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Mother of Guelph girl with ‘rare’ genetic mutation looks for help, and hope – GuelphMercury.com

March 10th, 2020 7:48 pm

"I walked into the geneticist's office, and she, with tears in her eyes, asked me how Riana's walking was doing, and she told me that (she) would lose her mobility, that she's been diagnosed with a really rare gene disorder: KCNB1," Francisco said.

"I think I blacked out after that. Nothing registered, literally."

Later, Francisco said she would remember being relieved that they knew what the problem was. Later still, even that small comfort would evaporate, as she realized how little was known about her daughter's newly-named disorder.

Renzo Guerrini is a professor of neuroscience at the University of Florence, Italy, and a leading expert in the study of epilepsy.

Reached by phone in Florence, he said KCNB1 is caused by a genetic mutation, and can be considered a spectrum disorder meaning that symptoms exist on a spectrum and can be more or less severe, depending on the person.

However, there are some common symptoms among the 70 patient-cases he's studied.

"All patients have developmental delay, and about 85 per cent also have epilepsy," he said.

In Riana Faith's case, she's also limited in how she can communicate. While she speaks a few words here and there, like asking for "bubbles" to play with, or demanding a "kiss" from mom, she also relies on a tablet-talker to help express herself. For instance, if asked what colour red was, she could point to a red object. But when asked what colour a red object was, she would say purple. With the tablet, she could press a button that would say "red" for her.

"That's a major feature which has been underlined,"Guerrini said. "About 50 per cent do not develop any language. They are non-verbal," he said, adding that all cases have a major language impairment of some kind.

Riana Faith is also extremely active. On a recent day home from school due to teacher strikes, the six-year-old bounced around the room, her attention careening from toys, to pens, to yogurt and whatever else she could grasp in the space of a few minutes.

She also loves to sing. Her mother calls her "the most patriotic girl ever" because she always tries to hum/sing along with "O Canada."

Ironically, some of the only time Riana Faith focuses is with the music blaring, the TV on in the background, while bouncing up and down dancing with her toy guitar and singing "we're gonna rock, rock, rock, rock, rock, and roll. Repetitively ..." Francisco said.

"I'm constantly apologizing."

As far as treatment is concerned, Guerrini said there isn't any specific treatment established for a KCNB1 diagnoses. Doctors have only known about the genetic mutation for about six years, and there isn't enough information to reach definitive conclusions.

"For example, in a centre like ours, which is one of the main centres in (Italy), we have seen seven cases," he said.

Likewise, Francisco says there are less than five cases in Canada, and she hasn't come across anyone focusing on KCNB1 research here.

So, while her doctors can try to treat symptoms, such as assigning medication for different types of seizures, there is no way to directly treat the disorder.

"And there's no indication that the behavioural problems, the language problems, can benefit from any specific program or type of approach," Guerrini said.

His recommendation for people with rare gene disorders is to take advantage of the internet, "start a club" where people with the diagnoses can share information, and get the word out about their struggle.

As someone struggling for answers, Francisco says she's already gone that route. Her daughter's story is posted to KCNB1.org, a website that tries to shed light on the disorder.

It was there the mother found comfort in reading stories from people with like experiences. For instance, other parents of children diagnosed with KCNB1 have said a complete loss of mobility may not be inevitable.

It was also in the KCNB1 community that she learned about an upcoming conference in Chicago, where Faith can get time with doctors specializing in her rare condition.

Francisco is hoping to raise $2,500 to cover the trip. You can click hereto be taken to her GoFundMe page.

Riana Faith might have everything she needs to be happy bubbles, some Splash'N Boots (a musical duo), maybe a pudding, if mom says it's OK. She's even been given a wish fund from the Guelph Wish Fund for Children, says executive director Sharon Rice.

But it's her mother who really stands to benefit from the Chicago trip.

"That's the thing, I don't want anyone to feel sorry for her. She is a very happy child. There's nothing I won't do for this kid," Francisco said.

"(In Chicago,) they're going to see our children, one-on-one. That, for me, I need."

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From Iceland COVID-19 In Iceland: deCODE Genetics Will Screen General Population For Virus – Reykjavk Grapevine

March 10th, 2020 7:48 pm

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Magns Andersen

CEO of deCODE Genetics Kri Stefnsson (shown above) intends to screen the entire Icelandic population for COVID-19, of which there have been 60 confirmed cases at the time of this writing.

While almost all of these cases come from three flights returning from Italy and Austria, with the arrivals put in quarantine while testing is underway, the virus has unfortunately found its way into the general population.

Kris desire to screen the general population was not without controversy, as both the Data Protection Authority and the Scientific Ethics Committee initially believed Kri required a special permit in order to conduct the screening. However, Frttablai now reports that both bodies have reversed their position on the matter, as the screening is considered clinical work; not a scientific study.

In fact, a statement from deCODE emphasises that peoples personal data will not be permanently recorded nor put in the companys general knowledge bank. Rather, the purpose of the screening is meant to inform those who have symptoms whether or not they have COVID-19, in conjunction with the Directorate of Health, in order to assist already ongoing efforts.

This screening is expected to go forward within the next week.

Symptoms of COVID-19 include dry cough, fever, and aches in the bones. If you are worried you may have COVID-19, have been to any of the high-risk areas or in contact with anyone who has within the last 14 days, you are urged to call 1700 from an Icelandic phone number or +354 544 4113 from any other phone, where a health care professional will give you further information and guidance.

To prevent transmission or contact with the virus, the cardinal rule is to wash your hands frequently before eating and after touching common surfaces, and avoid touching your face. If you must sneeze or cough, do so into the crook of your elbow or into a tissue. It also naturally follows that you should avoid contact with sick people.

The Directorate of Health in fact has extensive information in English on COVID-19, including a handy FAQ.

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March: Predicting educational achievement | News and features – University of Bristol

March 10th, 2020 7:48 pm

Pupils' genetic data do not predict their educational outcomes with sufficient accuracy and shouldnt be used to design a genetically personalised curriculum or tailor teaching, according to a new University of Bristol study. The findings, which compared the genetic scores of 3,500 pupils with their exam results, are published in the journal eLife today [10 March].

Despite some claims that differences in pupils' genetic data could be used to 'personalise' their education or identify those who are likely to struggle or thrive at school, few studies have investigated how accurately genetic measures known as polygenic scores (which combine information from all genetic material across the entire genome) can predict future educational performance better than other measures of student aptitude.

To measure whether genetic data could predict a pupils achievement, researchers from the Bristol Medical School and the MRC Integrative Epidemiology Unit took genetic and educational data from 3,500 children in Bristols Children of the 90s study. They compared pupils polygenic scores with their educational exam results at ages 7, 11, 14 and 16.

