saturated fat, giving him a better indication of an appropriate diet that helped him lose weight. Another client discovered that his genes may have an impact on his cholesterol. Another learned he was at risk of developing diabetes.

Ideally, this type of preventive care will soon be covered by insurance, Lovejoy says. The thinking is that preventing disease will bring down the cost of health care overall, making insurers likely to cover more preventive care, "but we have to prove it," Lovejoy says. Researchers are conducting studies and trials to do just that, and if they can prove it, then genetic testing could soon be routine in health care.

"If you think about what health care should mean, it should mean, one, the ability to deal with disease and that's what everyone does today," Arivale co-founder Leroy Hood said at a press conference in April announcing the company's partnership with WSU. "But two, it should mean the ability to optimize wellness for each individual. That is, improving their health and/or letting them avoid disease." That's a concept Hood calls "scientific wellness, and he thinks it could lead to "a whole new health care industry in the future."

Tomkowiak, of WSU's College of Medicine, agrees: "The concept of scientific wellness has the potential to disrupt the entire industry by shifting the cost curve, by keeping people healthier and reducing the cost of health care overall."

Regardless of whether or not Arivale becomes an industry leader, Tomkowiak believes that the practice of medicine will be fundamentally altered in the near future.

"We absolutely believe that seven years from now, the practice of scientific medicine and scientific wellness will be common," he says. "Instead of being behind the curve, we want... to be leading this effort."

For about $3,500, clients can sign up for Arivale's program. The fee includes whole genome sequencing, which is also available from other sources. So how do Arivale clients achieve "scientific wellness"? Here are the elements of their program:

Welcome package: Clients get a welcome package with a Fitbit to track sleep, activity and heart rate. The package asks for information to help understand a client's bacteria in their gut, and asks for a sample of saliva to measure a person's stress level.

Online test: Clients take a series of online assessments about their goals, health history, lifestyle, stress, personality and happiness.

Call from coach: You'll talk to a coach who will get to know what you want to accomplish and give you a personalized action plan.

Labs: You'll take blood tests so your coach can understand your current health. While you're there, they'll take your vital signs.

A picture emerges: The various test create a picture of you, which an Arivale coach will use to provide a step-by-step plan to "optimize your wellness," according to the company.

Follow-up: You're not done yet. You'll be contacted by your coach regularly to review your action plan, and Arivale will provide reports on how you're progressing. Every six months, you'll complete another set of clinical labs.

Source: arivale.com/your-journey

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What's In Your Genes? - Pacific Northwest Inlander

Genetic sequencing could influence treatment for nearly 3/4 of advanced cancer patients – Medical Xpress

June 2, 2017

A new analysis finds that nearly three-quarters of 500 patients with advanced cancer could be referred to a potential targeted treatment based on the results of a comprehensive analysis of their tumor's genetic landscape.

The study suggests the value of so-called next generation sequencing, a sophisticated method of evaluating the DNA and RNA of a tumor to help direct treatment.

A report on the first 500 patients with advanced solid tumors to go through the University of Michigan Comprehensive Cancer Center's sequencing program found that 72 percent qualified for a clinical trial based on a genetic marker in their tumor.

While not all of those patients were able to enroll in a trial based on other eligibility factors and trial location, the number who did enroll doubled from approximately 5 percent of patients in 2012 to 11 percent in 2016. Increased trial enrollment occurred as several major national biomarker-based studies opened.

"Availability of biomarker trials is crucial for being able to act on these results. Over time, we became better at matching patients to clinical trials as more of these basket trials opened," says Erin Cobain, M.D., clinical lecturer of hematology/oncology at the University of Michigan Medical School.

Cobain will present these findings at the American Society of Clinical Oncology annual meeting.

The Michigan Oncology Sequencing Center began in 2011, sequencing the DNA and RNA of metastatic cancers and normal tissue to identify alterations that could help drive treatment. About 900 patients with advanced cancer have enrolled to date. The analysis presented at ASCO focuses on the first 500 patients with solid tumors.

Precision medicine in action

Patients with stage 4 cancer undergo a biopsy and provide a blood sample to test their normal DNA. Patients also receive genetic counseling.

Results of the sequencing are discussed by a team of oncologists, genetics specialists, pathologists, bioinformatics specialists and genetic counselors, among others, at a precision medicine tumor board. This group discusses all results and assesses the feasibility of pursuing treatment options based on the genomic findings.

Genetic sequencing involves looking at all of the DNA and RNA expressed within a tumor. Scientists comb through this enormous amount of data to identify anomalies that may prove to be targets for existing approved or experimental therapies.

In addition, the program sequences patients' normal genome. This means it's able to identify hereditary genetic variations - those inherited from a mother or father and potentially passed down to children. Researchers found these hereditary variations in 11 percent of patients, none of which had been previously identified through family history.

"That was a major surprise. That 11 percent of patients had a genetic change that increases cancer risk is much higher than we would expect. This has significant impact not only on the patients, but on their families, who may also carry a genetic susceptibility to cancer," Cobain says.

A more comprehensive approach

Mi-ONCOSEQ, which is run as a research study, requires a fresh biopsy, where many commercial sequencing tools can use frozen tissue samples. However, those tests analyze only a limited panel of genes. The goal with Mi-ONCOSEQ was to obtain a large enough sample so that researchers could perform extensive sequencing of both DNA and RNA.

The more-thorough analysis, which covers at least 1,700 genes, meant that many anomalies were identified that would not have been found on panel-based tests that typically cover about 350 genes. Because Mi-ONCOSEQ is run as a research study, patients did not pay for sequencing.

Cobain cites an example of a patient with cholangiocarcinoma, a cancer of the bile duct. Sequencing revealed a novel gene fusion that would not have been identified through panel-based tests. The patient was able to enroll on a clinical trial targeting the gene fusion and had an excellent response to that therapy.

"This would not have been found by a commercial assay," Cobain says. "Sequencing is beginning to have a real impact on treatment recommendations. It's important to consider this testing early in the patient's clinical course in order to improve our ability to act on the results and impact the patient's course."

Explore further: Genetic alterations more common in tumors of older patients with metastatic breast cancer

More information: Reference: ASCO Annual Meeting, June 2-6, 2017, abstract 101

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What is Pompe disease? 5 things to know about the rare gene mutation – Today.com

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During his address to Congress last night, President Donald Trump introduced Megan Crowley, a 20-year-old woman with a rare disease.

Crowley, who has a neuromuscular disorder known as Pompe disease, credits her survival to her father's small biotechnology company for developing and producing a therapy for the rare genetic mutation.

During the speech, the President suggested that Crowleys story highlighted the need to scale back regulations and to streamline the processes of the Food and Drug Administration. While Crowley's doctor welcomed the spotlight shown on Pompe disease and on rare diseases, in general, others cautioned that rushing experimental treatments through the Food and Drug Administration could have disastrous results.

Related: Speed up drug approvals? The FDA already did

The big problem isnt with the FDAs procedures, but rather a shortage of funds and the small numbers of people in whom scientists can study the ailments, researcher Dr. Puneet Opal told TODAY.

FDA drug approval procedures are intended to prevent patient deaths from experimental treatments, said Opal, a professor of neurology at Northwestern Universitys Feinberg School of Medicine.

"You do need the FDA to be the police dog," said Opal.

Crowleys physician, Dr. Priya Sunil Kishnani, division chief of medical genetics at the Duke University Medical Center, was excited to have rare diseases given such high-profile attention.

We diagnosed Megan at Duke in 1998 when she was just 15 months old. Its been an amazing journey to see how she has not just survived but is thriving despite her limitations, Kishnani, who is also professor of pediatrics and division chief of medical genetics, told TODAY.