Their analysis showed that while the genetic scores modestly predicted educational achievement at each age, these predictions were little better than using standard information known to predict educational outcomes, such as achievement at younger ages, parents educational attainment or family socioeconomic position.

Dr Tim Morris, the studys lead author and Senior Researcher Associate from Bristol Medical School, said: Our analysis shows that some pupils with a low polygenic score are very high performers at age 16. Some of those who would be predicted from their genes to be in the bottom 5% are actually in the top 5% of performers. This contradicts the notion that it is possible to accurately predict how well any one child will perform in education from their DNA.

At the population level, researchers found that children with higher polygenic scores, on average, had higher exam scores than those with lower polygenic scores. They add that polygenic scores can be informative for identifying group level differences, but they currently have no practical use for predicting individual educational performance or for personalised education.

Dr Morris added: Educational achievement is incredibly complex and influenced by a large range of factors including parental characteristics, family environment, personality, intelligence, genetics, teachers, peers and schools, and - often overlooked - chance or random events. This complexity will make it perhaps irresolvably difficult to accurately predict how well any one pupil will do from their DNA.

The best piece of information we currently have for predicting how well a pupil will perform is how well they did in school earlier in childhood. Where we don't know this, such as at the start of schooling, we can make better predictions about a pupils future educational performance by knowing how educated their parents are than by knowing their DNA.

The researchers conclude that genes are insufficient for reliably predicting educational achievement at an individual level. The study was funded by the Economic & Social Research Council [ESRC], the Medical Research Council [MRC] and the Wellcome Trust.

Paper

Can education be personalised using pupils genetic data? by Tim T Morris, Neil M Davies, and George Davey Smith in eLife

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Lonza partners with three institutes on Cocoon system – BioPharma-Reporter.com

March 10th, 2020 7:47 pm

Institutes participating in the partnership include the Stanford University School of Medicine, the Fred Hutchinson Cancer Research Center, and Parker Institute for Cancer Immunotherapy.

The Cocoon platform is a closed automated cell therapy manufacturing platform enabling decentralized process development. A transportable cassette that internalizes all of the media, agents, and consumables used in the process is attached inside and the Cocoon closes and begins processing.

Each Cocoon develops therapy for one patient, therefore the technology is patient-scale, and the process can be scaled with many Cocoons, attached on Cocoon trees operating at the same time.

Under the agreement, Lonzas experts will work collaboratively with research teams of the partners to transfer some of their existing cell-based immunotherapies, which are in pre-clinical phase, to the Cocoon bioprocessing system.

Subsequently, the process development will be shared between the partners facilities and Lonzas R&D site in Shady Grove (MD), US.

Once these therapies enter the clinic, whether manufacturing is at the institutes or elsewhere, the Cocoon platform will enable this, Eytan Abraham, head of personalized medicine at Lonza, told us.

Asked about the potential immunotherapies examined, Abraham said that they target a combination of hematological malignancies, solid malignancies, and processes that use non-viral delivery of the gene of interest.

Use of the Cocoon technology can potentially benefit the organizations development projects in several ways, including increased process control, reductions in costs, manpower, time and space requirements, as well as offering superior scalability thereby enabling treatment of larger patient populations.

Further than that, Lonza expects the partnerships to help assess the technology and evaluate the platforms potential to manufacture a range of cell therapies comparable to those manufactured through other processes currently available.

Through these collaborations we are both showcasing the Cocoon advantages and capabilities, but also learning what is needed for decentralized based manufacturing of the next wave of patient scale cell therapies, Abraham told us.

He added that, accordingly, the company will continue to evolve the system to answer these needs, whether they increase cell numbers, improve in-process analytics, integration of additional technologies, such as magnetic cell separation and electroporation, or scaling technologies.

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Genomics Research Market Worth to Exceed $31 Billion by 2027 – Clinical OMICs News

March 10th, 2020 7:47 pm

The field of genomics has made fantastic progress in the fields of biomedical research and clinical development. This is good news for patients and excellent news for investors, as the field of genomics is expected to pay large dividends in finance in the coming decade.

Despite being a relatively new field in the space of biology research, genomics has made massive advances in science and medicine in the past few years. Research into the human genome has led to the development of personalized medicine, changing the clinical landscape for cancer treatment and rare genetic diseases, in particular. The cost associated with mapping one genome has dramatically dropped in a very short space of time, costing millions of dollars and years of effort at the start to now costing in the hundreds of dollars per sequence that is delivered in a matter of days. This has allowed worldwide entry into this space, and an explosion of new discoveries and advances.

The global genomics market size is expected to reach USD 31.1 billion by 2027, registering a CAGR of 7.7% over the forecast period, according to a new report by Grand View Research, Inc. Significant changes in disease management processes along with advancements in genomics and personalized medicine are expected to propel the market.

Grand View Research is a U.S.-based market research and consulting company, providing syndicated as well as customized research reports and consulting services. Headquartered in San Francisco, the companys analysts and consultants report in-depth analysis on 46 industries across 25 major countries worldwide. With the help of an interactive market intelligence platform, Grand View Research helps Fortune 500 companies and renowned academic institutes understand the global and regional business environment.

The report that was recently published makes several suggestions as to what is anticipated to be leading this growth. The consumables and reagents deliverable segment is expected to register the highest growth rate, owing to high costs and volume associated with reagents needed for sequencing. This field is filled by companies that service actual research companies, and oftentimes are the main operating costs of lab testing.

The computational services deliverable segment is also set to expand at a considerable CAGR from 20202027 owing to the increasing demand for computational sequence alignment and analysis among molecular biologists. Interpreting sequencing data is a somewhat complicated process, and software and people capable of interpreting the results are at an ever-increasing demand in this space.

In terms of investment into future research and development for predictive biomarkers targeted toward diagnosis and patient monitoring, substantial investments by biotechnology and pharmaceutical companies have contributed significantly to the revenue generated by the biomarker discovery application segment. Clinical trials using genomics sequencing have oftentimes been wildly successful, driving more and more disease-based research to consider its use for new treatment strategies, as well as a search for biomarkers at a breakneck speed.

The success of use of genomic sequencing is a worldwide affair, and the Asian Pacific region is a potentially lucrative market for genomics, and is anticipated to expand at the highest CAGR of 9.1%. Regionally, genomics is being used everywhere, particularly in North America and Europe, but also in Asia, South America, the Middle East, and Africa.

Key companies in the genomics market tend to be located in the United States or Europe, and the largest players include 23andMe; F. Hoffmann-La Roche Ltd.; BGI; Myriad Genetics Inc.; Danaher.; Pacific Biosciences; Illumina; Agilent Technologies; Thermo Fisher Scientific, Inc.; Foundation Medicine; Oxford Nanopore Technologies; and Bio-Rad Laboratories.

Of these companies, an increasing pool of market innovators mostly from 23andMe, Oxford Nanopore Technologies, and Veritas Genetics (each having launched breakthrough genomic technologies in recent years) are also contributing toward market development. 23andMe in particular has expertise in developing direct-to-consumer genomic tests targeted toward disease prognosis and has received FDA approval for its commercialization.

MinION, a sequencing device from Oxford Nanopore Technologies, is witnessing significant traction owing to its ability to sequence any fragment length of DNA in real time. In the same field, Veritas Genetics is offering an affordable solution for a complete readout of a genomic sequence. A few years ago, it was only possible to procure this information if ordered by a doctor, but now these tests can be taken by anyone curious about their DNA and costs approximately USD 1,000. Veritas Genetics has also begun the commercialization of this technique for newborns genomic sequencing applications in China.

Genomic sequencing and biomarker identification is hardly the only source of income in the field of genomics. Other deliverables besides products and services include functional genomics in basic laboratory research and aspects of costs associated; the study of epigenetics and computer data analysis associated with large data sets; and genomics end-use, in clinical and research laboratories, academic and government institutes, hospitals and clinics, and of course pharmaceutical and biotechnology companies.

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ImmersiveTouch Partners with HP on Virtual Reality and 3D Printing for Personalized Health Care Solutions – Yahoo Finance

March 10th, 2020 7:47 pm

Collaboration to focus on improving outcomes, increasing patient satisfaction and reducing costs

CHICAGO, March 5, 2020 /PRNewswire/ -- ImmersiveTouch has announced a collaboration with HP that strives to unleash the power of personalized medicine by providing the missing link between medical imaging and real-time surgery. This collaboration will pair ImmersiveTouch clinical software with HP hardware to create better healthcare outcomes at reduced costs. The companies will jointly showcase their technologies at the annual HIMSS conference in Booth 1541 from March 10th-12th.

ImmersiveTouch is revolutionizing personalized care by designing technology that more accurately simulates each patient's specific anatomy in 360 VR. Surgeons can feed traditional CT and MRI scans into ImmersiveTouch software, strap on virtual reality headsets, and then virtually fly through simulations of muscles, bones and blood vessels, exploring the specific dimensions of the disease they must attack from every angle. ImmersiveTouch continually strives towards increased patient satisfaction and improved surgical planning, and away from longer procedure times, sub-optimal patient outcomes and readmissions.

From radiology to surgery, the companies plan to combine their clinical software and hardware expertise to market products and solutions that can be customized to the needs of an individual patient. In the near-term, the collaboration will focus on promoting ImmersiveTouch software powered by HP's Reverb Pro VR headsets and connected to HP Jet Fusion 3D printers.

"ImmersiveTouch and HP together will shift the paradigm for high quality virtual reality experiences in healthcare," said Jay Banerjee, COO of ImmersiveTouch. "We are immersing surgeons to train and rehearse for mission-critical situations. The industry is poised to enter a new era of personalized care."

ImmersiveTouch has been installed in over 100 hospitals globally and is proud to facilitate personalized care through its technological innovation.

Recently at MetroHealth Hospital in Cleveland, a neurosurgeon was able to confirm his suspicion from the initial radiological report after reviewing the case with ImmersiveTouch. After the immersive planning session, the surgeon altered his surgical approach and was more accurately prepared.

In the spirit of the HIMSSmission to "realize the full health potential of every human, everywhere", ImmersiveTouch will invite one of its pioneer enterprise customers, Dr. Shafiq Rab, CIO of Rush Hospital, to speak on the HIMSS panel session titled "3D Print & VR: Improving Surgical Outcomes & Informed Consent".

About ImmersiveTouch Inc.

ImmersiveTouch strives to strengthen human life and unleash the power of personalized care by providing the missing link between medical imaging and real-time surgery. ImmersiveTouch is using the latest advancements in computer vision,artificial intelligenceand AR/VR to develop FDA cleared medical technology. The company provides a fullsoftware suite for surgical planning, surgery skills training, and informed patient consent. http://www.immersivetouch.com

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Global Biomarkers Market Outlook, 2020-2027 – Featuring Profiles of Key Players Abbott, Roche, Qiagen, Siemens Healthcare, Thermo Fisher Scientific,…

March 10th, 2020 7:47 pm

Dublin, March 10, 2020 (GLOBE NEWSWIRE) -- The "Biomarkers Market Size, Share & Trends Analysis Report by Type (Safety, Efficacy, Validation), by Application (Diagnostic, Drug Development, Personalized Medicine), by Disease, and Segment Forecasts, 2020-2027" report has been added to ResearchAndMarkets.com's offering.

The global biomarkers market size is expected to reach over USD 129.4 billion by 2027. It is anticipated to exhibiting a CAGR of 13.7%, during the forecast period. Factors, such as increasing collaborations and funds for R&D activities, rising consumer awareness, a widening patient base, and technological advancements collectively augmenting market growth.

The drug discovery segment contributed the highest revenue in 2019. Pharmaceutical companies focus on extensive R&D initiatives for the development of targeted therapeutics. Coordinated strategic efforts on biomarker development remain a searing trend among drug manufacturers, academic research institutions, commercial R&D organizations, non-profitable health foundations, and federal government biomedical regulatory and research agencies.

North America continued to lead the biomarkers market in 2019, driven by an amplifying demand for personalized medicines, high disease prevalence, and proactive government initiatives. It is expected to maintain its lead over the forecast period. Asia Pacific is positioned to witness the fastest CAGR, over the forecast period, spearheaded by India.

Some key market players include Abbott, Roche, Qiagen, Siemens Healthcare, Thermo Fisher Scientific, Bio-Rad Laboratories, Johnson & Johnson Services, Agilent Technologies, and Epigenomics. The players are developing novel kits and therapies and drugs to target population in the areas with high unmet clinical needs.