Pompe disease occurs in an estimated 1 in 12,000 to 20,000 babies and people with an adult-onset form, according to Duke University experts. Crowley's fathers struggle to find a cure for the disease was profiled in the book The Cure: How a Father Raised $100 Million and Bucked the Medical Establishment in a Quest to Save His Children and also inspired a 2010 movie called Extraordinary Measures.

Megan Crowley listens as President Donald Trump addresses Congress.

Related: Parents race to save girl with rare, deadly disease

For those not familiar with Pompe, here are five things to know:

That means that a child must inherit two copies one from each parent to be affected by it. Children born with just one copy of the mutated gene are healthy and generally are completely unaware they have it.

When someone has both copies of the mutated gene, the body lacks enough of an enzyme that breaks down the starch glycogen into glucose, a form of sugar that fuels the muscles. The result is a damaging overabundance of glycogen.

Because the heart is also a muscle, damage to it is what generally kills patients even before there is respiratory distress, Opal said.

In babies, the earliest symptoms are not meeting motor milestones, Kishnani said. Babies might not hold their heads up or start rolling over at the expected age. They may not have the same strength as other babies of similar age.

"When you pick them up you feel like theyre almost slipping through your fingers," said Kishnani.

Respiratory symptoms or pneumonia might reveal a massively enlarged heart.

The severity of the symptoms and when they appear depend on the exact type of mutation. There are children who show up with worse symptoms than Crowley and others who show up with milder ones, Kishnani said.

The treatment isnt a cure for the disease, but it is lifesaving. Crowley is confined to a wheelchair and must use a ventilator to breathe.

These individuals do have a life," said Kishnani, talking about Megan's spunk and passion.

"She has life goals. People should not just look past her ... and think there are not going to be any cognitive abilities.

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San Diego Genomic Medicine Conference Kicks Off Thursday – KPBS

Scientists and doctors will gather in La Jolla this week for a conference about how medicine could change and in some cases, how it's already starting to change thanks to advances in genomics.

The 10th annual Future of Genomic Medicine conference organized by the Scripps Translational Science Institute and held at the Scripps Institution of Oceanography is being held at a time when genomic breakthroughs have increasingly become the subject of high-profile intellectual property disputes, ethical debates and major industry investments.

One panel focussed on the gene editing tool CRISPR will feature MIT scientist Feng Zhang, who recently came out ahead of UC Berkeley scientists in a patent battle over who deserves credit for developing a tool that could be used to fight cancer, malaria and a host of other genetic diseases.

"I think it can't really be overstated how big of a revolution CRISPR is in terms of manipulating the genome," said Scripps Translational Science Institute researcher Ali Torkamani, who will moderate the CRISPR panel.

"It's exciting to the public and it is really exciting to scientists as well," he said.

Other panels will cover the federal Precision Medicine Initiative, which is still in nascent stages, and attempts to develop blood-based screening tests meant to catch cancer in early stages. Grail, a spinoff company of San Diego-based Illumina, announced on Wednesday that it has raised $900 million to develop such "liquid biopsies."

Razelle Kurzrock of the UCSD School of Medicine will give a presentation about fighting cancer by better understanding a patient's unique DNA and the unique DNA of their tumor.

"By understanding genomics and each patient's cancer, we are learning how to customize precision treatments for patients," Kurzrock wrote in an email to KPBS. "The immune system, once reactivated by our new drugs, differentiates between tumor and normal cells by the mutations that tumor cells harbor."

More than 600 people are scheduled to attend the conference, which begins Thursday morning and wraps on Friday afternoon.

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Gene therapy tried in dogs with muscle disease could prove useful for people – FierceBiotech

Theres a rare disorder that occurs when a gene mutation halts the production of myotubularina protein that facilitates normal muscle function. The disease, called myotubular myopathy (MTM), only affects males, and its ultimately fatal because it causes breathing difficulties.

Dogs get MTM, tooand that spelled opportunity for scientists at the University of Washington Medicine Institute for Stem Cell and Regenerative Medicine. In collaboration with five other academic institutions, they found a way to replace the faulty MTM gene with a functioning gene in dogs with the disease, they reported in the journal Molecular Therapy.

It worked: After a single infusion of genes, muscle strength was restored in the dogs, according to a press release. One year later, the dogs were indistinguishable from healthy animals, they said. "This regenerative technology allowed dogs that otherwise would have perished to complete restoration of normal health," said Dr. Martin K. "Casey" Childers, UW Medicine researcher and physician.

The researchers used a viral vector called adeno-associated virus serotype 8 (rAAV8) to deliver a healthy canine version of the MTM gene in dogs that were 10 weeks old and already showing symptoms. They believe a similar trial could be designed in people.

Gene therapy is under investigation for a wide range of disorders, though much of the progress to date has occurred outside the realm of muscular disorders. BioMarin Pharmaceutical, for example, is in mid-stage trials of a gene therapy treatment for hemophilia A. UniQure is working on several gene therapy products to treat diseases including Huntingtons and congestive heart failure. Its most advanced project, a gene therapy product to treat hemophilia B, received breakthrough designation status from the FDA in January.

One company that has achieved some success with gene therapy in inherited muscle disorders is AveXis, which is gearing up for a pivotal trial of its treatment for spinal muscular atrophy. AveXis won breakthrough therapy designation for its gene product last year, and high hopes for the product have prompted its stock to more than triple since the company went public early last year.

UW Medicine-led team that worked on the canine MTM trial observed that as they increased the dosage of genes, survival rates improved, they reported. They believe the study proves the potential utility of gene therapy in a wide range of diseases that are linked to mutated genes.

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Gene therapy tried in dogs with muscle disease could prove useful for people - FierceBiotech

Gene editing could bring an end to all inherited disease and cancer, expert says – The Independent

All inherited diseases and cancers could be cured in the coming decades, according to a leading British expert.

Gene editing techniques that have been developed in recent years could be put to work to effectively end cancer and inherited diseases, according to DrEdze Westra

MrWestra believes that the ability to splice DNA into cells precisely a technology which is on the horizon, but is rejected on moral grounds by many will become super importantover the next 20 years.

It could completely transform the human race, he says so thatpeople are not affected by cancer, failing vision or the diseases of old age.

The bioscientist from the University of Exeter said: 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.

I think in the coming decades gene editing will become super important, and I think we will see it being used to cure all 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 germlineeggs, sperm and embryos should 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 designerbabies 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.

Mr 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 drivesthat 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 carriesthe disease to humans.

It could be a fantastic strategy to deal with some of the worlds biggest problems,said Mr Westra.

In terms of ethics we need to work out what happens if a genetically engineered insect flies out of the window of the lab. Trials into gene drives are already happening in labs for malaria.

The most promising form of gene editing, known as CRISPR/Cas9, was first demonstrated in 2012.

It employs a defence system bacteria useto protect themselves against viruses.

A carefully targeted enzyme is used as chemical scissorsthat cut through specific sections of double stranded DNA. Then the cells own DNA repair machinery can be exploited to insert the pastedgenetic material.

Mr 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.

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Gene editing could bring an end to all inherited disease and cancer, expert says - The Independent

There’s a fine red line between cures, enhancements using gene editing tech – BioWorld Online

By Nuala Moran Staff Writer

BOSTON The triumph of the Massachusetts Institute of Technology Broad Institute and its spinout company Editas Medicine Inc. in the case of CRISPR/Cas9 gene editing patents could impede the development of human therapies based on the technology, according to one of the leading researchers in the field.

George Church, professor of genetics at Harvard Medical School, said, "It definitely is an issue" if Editas maintains exclusivity in applying patents on using CRISPR/Cas9 to edit eukaryote genes. That would limit the freedom to operate of Editas' direct competitors, Intellia Therapeutics Inc. and Crispr Therapeutics AG.

Church added that even if all three companies are equally involved in translation, "that is not enough to handle all the benefits to come out of this. I would love to see more companies," he told AAAS attendees.