Further key findings from the study suggest:

Key Topics Covered

Chapter 1 Methodology and Scope

Chapter 2. Executive Summary

Chapter 3. Biomarkers Market Variables, Trends & Scope3.1. Biomarkers Market Lineage Outlook3.1.1. Clinical Diagnostics Market Outlook3.2. Penetration & Growth Prospect Mapping3.3. Regulatory Framework3.3.1. Reimbursement Framework3.3.2. Standards & Compliances3.4. Market Dynamics3.4.1. Market Driver Analysis3.4.1.1. Increasing Prevalence of Chronic Diseases3.4.1.2. Technological Advancements3.4.1.3. Funding for Biomarkers3.4.2. Market Restraint Analysis3.4.2.1. Reimbursement Policies3.5. Biomarkers Market Analysis Tools3.5.1. Industry Analysis - Porter's3.5.2. PESTEL Analysis3.5.3. Major Deals & Strategic Alliances Analysis

Chapter 4. Biomarkers Market - Competitive Analysis4.1. Recent Developments & Impact Analysis, by Key Market Participants4.2. Company/Competition Categorization (Key Innovators, Market Leaders, Emerging Players)4.3. Vendor Landscape4.3.1. List of Key Distributors and Channel Partners4.3.2. Key Company Market Share Analysis, 20194.4. Public Companies4.4.1. Company Market Position Analysis (Revenue, Geographic Presence, Product Portfolio, Key Serviceable Industries, Key Alliances)4.4.2. Company Market Share4.4.3. Competitive Dashboard Analysis4.4.4. Market Differentiators4.4.5. Synergy Analysis: Major Deals & Strategic Alliances4.5. Private Companies4.5.1. List of Key Emerging Companies4.5.2. Regional Network Map4.5.3. Company Market Position Analysis (Geographic Presence, Product Portfolio, Key Alliance, Industry Experience)

Chapter 5. Biomarkers Market: Type Estimates & Trend Analysis5.1. Definitions & Scope5.2. Type Market Share Analysis, 2019 & 20275.3. Biomarkers Market, by Type, 2015 to 20275.4. Market Size & Forecasts and Trend Analyses, 2015 to 2027 for the following:5.4.1. Safety5.4.2. Efficacy5.4.3. Validation

Chapter 6. Biomarkers Market: Application Estimates & Trend Analysis6.1. Definitions & Scope6.2. Application Market Share Analysis, 2019 & 20276.3. Biomarkers Market, by Application, 2015 to 20276.4. Market Size & Forecasts and Trend Analyses, 2015 to 2027 for the following:6.4.1. Diagnostics6.4.2. Drug Development6.4.3. Personalized Medicine

Chapter 7. Biomarkers Market: Disease Estimates & Trend Analysis7.1. Definitions & Scope7.2. Disease Market Share Analysis, 2019 & 20277.3. Biomarkers Market, by Disease, 2015 to 20277.4. Market Size & Forecasts and Trend Analyses, 2015 to 2027 for the following:7.4.1. Cancer7.4.2. Cardiovascular Disease7.4.3. Neurological Disease7.4.4. Immunological Disease7.4.5. Others7.5. Disease Market, by Type, 2015-2027:7.5.1. Cancer7.5.2. Cardiovascular Diseases7.5.3. Neurological Disease7.5.4. Imunological Disease7.5.5. Others

Chapter 8 Biomarkers Market: Regional Estimates & Trend Analysis8.1 Biomarkers Market: Regional Movement Analysis, 2019 & 20278.2 Biomarkers Market: Leading Players, 20198.3 SWOT Analysis, by Factor (Political & Legal, Economic and Technological)8.4 North America8.5 Europe8.6 Asia-Pacific8.7 Latin America8.8 MEA

Chapter 9 Competitive Landscape9.1 Strategy Framework9.2 Heat Map Analysis of Private Companies9.3 F-Hoffman La Roche Ltd.9.4 Abbott9.5 Epigenomics AG9.6 General Electric Company9.7 Johnson & Johnson9.8 Thermo Fisher Scientific Inc.9.9 Bio-Rad Laboratories Inc.9.10 Siemens Healthcare Private Limited9.11 Qiagen

For more information about this report visit https://www.researchandmarkets.com/r/1r1wle

Research and Markets also offers Custom Research services providing focused, comprehensive and tailored research.

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Brekky Wrap: Businessman Failed To Pull Over In Police Chase Because He Was ‘Having Sex In The Back Seat’ – 10 daily

March 10th, 2020 7:46 pm

All the news you need to know this Wednesday morning.

A man who led police on a car chase said he told his chauffeur to keep driving because he was having sex in the backseat with a woman who was not his wife.

Maurice Sines, from Britain, was in his 405,000 (about $800,000) Rolls Royce Phantom with "a bird in the back" when police approached the vehicle, a UK court has heard.

He argued that he didn't want to get caught because he'd just rekindled his relationship with his wife.

But CCTV proved Sines' recollection of the incident was completely false. Video footage showed him getting into the car and he confessed to driving while disqualified.

Judge Robert Fraser told Guildford Crown Court he had given "what was clearly and utterly a false account", The Mirror reports.

The chase started after a golf tournament in Surrey in May 2018.

The 57-year-old has been slapped with an eight-month sentence -- suspended for two years, as well as a two-year driving ban and a three-month tagged curfew.

He was also ordered to pay a 5,000 penalty and 4,200 in court costs.

The Climate Council's Summer of Crisis report says climate change fanned the unprecedented impacts of Australia's recent bushfire crisis.

Former Fire and Rescue NSW Commissioner Greg Mullins said the bushfires produced more greenhouse gases than Australia typically emits in a year.

"The data contained in this new report confirms what we all suspected," he said in a statement.

"The bushfire season was the worst on record for NSW in terms of the scale of the bushfires, the number of properties lost and the amount of area burned. Climate change fuelled the unprecedented fires."

Politics

Now That The Bushfires Are Out, It's Time To Discuss What Caused Them

For the first time in eight months, all the NSW fires are out. Now, a ground-breaking report has ruled climate change was a massive factor in the extreme fire conditions that devastated Australia this summer.

More than 2400 NSW homes were destroyed over the summer, almost ten times more than the previous worst season for bushfire property damage which was in 2013.

About 5.4 million hectares of land were also scorched, which is equivalent to more than six per cent of NSW's total land area.

The report also found the bushfires have taken a huge economic toll on Australia, with the tourism sector predicted to have lost more than $4 billion.

Doctors in Britain claim a man from London is the second person to be cured of HIV, ever.

BBC News reports Adam Castillejo has been free of the virus for more than 30 months after stopping anti-retroviral therapy.

According to the Lancet HIV journal, he was not cured by HIV drugs but instead by a stem-cell treatment he received for an unrelated cancer diagnosis.

It is understood donors of those particular stem cells have a very uncommon gene that gives them protection against HIV -- that protection has now been passed on toCastillejo, 40.

Timothy Brown became the first person to be reportedly cured of HIV in 2011, three and a half years after having similar treatment.

Stem-cell transplants are believed to stop the virus from replicating inside the body by replacing the patient's own immune cells with donor ones.

Hobart could become the first Australian city to ban single-use plastic packaging on takeaway food.

According to The Mercury, new laws to ban this type of packaging will be enforced by the City of Hobart from next year.

The move comes after the city banned petroleum-based plastic containers and utensils as part of the City of Hobart's zero-waste strategy last year.

The new law will apply to plastic cups, lids, utensils, straws and condiment sachets with the council expecting the introduction to result in a600-tonne annual reduction in single-use plastics to landfill.

City of Hobart council is pleading for the State Government to take the initiative statewide.

Dutch prosecutors have made explosive claims that Russian spies interfered in the MH17 investigation and were behind a disinformation campaign.

Defendant Oleg Pulatov has applied to take away the legal anonymity of several threatened witnesses, who still fear for their lives both in Ukraine and abroad.

Prosecutors said those fears are legitimate as separatists have put areas of Ukraine "under a rule of violence", while Russian spies have recently been accused of murders in the UK, Germany, Turkey, and Bulgaria.

World

Judge Says Downing Of MH17 'Almost Incomprehensible' As Murder Trial Begins

A Dutch judge described as almost incomprehensible the 2014 shooting down of a Malaysian airliner that killed all 298 passengers and crew on board, as the trial of three fugitive Russians and a Ukrainian began on Monday.

They added Australian Federal Police case files were leaked on a Russian-linked website as part of the disinformation campaign. Only parts of the police report were released selectively to spread disinformation.

Australian Jon O'Brien, whose son died in the attack, said: "It's a bit embarrassing on one level if it wasn't so offensive and had such malicious intent."

"That (the disinformation campaign) is not helpful for the next of kin, I don't think it assists their grieving and ability to follow the trial and know what the facts are,"Australian police officer David Nelson added.

Kale chips might look like a healthy snack but experts warn vegetable crisps are packed with salt and Australians should watch out.

Heart Foundation dietitian Sian Armstrong said while they might look healthy, they contain "alarming" amounts of salt.

"They might be found in the health aisle or say 'organic' or something but this doesn't always mean they're actually a healthy option," she told AAP.

A George Institute survey released on Wednesday revealed some veggie chips -- like kale or legume-based crisps -- had 26 times more salt than less-salty veggie chips.

Armstrong said the rule of thumb is 120 milligrams of sodium per 100 grams are the best products and under 400 milligrams is okay but anything above is unhealthy.

"Most Australians are consuming double the amount of salt than they should be," she said. "A lot of the time, you can't even taste it. Things don't even taste that salty at all."

David Warner told teammates he'd reflected on how to be a better member of the squad in his first meeting with Australian players after the ball-tampering ban last year.

Warner and Steve Smith's comebacks are a key subject of an eight-part documentary labelled The Test, will be released on Amazon on Thursday.

The pair's first meeting back with the team -- in Dubai last March -- is shown in detail, which proved a key component for their returns in both the World Cup and Ashes.

In the meeting, Smith confessed to teammates he at times felt like walking away from the game during his year-long suspension.

Warner also said he'd completed plenty of self-reflection in his time away, but believed he was returning to a different team than the one he left in South Africa a year earlier.

"In the last 12 months I have had a lot of reflecting to do," Warner said in the Dubai meeting.

"With cricket and what happened in the past and getting better as a team person as well.

"From looking the outside in, you can see the whole team... we have grown a lot."

And you're all caught up on 10 daily.

With AAP.

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Henry Ford to expand precision medicine program with help of $25 million donation – ModernHealthcare.com

March 10th, 2020 7:45 pm

Henry Ford Health System plans to rapidly expand its life-extending precision medicine program in Detroit after the Jeffries family pledged $25 million to create a specialized center.

The $25 million donation, provided by developer Chris Jeffries and his wife, Lisa, is the largest single gift from individuals in Henry Ford's 105-year history and one of the largest in the nation for a precision medicine program, Henry Ford officials said.

"We are incredibly grateful to Lisa and Chris Jeffries for their generosity," Wright Lassiter III, president and CEO of Henry Ford Health System, said in a statement. "We are experiencing a momentous era in medicine, a radical shift from the traditional approach to cancer care. This gift will help us consolidate and advance our collective efforts to create unprecedented access to advanced, highly personalized treatments for our patients and members."

But in the past three months, precision medicine or precision health, as neurosurgeon Steven Kalkanis, M.D., CEO of the Henry Ford Medical Group, likes to call it is now available for a whole host of new treatments besides those for cancer.

"Hot off the press. There have been animal studies and now clinical studies, only in the last several months, where precision health is ready for prime time and for human beings," said Kalkanis, who also is Henry Ford's chief academic officer.

Over the past decade, precision medicine has been evolving as a new type of medical care that initially focused on treating patients with various forms of cancer, including brain, lung, colon and pancreatic. It works like this: By analyzing patients' own molecular profile and the genetic mutations of their tumors, doctors are able to use the information to develop personalized treatments that could be more effective than standard care.

Doctors are now using precision medicine approaches to treat many other conditions, including cystic fibrosis, asthma, depression, heart disease, autoimmune diseases and multiple sclerosis, Kalkanis said.

"We have a whole era opening up to treat a host of other chronic diseases, using precision medicine to identify patients' molecular profiles, but potentially using existing drugs for everything from asthma to high blood pressure to depression," Kalkanis said. "However, the majority (of precision medicine) is still about designing a tailored drug regimen for individual patients."

Kalkanis said patients with some chronic conditions will one day soon be able to take a blood test and have their molecular profile entered into a database of existing drugs that may be able to match to an existing drug or to new ones being created in real time.

"We have found, in one of our clinical trials, that a (patient had a) rare type of brain cancer with a mutation impacting glucose levels. We used an existing diabetes drug and the patient went into remission," Kalkanis said.

Why the Jeffries donated

Chris Jeffries' father, Gerald was diagnosed with a highly malignant brain tumor in 2001.

Treated initially by neuro-oncologist Tom Mikkelsen and later Kalkanis and the Hermelin Brain Tumor Center team, Gerald was given only nine to 11 months to live, but using a precision medicine approach, he lived another five years until he died in December 2006.

"That meant so much to us. It's impossible to describe," Chris Jeffries said in a statement. Lisa Jeffries also lost her stepfather to cancer.

A native of Flint, Chris Jeffries is co-founder of Millennium Partners, a real estate development company that specializes in mixed-use, urban living and entertainment centers in Boston; San Francisco; Miami; Washington D.C.; Los Angeles; and New York.

Last year, the Jeffries donated $33 million to the University of Michigan Law School, where Chris was a 1974 graduate. The donation is earmarked for student support, including scholarships and other forms of financial aid, summer funding programs, and debt management. It was the largest private donation to the law school in its history, UM said.