Church could be seen as having something of an axe to grind because he published a paper in the same issue of Science as Feng Zhang of the Broad Institute, on using CRISPR/Cas9 in human cells. It is that research of Zhang's on which the disputed patent hangs.

The decision on the high-profile CRISPR/Cas9 patents came a day after the Committee on Human Gene Editing of the National Academies of Sciences and Medicine issued a report concluding that clinical trials involving genome editing in gametes or early embryos could be permitted in the future for serious diseases or disabilities, under stringent oversight. (See BioWorld Today, Feb. 15, 2017, and Feb. 16, 2017.)

Church was one of the contributors to the international summit on gene editing held in Washington in December 2015 that led to the writing of the report. He said the report's proposals amounted to "a change in the red lines we are drawing." When talking about altering the inherited germline and the somatic cells of adults, "the line is now drawn on the seriousness of the disease," he said.

While the red line in germline modification is shifted, the line between using gene editing to cure disease and to enhance human traits becomes softer, Church suggested. For example, gene editing somatic cells to increase muscular strength in patients with muscular dystrophy could tip over into giving subjects greater than average strength.

Similarly, a somatic gene editing to improve cognition as a "cure" for Alzheimer's disease could result in patients having enhanced cognitive abilities.

Such modifications are far from becoming reality, but Church said other traits are more amenable to change. One example would be somatic modification to promote endogenous production of human growth hormone, which could be viewed both as a therapy and as a means of enhancement.

The Committee on Human Gene Editing was convened to try to get ahead of the curve in establishing regulations, before those types of modifications become feasible, as Richard Hynes, professor of cancer at MIT and co-chair of the committee, explained.

While he agreed it is difficult to draw the line between the use of somatic gene editing for treatment of disease and for enhancement, he said he firmly believes enhancement should be banned for now. "We should work out the risk/benefit for therapies first. It will take time to understand the risks. With enhancement, the benefits are debatable, but the risks are the same," Hynes said.

The concern is that, as with stem cell therapies, genetic enhancement through somatic gene editing will be on offer in rogue clinics and in countries where there is limited oversight.

Given that, one of the aims of the committee was to set out core principles that would be broadly influential and could be adopted as the basis for promulgating national laws governing the technology. "The principles are for application around the world, as part of a drive to try and harmonize international regulation," Hynes said.

That is all very well, but as Gary Marchant, of Arizona State University, also a member of the committee, noted, "There is a huge problem of international enforcement." Ways of trying to ensure compliance considered in the report include journals only publishing research that complies with international norms and withholding research grants if the rules are not upheld.

The committee did not consider patenting in its survey of gene editing. However, Marchant suggested refusing licenses could be another mechanism in attempts to ensure appropriate use of the technology worldwide. That "may have more currency at an international level," he said.

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There's a fine red line between cures, enhancements using gene editing tech - BioWorld Online

Stepping up the hunt for genetic diseases – Medical Xpress

February 16, 2017 Credit: UNIGE

When a child is conceived, he or she receives DNA from both parents. The child's own genome thus consists of a maternal and a paternal genome. However, some genesabout 100 out of the 20,000 encoded genes are exclusively expressed either from the maternal or from the paternal genome, with the other copy of the gene remaining silent. We know that these imprinted genes are more likely to lead to serious genetic diseases, such as PraderWilli or Angelman syndrome. Researchers at the University of Geneva (UNIGE), Switzerland, have devised a new technique, based on a combination of biology and bioinformatics, to quickly and accurately detect the imprinted genes expressed in each of the cell types that constitute the human organs. This major breakthrough will improve our understanding and diagnosis of genetic diseases. The study can be read in full in the American Journal of Human Genetics.

The research team, led by Professor Stylianos Antonarakis from the Department of Genetic Medicine and Development in the Faculty of Medicine at UNIGE, focused on genomic imprinting. This is a set of genes exclusively expressed from the genetic code inherited either from the father (the paternal allele) or from the mother (maternal allele). Why is there so much interest in the identification of the imprinted genes? Because if a deleterious mutation affects the functional allele, it cannot be compensated by the expression of the second silent allele, likely causing a serious genetic disease. The goal, therefore, is to determine the imprinted genes in all cell types of human body tissues that are liable to cause these kind of diseases.

Until recently, millions of cells were analysed together without distinction. "We have now developed a new technique with a better resolution, known as Human Single-Cell Allele-Specific Gene Expression," explains Christelle Borel, UNIGE researcher. "The process can be used to simultaneously examine the expression of the two alleles, paternal and maternal, of all known genes in each individual cell. The method is fast and can be carried out on thousands of single cells with the utmost precision using next-generation sequencing technology." The heterogeneity of each tissue of the body is thus analysed in detail while searching for imprinted genes in disease-relevant tissue. The individual's genome is sequenced, as is the genome of both parents, in order to identify the parental origin of the alleles transcribed in the person's single cell.

Each cell is unique

Federico Santoni, first author of the study and researcher at UNIGE and HUG (Geneva University Hospitals) further explains, "We establish the profile of the allelic expression for thousands of genes in each single cell. We then process this data with a novel computational and statistical framework to identify the specific signature of each imprinted gene, enabling us to accurately record them." This new technique redefines the landscape of imprinted genes by examining all cell types, and can be applied to all tissues affected by diseases, such as cardiac and brain tissue. Moreover, the scientists have discovered novel imprinted genes and demonstrated that some were restricted to certain tissues or cell types.

This technique focuses on the specific characteristics of each individual by treating each cell as a single entity. This concept, called Single-cell Genomics, is part of an emerging field that is assuming an all-important role at UNIGE, which sees it as the future of medicine that will be personalised rather than generalised. Thanks to the technique pioneered by UNIGE researchers, it will be possible to identify new disease causing genes and to adapt a specific and targeted treatment for individual patients.

Explore further: Expanding the brain: Research identifies more than 40 new imprinted genes

More information: Federico A. Santoni et al. Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression, The American Journal of Human Genetics (2017). DOI: 10.1016/j.ajhg.2017.01.028

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Stepping up the hunt for genetic diseases - Medical Xpress

Rare Muscle Disease Treated Successfully with Gene Therapy – Genetic Engineering & Biotechnology News

Work on gene therapy is showing significant progress for restoring muscle strength and prolonging lives in dogs with a previously incurable, inherited neuromuscular disease, according to scientists at the University of Washington (UW) Medicine Institute for Stem Cell and Regenerative Medicine.

The disease arises from a mutation in genes that normally make myotubularin, a protein essential for proper muscle function. Puppies with this naturally occurring mutation exhibit several features of babies with the same defective gene. The rare disorder, called X-linked myotubular myopathy, or XLMTM, affects only males. It causes fatal muscle wasting. Both dogs and boys with the disease typically succumb in early life due to breathing difficulties.

For decades, researchers have struggled to find suitable treatments for genetic muscle diseases like this one. Collaborating research groups in the United States and France found a way to safely replace the disease-causing MTM gene with a healthy gene throughout the entire musculature of affected dogs.

Their most recent findings ("Systemic AAV8-Mediated Gene Therapy Drives Whole-Body Correction of Myotubular Myopathy in Dogs") werepublished online inMolecular Therapy.The paper reports that diseased dogs treated with a single infusion of the corrective therapy were indistinguishable from normal animals 1 year later.

"This regenerative technology allowed dogs that otherwise would have perished to complete restoration of normal health," said Martin K. "Casey" Childers, Ph.D., UW medicine researcher and physician. Dr. Childers is a professor of rehabilitation medicine at the University of Washington School of Medicine and co-director of the Institute for Stem Cell and Regenerative Medicine.

Gene therapy holds the promise to treat many inherited diseases. To date, this approach has not been widely translated into treatment of skeletal muscle disorders.