Kalkanis said Gerald Jeffries was one of the first cohorts of patients in Henry Ford's personalized medicine program long before it was called precision medicine, in the early 2000s.

"He was enrolled in a clinical trial at Henry Ford 10 to 15 years ago and treated with a novel drug based on his unique cancer characteristics," Kalkanis said. "Because of that, he lived way beyond his life expectancy. The family was very supportive of our program and especially wanted to provide this same hope to others once they learned of the enhanced capability of precision medicine."

Since Gerald Jeffries was treated and Henry Ford developed its precision medicine approach, Kalkanis said there have been a number of patients who have outlived their prognoses. He said doctors can now give patients and families more hope than ever.

"We went through the precision medicine protocol, based on his own unique biomarkers and using a novel drug," he said. "Today these tests have become much more accessible. (For instance), a decade ago, it cost $5,000 (for testing). Now it costs several hundred for the tests" that can lead to the novel, personalized treatment.

Henry Ford's precision medicine program

For years, Henry Ford has been at the forefront of the precision medicine revolution, making world-class, targeted cancer treatments available at its national destination referral center, the Henry Ford Cancer Institute, officials said.

"By analyzing genetic and non-genetic factors, we can gain a better understanding of how a disease forms, progresses and can be treated in a specific patient," Mikkelsen, who is Henry Ford's medical director of the Precision Medicine Program and Clinical Trials Office, said in a statement.

"As of now, we can check for more than 500 genomic markers, which helps us understand the pattern of changes in a patient's tumor cells that influence how cancer grows and spreads," Mikkelsen said. "I'm confident this gift will lead to advancements that provide hope for patients with even the most complex diagnoses."

Kalkanis said the $25 million donation, which is expected to be received over the next several years, will enable Henry Ford to do a number of things.

"It takes investment to build out our biodepository with tissue samples, test them, look for biomarkers and see if (patients are) eligible for certain drugs," Kalkanis said. "We need to design our lab platform that is FDA-approved and recruit the best and brightest scientists and clinicians (specializing in) other cancer types."

Based on the current projection of about four to five chronic diseases and about 10 subspecialties that can be addressed by precision medicine, Kalkanis estimated Henry Ford will recruit two to three scientists and clinicians each year for the next few years.

"We are launching the search process for key researchers and working with the lab and pathology group for tests this calendar year," he said. "We should be up and running over the next year."

Adnan Munkarah, M.D., Henry Ford's executive vice president and chief clinical officer, said taking research in the lab and translating it to patient care is a standard process at Henry Ford.

"(It) is a critical element to help us treat many of the most challenging conditions our patients face," Munkarah said in a statement. "Translational research is bench-to-bedside, meaning it allows patients to benefit from discoveries in real time. That is an essential part of our history and commitment to medicine and academics not only offering the latest innovations in medicine, but also playing a leading role in their development."

Precision medicine is an approach to patient care that allows doctors to select treatments most likely to help patients based on a genetic understanding of their disease.

"The support of our donors is the fuel behind our clinical innovations and the breakthroughs that are improving people's lives," Mary Jane Vogt, Henry Ford's senior vice president and chief development officer, said in a statement. "It is remarkable to work with donors who believe in a better tomorrow and the power of a unified approach to medicine."

The Jeffrieses said they believe Henry Ford will achieve transformational advancements in cancer treatment using precision medicine and personalized treatments.

"The team at Henry Ford is second to none," said Chris Jeffries. "We believe this gift will lead to other families having more time together, as I had with my father. Defeating cancer requires a concerted effort from everyone and we hope to make as big an impact on that goal as possible."

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Henry Ford to expand precision medicine program with help of $25 million donation - ModernHealthcare.com

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Collaborative Review of Scientific Evidence Announced By FDA – JD Supra

March 10th, 2020 7:45 pm

Updated: May 25, 2018:

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Collaborative Review of Scientific Evidence Announced By FDA - JD Supra

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New UNC computational tool boosts understanding of genetic disorders affecting the brain – WRAL Tech Wire

March 10th, 2020 7:45 pm

CHAPEL HILL Scientists at the UNC School of Medicine and colleagues created a new computational tool called H-MAGMA to study the genetic underpinnings of nine brain disorders, including the identification of new genes associated with each disorder.

The research,published inNature Neuroscience, revealed that genes associated with psychiatric disorders are typically expressed early in life, highlighting the likelihood of this early period of life as critical in the development of psychiatric illnesses. The researchers also discovered that neurodegenerative disorder-associated genes are expressed later in life. Lastly, the scientists linked these disorder-associated genes to specific brain cell types.

By using H-MAGMA, we were able to link non-coding variants to their target genes, a challenge that had previously limited scientists ability to derive biologically meaningful hypotheses from genome-wide association studies of brain disorders, said study senior authorHyejung Won, PhD, assistant professor of genetics at the UNC School of Medicine and member of the UNC Neuroscience Center. Additionally, we uncovered important biology underlying the genetics of brain disorders, and we think these molecular mechanisms could serve as potential targets for treatment.

Hyejung Won, PhD UNC photo)

Brain disorders such as schizophrenia and Alzheimers disease are among the most burdensome disorders worldwide. But there are few treatment options, largely due to our limited understanding of their genetics and neurobiological mechanisms. Genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture related to many health conditions, including brain-related disorders. GWAS is a technique that allows researchers to compare genetic sequences of individuals with a particular trait such as a disorder to control subjects. Researchers do this by analyzing the genetic sequences of thousands of people.

To date, we know of hundreds of genomic regions associated with a persons risk of developing a disorder, Won said. However, understanding how those genetic variants impact health remained a challenge because the majority of the variants are located in regions of the genome that do not make proteins. They are called non-coding genetic variants. Thus, their specific roles have not been clearly defined.

Prior research suggested that while non-coding variants might not directly encode proteins, they can interact with and regulate gene expression. That is, these variants help regulate how genes create proteins, even though these variants do not directly lead to or code for the creation of proteins.

Given the importance of non-coding variants, and that they make up a large proportion of GWAS findings, we sought to link them to the genes they interact with, using a map of chromatin interaction in the human brain, Won said. Chromatin is the tightly packed structure of DNA and proteins inside cells, folded in the nucleus in a way to maintain normal human health.

Won and colleagues used this map to identify genes and biological principles underlying nine different brain disorders, including psychiatric conditions such as schizophrenia, autism, depression, and bipolar disorder; and neurodegenerative disorders such as Alzheimers, Parkinsons, amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS).

Using the computational tool H-MAGMA, Won and colleagues could link non-coding variants to their interacting genes the genes already implicated in previous GWAS findings.

Another important question in brain disorders is to identify cellular etiology the cells involved in the root cause of disease. This is especially critical as the brain is a complex organ with many different cell types that may act differently in response to treatment. In the attempt of finding critical cell types for each brain disorder, the researchers found that genes associated with psychiatric disorders are highly expressed in glutamatergic neurons, whereas genes associated with neurodegenerative disorders are highly expressed in glia, further demonstrating how the two disorder clusters diverge from each other.

Moreover, we classified biological processes central to the disorders, Won said. From this analysis, we found that the generation of new brain cells, transcriptional regulation, and immune response as being essential to many brain disorders.

Won and colleagues also generated a list of shared genes across psychiatric disorders to describe common biological principles that link psychiatric disorders.

Amongst the shared genes, we once again identified the brains early developmental process as being critical and upper layer neurons as being the fundamental cell-types involved, Won said We unveiled the molecular mechanism that underscores how one gene can affect two or more psychiatric diseases.

H-MAGMA is publicly available so that the tool can be widely applicable and available to the genetics and neuroscience community to help expand research, with the ultimate goal of helping people who suffer with brain-related conditions.

The National Institute of Mental Health, the Brain and Behavior Research Foundation, and the Simons Foundation Autism Research Initiative funded this research.

Other authors were Nancy Sey, Benxia Hu, Won Mah, Harper Fauni, Jessica McAfee, all from UNC-Chapel Hill, and Prashanth Rajarajan, Kristen Brennand, and Schahram Akbarian from Mount Sinai Health System.

(C) UNC-Chapel Hill

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New UNC computational tool boosts understanding of genetic disorders affecting the brain - WRAL Tech Wire

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Invitae to Acquire YouScript and Genelex to Make it Easier to Use Pharmacogenetic Information at the Point of Care – PRNewswire

March 10th, 2020 7:45 pm

SAN FRANCISCO, March 10, 2020 /PRNewswire/ --Invitae Corporation(NYSE: NVTA), a leading medical genetics company, today announced it has entered into definitive agreements to acquire YouScript, a privately held clinical decision support and analytics platform, and Genelex, a privately held pharmacogenetic testing company, to bring best-in-class pharmacogenetic testing, and robust, integrated clinical decision support to Invitae. Pharmacogenetic testing evaluates genetic variations that can impact how an individual responds to prescription medication.

"Adding pharmacogenetics to Invitae's services enables us to offer greater value to our existing customers and helps us expand into new customer types and clinical areas," said Sean George, co-founder and chief executive officer of Invitae. "Despite its broad utility, the incorporation of pharmacogenetic information into routine medical care has been slow. We believe that Invitae's business model and technological capabilities, combined with an offering designed for ease of use in supporting clinical care, can accelerate the use of pharmacogenetic information. This is an exciting next step in our mission to bring comprehensive genetic information into mainstream medical care."

Pharmacogenetic variants with medical implications are very common. For example, a cross-sectional study of more than 7.7 million U.S. veterans published in 2019 found that 99% of individuals in the Veteran Health Administration system carry at least one actionable pharmacogenetic variant. Furthermore, over half of the individuals had been prescribed a drug for which deciding to use the drug or determining the proper dosage would be affected by relevant pharmacogenetic information.1 Routine pharmacogenetic testing can provide clinicians with information to improve treatment and reduce the possibility of adverse events, particularly for patients with complex medication regimens or co-existing conditions.

"Pharmacogenetic information becomes clinically actionable when the complex web of multifactor interactions, including drug-drug and drug-gene, is used to characterize risk and benefit," said Robert Nussbaum, M.D., chief medical officer of Invitae. "Simply detecting pharmacogenetic variation is not nearly enough to make the information clinically useful. Combining Genelex testing with clinical decision support in the EMR using YouScript software enables clinicians to easily navigate this information when making prescription choices at the point of care."

YouScript offers an innovative clinical decision support tool for healthcare providers that can assist in patient medication management at the point of care. The software pairs a patient's pharmacogenetic profile with published drug and gene interaction information to assess the risk for adverse drug events and possible side effects. Clinicians receive information, alerts, and possible medication alternatives in real-time through a clear and concise interactive interface to help optimize medication choice to improve patient care. YouScript is integrated with major electronic medical record (EMR) systems, including Epic, Cerner, and Allscripts.

In addition to providing clinical support at the patient level, health systems can use YouScript at population scale to identify patient populations at highest risk for adverse events. The software identifies those patients who are most likely to benefit from pharmacogenetic testing based on their drug regimen. The utilization of YouScript's software, in combination with Genelex pharmacogenetic testing, has been shown to reduce adverse events, costs and hospital readmissions in peer-reviewed published studies.

"Our clinical decision support tool is focused on giving clinicians the most comprehensive, evidence-based information in an actionable, easy-to-use format. This enables the safest, most informed decision for their patient in real time, within the workflow," said Kristine Ashcraft, chief executive officer of YouScript. "Joining forces with Genelex and Invitae will allow us to help a larger number of clinicians use genetics not just for the few but as a routine practice for all their patients."

Genelex offers pharmacogenetic testing that analyzes the genes that are important for understanding variation in how people metabolize and respond differently to prescription medications. The testing process includes pharmacist review, patient- and clinician-facing reports, as well as access to clinical decision support for the treating provider.

"Accelerating the use of genetic information to inform treatment choices is essential for realizing the power of genetics in mainstream medicine," said Chris Howlett, chief executive officer of Genelex."The combination of Genelex's expertise in pharmacogenetics, YouScript's advanced clinical decision support and Invitae's expertise in delivering genetic information that is affordable and accessible at scale enables us to help more clinicians and their patients benefit from genetics-informed treatment choice."

Under the definitive agreements, Invitae will acquire YouScript for approximately $79.3 million, subject to certain adjustments, consisting of $25 million in cash and the remaining in Invitae common stock (based upon a trailing average trading price as of the agreement date), and Invitae will acquire Genelex for approximately $20.7 million in upfront shares of Invitae common stock (based upon a trailing average trading price as of the agreement date) plus additional shares of Invitae common stock in the event that certain milestones are achieved. The acquisitions are expected to close in the coming weeks, pending customary closing conditions. The acquisitions are not expected to materially change previously shared guidance on revenue and volume for 2020.

Conference Call and Webcast Details

Management will host a conference call and webcast today at 2:00 p.m. Pacific / 5:00 p.m. Eastern to discuss the acquisitions. The dial-in numbers for the conference call are (866) 393-4306 for domestic callers and (734) 385-2616 for international callers, and the reservation number for both is 4663118. Following prepared remarks, management will respond to questions from investors and analysts, subject to time limitations.