"We report here a gene therapy dose-finding study in a large animal model of a severe muscle disease where a single treatment resulted in dramatic rescue," said Dr. Childers. The findings demonstrate potential application across a wide range of diseases and broadly translate to human studies. The data supports the development of gene therapy clinical trials for myotubular myopathy, the researchers concluded.

The study was conducted in collaboration with Harvard University, Medical College of Wisconsin, Virginia Tech, INSERM, and Genethon.

Excerpt from:
Rare Muscle Disease Treated Successfully with Gene Therapy - Genetic Engineering & Biotechnology News

To prevent serious medical conditions, scientists should be able to edit people’s DNA, panel says – Los Angeles Times

Scientists should be allowed to altera persons DNA in ways that will be passed on to future generations, but only to prevent serious and strongly heritable diseases, according to a new report from the National Academy of Sciences and the National Academy of Medicine.

However, tinkering with these genes in orderto enhance or alter traits such as strength, intelligence or beauty should remain off-limits, the report authors concluded.

Changing theso-called germline effectively, editing humanitys future by altering genes in human reproductive cells is illegal in the United States. It has largely been considered ethically off-limits here as well, at least whilebioethicists and scientists pondered the unforeseen effects and unexamined moral dilemmas of using new gene-editing technologies.

However, scientists have moved forward aggressively to explore the feasibility of altering disease genes in other adult human cells with a revolutionarytechnique known asCRISPR-Cas9. It is widely believed that gene editing of this sort could treat patients with metabolic disorders, certain cancers, anda range of otherdiseases that arise from genetic mutationswithout altering the germline.

Last year, Chinese scientists launched a trial that uses CRISPR-Cas9 in a treatment for lung cancer. While the trials outcome is awaited with high anticipation, scientists outside of China have expressed concern that ethical reservations in the United States and Europe will put themat a disadvantage.

CRISPR-Cas9 makesgene editing more straightforward, more precise and far more widespread. As such, the National Academies report acknowledgesthat changingheritable DNA ineggs, sperm and early embryosis fast becoming a realistic possibility that deserves serious consideration.

The 22-memberpanel of scientists and bioethicists who produced the report completed a comprehensive review of the issues raised by that prospect.

Clinical trials involving germline editing should onlybe pursuedto treat diseases that cannot be improvedwith reasonable alternatives, the committee said. In addition, they added,scientists should convincingly demonstratethey are targeting a gene that eithercauses or strongly predisposes a carrier to a serious disease or condition, and that they have weighed the likely risks and benefits of altering that gene.

These clinical trials should be conducted under public scrutiny that takes into account issues ofsocietal fairness, personal dignityand scientific integrity, the panel said.

Finally, scientists should conduct long-term follow-up studies to discern how gene editing affects subsequent generations.Public debate and discussion about the technologyshould continue, the panel added.

Genome editing research is very much an international endeavor, and all nations should ensure that any potential clinical applications reflect societal values and be subject to appropriate oversight and regulation, saidMIT cancer researcher Richard O.Hynes, who co-chaired the panel with University of Wisconsin-Madison bioethicist R. Alta Charo. These overarching principles and the responsibilities that flow from them should be reflected in each nations scientific community and regulatory processes.

Dr. J. Patrick Whelan, an immunologist and bioethicist who was not on the panel, said the grouphas asked the compelling questions, sparkinga conversation that must keep up with a rapid pace of scientific discovery in this field. He called the reportsrelease a fantastic development.

What theyre saying is, lets start the conversation, maintain ethical structures along the way, and hopefully do this the right way, said Whelan, who serves on the advisory board of USCs Institute for Advanced Catholic Studies.

The international panel included members from the U.S., China, France, Israel andItaly.Their report was underwritten in part by the Department of Defenses Advanced Research Projects Agency and the U.S. Food and Drug Administration.

melissa.healy@latimes.com

Follow me on Twitter @LATMelissaHealy and "like" Los Angeles Times Science & Health on Facebook.

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To prevent serious medical conditions, scientists should be able to edit people's DNA, panel says - Los Angeles Times

Human genome editing report strikes the right balance between risks and benefits – Medical Xpress

February 16, 2017 by Merlin Crossley, The Conversation Gene therapy is growing in its capabilities, but there should be limits to its use. Credit: Shutterstock

If you recognise the words "CRISPR-mediated gene editing", then you'll know that our ability to alter DNA has recently become much more efficient, faster and cheaper.

This has inevitably led to serious discussions about gene therapy, which is the direct modification of someone's DNA to rectify a genetic disorder, such as sickle cell anaemia or haemophilia. And you may also have heard of deliberate genetic enhancement, to realise a healthy person's dreams of improving their genome.

Both of these issues have now been tackled in a comprehensive report on gene editing released today by the US National Academy of Science and National Academy of Medicine.

The message is fairly simple: relax, we've seen this all before, little if any harm has eventuated, and society is well placed to move forward together on this.

A definite maybe

Of all human technologies, recombinant DNA has arguably been one of the safest. There have been multiple benefits in both medicine and agriculture. And the legitimate concerns that arose when viruses were first mixed with bacterial genes, when cloning was first introduced, and when stem cells were developed, have not come to pass.

I cannot list all the benefits here, but if you have received the Hepatitis B vaccine or Australian Ian Fraser's Gardasil vaccine, which protects against cervical cancer viruses, you have been protected from disease thanks to recombinant DNA technology.

However, you probably haven't received somatic gene therapy, which is gene alteration directed at fixing one cell type, such as defective blood or liver cells. This is because this therapy only touches a tiny number of people, probably fewer than 1,000 worldwide, and again the benefits have outweighed the risks.

But there is one new message in the report that will grab the headlines.

That is the view on human germline gene therapy, which entails modifications that would be passed on to children and then to their children. This kind of gene therapy has been considered highly controversial. But this time, instead of a simple no thanks there's a definite maybe, provided the therapy is targeted at a severe disease as a last resort.

There will be alarm in some circles at the very mention of germline gene therapy, although perhaps not from the very few people who might be contemplating such treatment for the sake of their future children.

The authors of the report, who are among the mostly highly respected experts in the world, are well aware that many people will not be comfortable with the thought of germline gene therapy. They stress the need for extensive consultation, the meeting of strict criteria, and close regulation.

But in weighing up safety and efficacy, social and individual benefit, they clearly don't want to see a reflex ban put in place that may limit options if this technology can be used to make the life of some individuals better.

On one hand, they are right. This technology is not a threat to the fabric of society. Nor, I'd say, is this a genie that could not be put back in the bottle; gene editing could be reversed.

Nor, like the Sorcerer's Apprentice's broomsticks, will it multiply and spread when we try to restrain it. This is not like letting slip a virus, cane toads, oozing radioactive waste or carbon emissions into the atmosphere.

Seeking germline gene therapy in order to have a disease-free child would be a choice made at a personal level and those not wishing to participate should never feel compelled to do so.

Except, of course, the children who would not have a say in it. But also for them the risks might well outweigh the benefits. And, one way or another, parents already make life-determining choices for their children and sometimes for their children's children.

Even those seeking germline therapy for the sake of their children would mostly have alternatives, such as preimplantation diagnosis, which itself also has ethical considerations. There are no easy answers here.

So I can understand the report's conclusion, although I also believe there are risks, which I'll mention below.

Hard to abuse

There are other aspects of the report worth mentioning. It confirms that we already do properly regulate laboratory-based gene modifications, and we have learned so much from previous somatic gene therapy efforts that we are well placed to push on safely with both research and somatic treatments. I agree with this.

It also says that actual genetic enhancements should be avoided. There is evidence that society is uncomfortable with the idea of individuals, who are not suffering from disease, improving either themselves through somatic therapy or their bloodlines through germline genetic enhancement.

Some people might want more copies of the p53 tumour suppressing gene or to lose their CCR5 gene, which helps HIV invade cells, in order to give their children possible protection from cancer or HIV respectively, but I'd have to say it isn't worth the risk.

I would add that, ethical reservations aside, the sheer complexity of our genomes, and the rather involved and lengthy process of human reproduction, means that I have no concerns that even the craziest world leader could ever generate an army of super-mutants. Such an ambition would be defeated by not knowing which genes to alter, not to mention the requirement to assemble tens of thousands of surrogate mothers, then wait 20 years for the army to mature.

Yes, it is possible that someone somewhere will attempt germline gene enhancement as a stunt. That would be wrong and dangerous, and a risk for the child. But it would not threaten society any more deeply than many other obscene and regrettable individual crimes that sadly occur every day.

Germline gene therapy is illegal in many countries, and although there is a risk that unfortunate "medical tourism" may occur at some stage, I don't expect this to be a greater problem than the already widespread snake-oil selling that is a feature of many economies.

No emergency

So am I comfortable with this report and confident that it covers the ethical issues? I think it is superbly written. It is accurate, up to date, balanced, thoughtful, and covers experiments, somatic therapy, germline therapy, genetic enhancement, societal responses, and the need for public consultation and careful regulation. There is no emergency here.

My main concern is that raising the prospect of germline gene therapy will trigger discussions that will divert us from more pressing issues.

I do worry that introducing this apex concept as a possibility may increase the number of people who fixate on what gene therapy could deliver and thus may be lured into medical tourism, both desperate patients and also foolish investors, and all the while charlatans will profit from peddling promise.

I worry that raising hopes too high too quickly will ultimately cause a backlash against more moderate science.

I also worry that even conventional funding bodies will succumb to understandable pressures to fund translational research prematurely and this will actually waste large amounts of valuable public money.

And I worry about a hysterical reaction that could divide society along political lines with people lining up for or against germline gene therapy based on their political positions or personal beliefs rather than a sober examination of the facts, risks and contexts.

Finally, I worry that the focus on human modification will distract us from other issues, such as the use of CRISPR-mediated gene drives that could be used to eradicate rapidly reproducing organisms such as mosquitoes, and could thus be used for both great good or great harm.

But I don't feel the burden of worry too much because I know that, as a scientist, I can and should share the weight of my concerns with society.

Explore further: With stringent oversight, heritable human genome editing could be allowed: report

This article was originally published on The Conversation. Read the original article.

Clinical trials for genome editing of the human germline - adding, removing, or replacing DNA base pairs in gametes or early embryos - could be permitted in the future, but only for serious conditions under stringent oversight, ...

Recent evidence demonstrating the feasibility of using novel CRISPR/Cas9 gene editing technology to make targeted changes in the DNA of human embryos is forcing researchers, clinicians, and ethicists to revisit the highly ...

The National Academy of Sciences and National Academy of Medicine issued a 258-page report Tuesday (Feb. 14) focused on human genome editing. It lays out principles and recommendations for the U.S. government and governments ...

At the conclusion of the recent International Summit on Human Gene Editing in Washington, DC, its organizing committee released a much-anticipated statement recommending how human genetic engineering should be regulated. ...

Don't expect designer babies any time soonbut a major new ethics report leaves open the possibility of one day altering human heredity to fight genetic diseases, with stringent oversight, using new tools that precisely ...

Personalized medicine, which involves tailoring health care to each person's unique genetic makeup, has the potential to transform how we diagnose, prevent and treat disease. After all, no two people are alike. Mapping a ...

Work on gene therapy is showing significant progress for restoring muscle strength and prolonging lives in dogs with a previously incurable, inherited neuromuscular disease. UW Medicine Institute for Stem Cell and Regenerative ...

A genomic study of baldness identified more than 200 genetic regions involved in this common but potentially embarrassing condition. These genetic variants could be used to predict a man's chance of severe hair loss. The ...

Purdue University and Indiana University School of Medicine scientists were able to force an epigenetic reaction that turns on and off a gene known to determine the fate of the neural stem cells, a finding that could lead ...

Just before Rare Disease Day 2017, a study from the Monell Center and collaborating institutions provides new insight into the causes of trimethylaminura (TMAU), a genetically-transmitted metabolic disorder that leads to ...

Monash University and Danish researchers have discovered a gene in worms that could help break the cycle of overeating and under-exercising that can lead to obesity.

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

Read more:
Human genome editing report strikes the right balance between risks and benefits - Medical Xpress

Cancer could be wiped off the face of the earth with new gene editing techniques – Metro

We could be about to see a golden age of health (Picture: Getty)

Gene editing techniques developed in the last five years could usher in a golden age of health with an effective end to the scourge of cancer and inherited disease being banished forever, a leading British expert predicts.

Dr Edze Westra believes the ability to splice selected DNA into cells with great precision is destined to become super important in the next two decades.

He foresees it transforming the human race by creating generations of people for whom cancer, failing vision, and the diseases of old age or bad genes are distant memories.

The bioscientist from the University of Exeter said: 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.

I think in the coming decades gene editing will become super important, and I think we will see it being used to cure all 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 embryos should 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.

It could be a fantastic strategy to deal with some of the worlds biggest problems, said Dr Westra.

In terms of ethics we need to work out what happens if a genetically engineered insect flies out of the window of the lab. Trials into gene drives are already happening in labs for malaria.

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 cells 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.

Read the original here:
Cancer could be wiped off the face of the earth with new gene editing techniques - Metro

Bridging the gap study sequences Asian genomes to diversify genetic databases – University of Virginia The Cavalier Daily

Though the number of human genomes sequenced continues to rise rapidly since the completion of the Human Genome Project a scientific endeavor spanning multiple decades and countries aimed at detailing human DNA in 2003, less than 10 percent of those genomes to date correspond to individuals of Asian descent. The GenomeAsia 100K Project, a non-profit consortium, seeks to change this lack of knowledge surrounding a major portion of the worlds ethnicities. The conglomeration of researchers and private sector executives from around the world from Seoul, South Korea to the University plans to add 100,000 novel genomes from individuals of Asian ethnicity to new open-access databases.

Academic institutions and private sector companies came together in 2016 to launch the GenomeAsia 100K Project. While the research organization MedGenome and Nanyang Technological University in Singapore originally founded the non-profit consortium, representatives from other businesses and schools including Genentech, Macrogen and the University of California, San Francisco have joined the association.

Since genome sequencing can reveal the unique characteristics of each persons genetic material, it can help determine a persons ancestry and the propensity for certain medical conditions. According to GenomeAsia 100K, Asians constitute nearly half of the worlds population, and the distinct ethnicities and communities offer a relatively untapped repository of genetic diversity. The project hopes to provide new insights into inherited diseases as well as those caused by a combination of genetic and environmental factors.

Aakrosh Ratan, assistant professor of public health sciences and researcher for GenomeAsia 100K, explained that in particular, the information the initiative collects may help develop medical treatments based on peoples specific genetic makeup, instead of relying on traditional general treatments that may not target the unique root cause of each patients form of a disease.

The goal of precision medicine is to tailor treatment towards a persons genetic background, and that dream cannot be realized until you have the proper reference databases, Ratan said.

Mutations in humans DNA sequences lead to different copies of the same gene within a person and amongst ethnicities. These different versions of a gene can act as markers of diseases that are inherited or influenced by genetic makeup. For example, the disorder sickle cell anemia is caused by the change of a single point in the DNA sequence. When someone is born with copies of this particular gene from both parents contain the mutation, he or she will suffer from often debilitating pain resulting from red blood cells that cannot effectively transport oxygen.

Ratan explained that genome sequencing can highlight mutations in a persons DNA that may cause illnesses such as sickle cell anemia.

One of the ways we identify the mutations that drive a rare disease is by identifying the mutations and then prioritizing those mutations based on their prevalence in healthy populations, Ratan said. With the medical datasets we have compiled, we can actually improve such analyses for patients of Asian descent.

As of December 2019, the GenomeAsia 100K Project has completed the analysis of 1,739 genomes from 219 populations and 64 countries worldwide. Preliminary findings appeared that same month in the scientific journal Nature. The paper concluded that the sample provided a reasonable framework for sequencing practices and studying the history and health of Asian populations. Ratan and his lab at the University supervised the identification and contributed to the analysis of these genetic variants.

Once the 100,000 genomes have been collected and sequenced, the data will be publicly available as a controlled dataset. As a result, experts investigating topics from heart disease to human evolution can easily access the genome sequences.

One of the real gaps in human genetics studies of disease has been the underrepresentation of non-Europeans, Charles Farber, associate professor of public health sciences, said in an email to The Cavalier Daily. The work of the GenomeAsia 100K Consortium provided critical insight into the extent and nature of genome variation in individuals of Asian ancestry and will be critical in making disease genetic studies more inclusive of all global populations.

Ani Manichaikul, assistant professor of public health sciences in the Center for Public Health Genomics, expressed enthusiasm for the GenomeAsia 100K Project. She claimed that the additional genetic information could augment her research as part of the Multi-Ethnic Study of Atherosclerosis, a cardiovascular disease where fatty deposits accumulate and potentially block arteries. The study currently focuses on Caucasian, African American, Hispanic and Chinese American individuals.

The GenomeAsia project is very useful because there are some instances where particular genetic variants are only observed in particular genetic groups, Manichaikul said. Those markers can be unique to those sequenced through the project, which means we would not have necessarily have observed those particular variants otherwise.

Manichaikul also suggested that expanding existing repositories of hereditary statistics would improve methods of assigning people risk scores for diseases based on their DNA. The National Human Genome Research Institute describes polygenic risk score, which indicates a persons likelihood of certain diseases based on the presence of mutations known to be associated with a given disorder. Companies such as 23andMe have started to provide consumers with this metric, but without a comprehensive database of genomes from different populations, score reliability can decrease.

Since indicators of genetically-linked conditions often appear in certain alleles, or different versions of a gene, knowing whether one has a disease marker can help patients take preventative measures if need be. However, in the absence of comprehensive information on the range of disease markers that appear in different ethnicities, whole populations may lack the potential benefits of this burgeoning healthcare statistic.

The only way we can create risk prediction models that are accurate across populations is if we also have corresponding databases available with individuals that represent that diversity, Manichaikul said.

Following the findings in the preliminary study, GenomeAsia 100K Project collaborators will continue to sequence more genomes of Asian individuals. The hope is that, once researchers have access to the data, insights from 100,000 genomes will drive the development of new therapeutic strategies that will benefit people around the world.

I would like more researchers to have access to this data, Ratan said. This is a resource. Were working to establish these reference datasets, and we would definitely like them to be used.

Continued here:
Bridging the gap study sequences Asian genomes to diversify genetic databases - University of Virginia The Cavalier Daily

Meet the PLOS ONE Cancer and Oncology Authors – PLoS Blogs

Today is World Cancer Day a day for raising the voices of cancer survivors, loved ones, and the people who are working endlessly to find solutions. This years theme is I am and I will: a recognition of the power each individual has to make an impact.

Each year, PLOS ONE publishes more than 1000 new research articles in cancer and oncology from authors who have dedicated their careers to studying this disease. In celebration of this years theme, were sharing their stories which inspired the science we use to understand and fight this disease.

My research group is mainly focused on the study of lung and pancreatic cancers, which are associated with high morbidity and mortality rates, worldwide. We use high throughput methods to identify new biomarkers and regulatory pathways and functional assays to improve our understanding of disease biology.

Patricia Pintor dos Reis, Faculty of Medicine, So Paulo State University UNESP Botucatu, SP, BRAZIL.

MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma.Tainara F. Felix, Rainer M. Lopez Lapa, Mrcio de Carvalho, Natlia Bertoni, Tomas Tokar, Rogrio A. Oliveira, et al

Bioinformatics is my tool and cancer research is my subject. My dad and many other people died of cancer and I want to uncover what causes cancer. And I love math and computers, which attracted me to become a bioinformatician. Now I am working for NCI initiative Ras program at Frederick National Lab for Cancer Research, which tries to tackle the most critical and ancient gene in cancer biology: Ras genes.

My last paper on PLOS ONE is about common pitfalls often seen in the survival analysis in the field. We wish to first alert researchers about the pitfalls when they perform survival analysis and to provided a novel method that shall help avoid the pitfalls.

Ming Yi, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America

GradientScanSurvAn exhaustive association test method for gene expression data with censored survival outcome.Ming Yi, Ruoqing Zhu, Robert M. Stephens

The goal of my research is to develop an agent that promotes apoptosis in cancer cells but not in normal cells. To accomplish this goal, I explored different protein targets and pathways that included but are not limited to matrix type-I metalloprotease I (MT1-MMP), tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), and oxidative stress.

Dmitri Rozanov, Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America

Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity.Dmitri Rozanov, Anton Cheltsov, Aaron Nilsen, Christopher Boniface, Isaac Forquer, et al

I focus on H&N/Skull base cancers and mechanisms of treatment resistance within HPV positive and negative cancers. Understanding mechanism of treatment resistance will enable us to target new pathways for improving patient outcomes.

Dukagjin Blakaj, The James Cancer Center, Ohio State University, Columbus, OH, United States of America

Association of an intact E2 gene with higher HPV viral load, higher viral oncogene expression, and improved clinical outcome in HPV16 positive head and neck squamous cell carcinoma.Nicole V. Anayannis, Nicolas F. Schlecht, Miriam Ben-Dayan, Richard V. Smith, Thomas J. Belbin, et al

My particular area of research is the staging of colon cancer, it is important because colon cancer is a top 3 killer (of all cancer types) and we need new treatment strategies. However without accurate staging (i.e. determining how advanced the tumor is), it is nearly impossible to develop these new strategies.

Elias Nerad, The Netherlands Cancer Institute, Amsterdam The Netherlands.

The Apparent Diffusion Coefficient (ADC) is a useful biomarker in predicting metastatic colon cancer using the ADC-value of the primary tumor.Elias Nerad, Andrea Delli Pizzi, Doenja M. J. Lambregts, Monique Maas, Sharan Wadhwani, et al

I have always wanted to understand the incredible organization of brain functions and how to cure patients with brain lesions. My research field focuses on brain anatomy, brain functions, neuroimaging and how all these aspects together can improve the treatment of patients with cerebral tumors. My work tried to change the standard topographical classification of brain tumors to a model including more detailed information regarding the tumor infiltration along the white matter fibers.

This model perfectly fits the open access principle because it is not based on expensive technology, rather on a basic idea merging anatomy neuroimaging and oncology. I believe that anyone in the world can reproduce this classification method with standard MRI pictures contributing to a more extensive and shared knowledge in this field.

Francesco Latini, Department of Neuroscience, Neurosurgery, Uppsala University, Uppsala, Sweden

A novel radiological classification system for cerebral gliomas: The Brain-Grid.Francesco Latini, Markus Fahlstrm, Shala G. Berntsson, Elna-Marie Larsson, Anja Smits, Mats Ryttlefors

Find out more about the causes of cancer and interventions to prevent and manage the disease in the PLOS Cancer Research Special Collection.

PLOS ONE will also be launching a Call for Papers for Cancer Metastasis research and invites submissions that report on the biochemical and cell biological basis of metastasis, including but not limited to cell adhesion, cell migration, cytoskeletal dynamics, cell polarity, tumour heterogeneity, tumour dormancy and the tumour microenvironment.

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Meet the PLOS ONE Cancer and Oncology Authors - PLoS Blogs

Ultra-Fast Genome Sequencing Could Save the Lives of Newborns – WIRED

Maverick Coltrin seemed like any other newborn when he first came home from the hospital, wearing his beanie cap with bear ears and blue-and-gray onesie and following the typical around-the-clock cycle of sleeping and breastfeeding. But within a couple of days, his parents noticed something was off. At 6 days old, Maverick completely stopped feeding. His arms and legs would stiffen and then release, the spasms punctuated by his cries.

His parents rushed him to Rady Childrens Hospital in San Diego, where EEG monitors recorded that he was having as many as 30 seizures an hour. Doctors scrambled to find the cause. Anti-seizure medicines didnt work, so he was sedated to stop the damage to his brain. His organs started to fail, and his skin turned a dusky blue. His mother, Kara Coltrin, walked into his empty nursery at home and cried.

So when doctors from Radys Institute for Genomic Medicine asked for permission to sequence Mavericks genome as part of a clinical trial of ultra-rapid sequencing for newborns who are critically ill from an unknown cause, Mavericks parents didnt hesitate. The doctors cautioned that they couldnt guarantee that they would pinpoint a genetic disorder or, if they did, that it could be treated. They gave the standard caveat about genetic testingthat identifying a genetic disorder could affect Mavericks eligibility for life insurance someday. But even if the sequencing didnt help him, his participation would contribute to a study that could benefit other babies. Obviously, the pros outweighed the cons manyfold, his mother says. We just wanted his pain to stop.

Within 36 hours, the Coltrins had an answer: Maverick has pyridoxine-dependent epilepsy, caused by a rare mutation of the ALDH7A1 gene, which codes for the enzyme antiquitin. By giving him high doses of vitamin B6 and controlling a couple of amino acids in his diet, doctors stopped the seizures. Maverick, now 2 years old, runs around like a normal, rambunctious toddler. He has hit all his developmental milestones, although they have been somewhat delayed. He hasnt had a seizure since his treatment began. Every once in a while, I think back on him being dusky blue and super skinny and hooked up to all these tubes, says Kara Coltrin. I look at him and its hard to believe that happened to him. People who see him on a normal basis would never know he was ever sick.

The technology that saved Mavericks life stretched the limits of bioinformatics, returning results far sooner than is typical for genetic testing. Rapid sequencing typically takes about seven days for a preliminary diagnosis, while Rady completes ultra-rapid sequencing in three days or less. (In 2018, Rady set a Guinness World Record by sequencing a babys genome in 20 hours and 10 minutes.)

But now ultra-rapid sequencing is moving from an investigational tool to a standard of care. Blue Shield of California is the first insurer to cover rapid and ultra-rapid sequencing of babies and children who have life-threatening and unexplained medical conditions. Since the new policy began in July 2019, 28 babies or children in California have received the testing through Blue Shield, which is just beginning to promote the new coverage.

Blue Shield expects that 250 to 500 newborns will be eligible for the whole genome sequencing each year, which represents about 10 percent of their insured babies treated in neonatal intensive care units in California. Company executive vice president Terry Gilliland said he will encourage other Blue Cross and Blue Shield plans around the country to adopt a similar policy. When you think about all the pain and suffering families go through with sick babies, this is going to be an enormous benefit, he says.

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Ultra-Fast Genome Sequencing Could Save the Lives of Newborns - WIRED

UPDATED: Decrying ‘arbitrary and capricious’ action, RegenxBio sues FDA over clinical holds on gene therapy – Endpoints News

When RegenxBio disclosed that the FDA had placed a partial clinical hold on one of its lead gene therapies, execs outlined several customary next steps: continuing assessment and monitoring, delaying a related IND filing, and working with the FDA to address the matter.

As it turned out, they were planning something much less mundane. Two days after announcing the hold in its Q3 update, RegenxBio filed a lawsuit seeking to set it aside, the FDA Law Blog noted.

The lawsuit shed light on the interactions between the biotech and regulators, revealing that there was actually a full clinical hold on the diabetic retinopathy trial in addition to the partial hold on wet age-related macular degeneration and RegenxBio withdrew the IND.

According to the complaint, the company had discussed results from its Phase I/IIa trial with the FDA and was on track to begin the next phase before the end of 2019.

But on October 18, 2019, without notice or explanation, FDA placed RGX-314 on a clinical hold, effectively halting REGENXBIOs development of this potentially life-altering treatment for retinal diseases that are leading causes of adult blindness. Since issuing the clinical hold order, FDA has rebuffed REGENXBIOs repeated attempts to obtain an explanation of the basis for the clinical hold.

Failing to provide advance warning or explanation for the hold, RegenxBio claims, is in violation of the FDAs own regulations. And that led to an arbitrary and capricious final decision, they wrote.

But thats not it.

Since they didnt get a chance to review or rebut the reasons for the hold, which harmed their reputation and property interest in RGX-314, RegenxBio believes the FDA violated the Fifth Amendments Due Process Clause. Furthermore, they charged a particular section of the Food, Drug, and Cosmetic Act represented an unconstitutional vesting of legislative power in the Secretary of Health and Human Services.

Along with the agency, the federal government, HHS Secretary Alex Azar, acting FDA commissioner Brett Giroir (who has taken over from Ned Sharpless while Stephen Hahn goes through the confirmation process), and FDA regulatory project manager Edward Thompson were also named as defendants. Thompson allegedly first notified RegenxBio of the holds citing issues associated with [RGX-314s] delivery systems.

Following multiple exchanges, the FDA apparently told RegenxBio that it would provide a written explanation of the basis for the hold by this Friday, November 15.

Why risk the ire of regulators when an update is due so soon? As a procedural matter to preserve their rights, the company said.

This action was taken on the recommendation from counsel as we continue to work with the FDA to address this matter, and we hope this step will help ensure the FDA will provide RegenxBio with their specific concerns about the unspecified device, it wrote in an email to Endpoints News.

Attorney Deborah Livornese offered this take on the FDA Law Blog:

While it seems unlikely that the merits of the clinical hold will be resolved through the judiciary process in a helpful timeframe, the complaint has likely increased the chances that FDA will respond with a thorough explanation of its reason for the hold when it does provide the written basis.

The biotech added that the plan is still to start the wet AMD trial and file an IND for diabetic retinopathy in Q2 2020, as we believe that there are readily available and suitable alternatives for all of the devices used in our studies.

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UPDATED: Decrying 'arbitrary and capricious' action, RegenxBio sues FDA over clinical holds on gene therapy - Endpoints News

BostonGene and Weill Cornell Medicine Reveal Results from Cancer Microenvironment Study – Business Wire

ORLANDO, Fla.--(BUSINESS WIRE)--BostonGene Corporation (BostonGene), a Boston-based biomedical software company, presented the results of its recent cancer microenvironment study during the 61st American Society of Hematology Annual Meeting and Exposition held on December 7-10, 2019. The research study examined the role of the tumor microenvironment of Diffuse Large B-Cell Lymphoma (DLBCL).

The study, conducted as part of BostonGenes collaboration with Weill Cornell Medicine, combined whole exome and transcriptome analyses from an integrated cohort of 3,026 DLBCL patients. The cohort includes publically available data as well as prospective patients.

The study revealed that a new classification based on the tumor microenvironment is associated with clinical outcomes independently of existing molecular subtypes.Computationally predicted results demonstrated a strong correlation with response therapy obtained in murine DLBCL models for subtypes based on stromal, immune and malignant composition.

Improving treatment outcomes for individual DLBCL patients by integrated analysis of large-scale next-generation sequencing (NGS) data including somatic variants and gene expression changes in the tumor and the tumor microenvironment is our top priority, said Leandro Cerchietti, M.D., Associate Professor of Medicine and a member of the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. These promising findings bring us one step closer to achieving that goal.

We are proud to collaborate with Weill Cornell Medicine to provide advanced computational analytics for the integration of big data sets generated for each patient, said Andrew Feinberg, President and CEO of BostonGene. We look forward to continuing our collaboration to further identify the best treatment options for cancer patients.

About BostonGene Corporation

BostonGene Corporation is pioneering the use of biomedical software for advanced patient analysis and personalized therapy decision making in the fight against cancer. BostonGenes unique solution performs sophisticated analytics to aid clinicians in their evaluation of viable treatment options for each patient's individual genetics, tumor and tumor microenvironment, clinical characteristics and disease profile. BostonGenes mission is to enable physicians to provide every patient with the highest probability of survival through optimal cancer treatments using advanced, personalized therapies. For more information, visit BostonGene at http://www.BostonGene.com.

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BostonGene and Weill Cornell Medicine Reveal Results from Cancer Microenvironment Study - Business Wire

How maternal Zika infection results in newborn microcephaly – Baylor College of Medicine News

The current study was initiated when a patient presented with a small brain size at birth and severe abnormalities in brain structures at the Baylor Hopkins Center for Mendelian Genomics (CMG), a center directed by Dr. Jim Lupski, professor of pediatrics, molecular and human genetics at Baylor College of Medicine and attending physician at Texas Childrens Hospital, said Dr. Hugo J. Bellen, professor at Baylor, investigator at the Howard Hughes Medical Institute and Jan and Dan Duncan Neurological Research Institute at Texas Childrens Hospital.

This patient and others in a cohort at CMG had not been infected by Zika virus in utero. They had a genetic defect that caused microcephaly. CMG scientists determined that the ANKLE2 gene was associated with the condition. Interestingly, a few years back the Bellen lab had discovered in the fruit fly model that ANKLE2 gene was associated with neurodevelopmental disorders. Knowing that Zika virus infection in utero can cause microcephaly in newborns, the team explored the possibility that Zika virus was mediating its effects in the brain via ANKLE2.

In a subsequent fruit fly study, the researchers demonstrated that overexpression of Zika protein NS4A causes microcephaly in the flies by inhibiting the function of ANKLE2, a cell cycle regulator that acts by suppressing the activity of VRK1 protein.

Since very little is known about the role of ANKLE2 or VRK1 in brain development, Bellen and his colleagues applied a multidisciplinary approach to tease apart the exact mechanism underlying ANKLE2-associated microcephaly.

The team found that fruit fly larvae with mutations in ANKLE2 gene had small brains with dramatically fewer neuroblasts brain cell precursors and could not survive into adulthood. Experimental expression of the normal human version of ANKLE2 gene in mutant larvae restored all the defects, establishing the loss of Ankle2 function as the underlying cause.

To understand why ANKLE2 mutants have fewer neuroblasts and significantly smaller brains, we probed deeper into asymmetric cell divisions, a fundamental process that produces and maintains neuroblasts, also called neural stem cells, in the developing brains of flies and humans, said first author Dr. Nichole Link, postdoctoral associate in the Bellen lab.

Asymmetric cell division is an exquisitely regulated process by which neuroblasts produce two different cell types. One is a copy of the neuroblast and the other is a cell programmed to become a different type of cell, such as a neuron or glia.

Proper asymmetric distribution and division of these cells is crucial to normal brain development, as they need to generate a correct number of neurons, produce diverse neuronal lineages and replenish the pool of neuroblasts for further rounds of division.

When flies had reduced levels of Ankle2, key proteins, such as Par complex proteins and Miranda, were misplaced in the neuroblasts of Ankle2 larvae. Moreover, live imaging analysis of these neuroblasts showed many obvious signs of defective or incomplete cell divisions. These observations indicated that Ankle2 is a critical regulator of asymmetric cell divisions, said Link.

Further analyses revealed more details about how Ankle2 regulates asymmetric neuroblast division. They found that Ankle2 protein interacts with VRK1 kinases, and that Ankle2 mutants alter this interaction in ways that disrupt asymmetric cell division.

Linking our findings to Zika virusassociated microcephaly, we found that expressing Zika virus protein NS4A in flies caused microcephaly by hijacking the Ankle2/VRK1 regulation of asymmetric neuroblast divisions. This offers an explanation to why the severe microcephaly observed in patients with defects in the ANKLE2 and VRK1 genes is strikingly similar to that of infants with in utero Zika virus infection, Link said.

For decades, researchers have been unsuccessful in finding experimental evidence between defects in asymmetric cell divisions and microcephaly in vertebrate models. The current work makes a giant leap in that direction and provides strong evidence that links a single evolutionarily conserved Ankle2/VRK1 pathway as a regulator of asymmetric division of neuroblasts and microcephaly, Bellen said. Moreover, it shows that irrespective of the nature of the initial triggering event, whether it is a Zika virus infection or congenital mutations, the microcephaly converges on the disruption of Ankle2 and VRK1, making them promising drug targets.

Another important takeaway from this work is that studying a rare disorder (which refers to those resulting from rare disease-causing variations in ANKLE2 or VRK1 genes) originally observed in a single patient can lead to valuable mechanistic insights and open up exciting therapeutic possibilities to solve common human genetic disorders and viral infections.

Others who contributed in this study are Hyunglok Chung, Angad Jolly, Marjorie Withers, Burak Tepe, Benjamin R. Arenkiel, Priya S. Shah, Nevan J. Krogan, Hatip Aydin, Bilgen B. Geckinli, Tulay Tos, Sedat Isikay, Beyhan Tuysuz, Ganesh H. Mochida, Ajay X. Thomas, Robin D. Clark and Ghayda M. Mirzaa. They are affiliated to one or more of the institutions: Baylor College of Medicine, Texas Childrens Hospital and the Jan and Dan Duncan Neurological Research Institute in Houston, TX; University of California at Davis and San Francisco; Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Marmara University School of Medicine, Istanbul, Turkey; Dr. Sami Ulus Research and Training Hospital of Women's and Children's Health and Diseases, Ankara, Turkey; Boston Childrens Hospital; Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA; Loma Linda University Medical Center, Loma Linda, CA; University of Washington, Seattle, WA; and Seattle Children's Research Institute, Seattle, WA.

The study was funded by the National Institutes of Healths F32NS092270, NIH/NINDS R35NS105078, NIH U54NS093793, NIH R24OD022005, NIH/NINDS K08NS092898, Howard Hughes Medical Institute (HHMI), Medical Research Fellowship, Jordans Guardian Angels, a jointly funded NHGRI and NHLBI grant to the Baylor-Hopkins Center for Mendelian Genomics (UM1 HG006542) and the Huffington Foundation.

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How maternal Zika infection results in newborn microcephaly - Baylor College of Medicine News

Intermountain preps precision medicine tool for commercialization – Healthcare IT News

Intermountain Healthcare on Monday announced that its stepping closer to bringing a version of its precision medicine tool for cancer to the open market.

The health system, in fact, is pumping an additional $15 million into its spin-out Navican Genomics, which makes the TheraMap technology for matching patients with prioritized treatment options or appropriate clinical trials.

[Also:Promise of precision medicine depends on overcoming big obstacles] While precision medicine has great potential to positively impact cancer patients, its use is currently fragmented at best, Navican CEO Ingo Chakravarty said in a statement. TheraMap will provide precision care for all cancer patients, not just a few.

Navican employs sequencing tests developed at Intermountain to determine exactly which gene mutations are causing the cancer. From there, TheraMap provides testing and treatment options for the greatest number of actionable gene mutations, the startup said.

Intermountains Innovations division launched Navican Genomics in October 2016.

Twitter: @Bernie_HITN Email the writer: bernie.monegain@himssmedia.com

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Intermountain preps precision medicine tool for commercialization - Healthcare IT News