The live webcast of the call and slide deck may be accessed by visiting the investors section of the company's website atir.invitae.com. A replay of the webcast and conference call will be available shortly after the conclusion of the call and will be archived on the company's website.

About InvitaeInvitae Corporation (NYSE: NVTA) is a leading medical genetics company whose mission is to bring comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Invitae's goal is to aggregate the world's genetic tests into a single service with higher quality, faster turnaround time, and lower prices. For more information, visit the company's website at invitae.com.

About YouScriptYouScript enables faster, more proactive personalized medication management to reduce avoidable adverse drug events. YouScript is a trusted partner to value-based healthcare organizations, providers, and payers who want to bend the healthcare cost curve with the power of precision medicine. Partners include Clover Health, Group Health of South-Central Wisconsin, Highmark BCBS, and TELUS Health. YouScript's technology synthesizes the evidence impacting drug response, including pharmacogenetic testing, to support doctors and pharmacists at the point of care. YouScript is the only clinically validated system that shows improved outcomes, reduced costs and high patient and provider satisfaction. YouScript is successfully integrated into the clinical workflow of Epic, Cerner, Allscripts, GraneRx and other leading healthcare technology providers. For more information about YouScript, please visit:www.youscript.com.

YouScript has not been reviewed or approved by the United States Food and Drug Administration and cannot be used to diagnose or treat any disease or other health condition.

About GenelexGenelex is one of the longest-standing laboratories in the United States, specializing in pharmacogenetics testing and was one of the first clinical laboratories to provide pharmacogenetic testing and interpretation as the creator of the patented, proprietary and powerful YouScript Personalized Prescribing System. Genelex pharmacogenetic tests reveal natural variations that determine how the body processes commonly prescribed medications.

Safe Harbor StatementThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to the potential benefits of the proposed acquisitions; the expected timing of the closing of the proposed acquisitions; the capabilities and benefits of YouScript and/or Genelex technology; the company's ability to integrate and expand the use of YouScript and/or Genelex technology and the impact thereof; and the company's business strategy, and its beliefs regarding the ways in which the proposed acquisitions will contribute to that strategy. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially, and reported results should not be considered as an indication of future performance. These risks and uncertainties include, but are not limited to: the parties' ability to satisfy the conditions precedent to the consummation of the proposed transactions, including the parties' ability to close the proposed acquisitions; the occurrence of any event that could give rise to the termination of one or both acquisition agreements; unanticipated difficulties or expenditures relating to the proposed transactions; the risk that expected benefits of the proposed transactions may not be achieved in a timely manner, or at all; the risk that the YouScript and/or Genelex technology may not be efficiently or successfully integrated into, or otherwise scale with, the company's platform; the company's history of losses; the company's ability to compete; the company's ability to manage growth effectively; the company's ability to use rapidly changing genetic data and technology to interpret test results accurately and consistently; security breaches, loss of data and other disruptions; laws and regulations applicable to the company's business; and the other risks set forth in the company's filings with the Securities and Exchange Commission, including the risks set forth in the company's Annual Report on Form 10-K for the year ended December 31 , 2019. These forward-looking statements speak only as of the date hereof, and Invitae Corporation disclaims any obligation to update these forward-looking statements.

Source: Invitae Corporation

Contact:Laura D'Angelo[emailprotected](628) 213-3283

SOURCE Invitae Corporation

http://invitae.com

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Invitae to Acquire YouScript and Genelex to Make it Easier to Use Pharmacogenetic Information at the Point of Care - PRNewswire

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Removing the Barriers to Broad Adoption of NGS in Diagnostics – Technology Networks

March 10th, 2020 7:45 pm

Credit: Online Marketing on Unsplash.

When it comes to applying genomic sequencing in diagnostic medicine, increasing evidence is demonstrating that whole exome sequencing (WES) can sometimes fall short. This is a particular issue when analyzing large segments of DNA from patients and can adversely impact a physician's diagnosis.An alternative to WES is the utilization of a smaller, more targeted genetic test that analyzes a specific panel of genes known to be associated with a certain pathology. These tests are less of a financial burden on healthcare systems and patients and can offer highly accurate results. Targeted NGS is enabling this testing approach, and we're seeing increased adoption of NGS in the clinical diagnostics space.

But what barriers still exist to the full implementation of NGS, and how can we remove them? Technology Networks recently spoke with Luca Quagliata, Ph.D., Global Director of Medical Affairs for Thermo Fisher Scientific, to learn more.Molly Campbell (MC): How is genome sequencing currently utilized in the oncology diagnostics space? What are its limitations?Luca Quagliata (LQ): Sequencing of DNA and RNA is currently used in routine molecular testing for two purposes. Firstly, they are used with the aim of supporting a diagnostic decision, i.e. differential diagnosis (such as PIDGFA mutation status in gastrointestinal stromal cancer. More commonly, they are adopted to complement a pathology report by adding information related to a clinically relevant genomic variant (e.g. mutations in the EGFR gene) that are directly associated with any specific approved drug treatment (for example, BRAF inhibitors for V600E BRAF mutated melanoma patients).Some of the major limitations of genomic testing are related to quality of the starting material for testing (generally known as pre-analytic issues, e.g. tissue fixation), the ability of a given sequencing method to generate usable results (not every sequencing approach is born equal), the capability of interpreting the results (e.g. is the observed genomic variant a pathogenic alteration or is simply benign?) and finally the economic aspect. Who should pay for the test?MC: Why does WES commonly fail to adequately analyze large segments of DNA?LQ: As above mentioned, not all sequencing methods are born equal, WES can be performed using a variety of library preparation kits, possibly leading to substantially different results.1 Unfortunately, no universally accepted standard has been established for WES, especially for oncology applications.Generally, one of the most common issue is related to the sequencing depth, also known as coverage. High coverage allows to gain higher confidence in the generated results, as the genomic examined regions are analyzed multiple times, thus increasing the robustness of the data. However, high coverage comes at the cost of increasing sequencing price. Plus, even in the absence of any financial constraints, increasing coverage indefinitely is simply not possible due to technical limitations, i.e. the input material will define the maximal reachable coverage.

Furthermore, it is well established that, in certain situations, even pushing the coverage a 100-fold higher does not generate any tangible benefit in terms of data analysis output. Finally, a variety of alignment and calling algorithms can be deployed to identify large DNA segments rearrangements. Once again, no standard is strictly defined, thus the varying ability of different algorithms will greatly impact the final result. To conclude, while robust approaches are in place for single nucleotide variants (SNV) or multiple nucleotide variants (MNP), as well as insertions and deletions (INDEL), this is not the case when applying WES to study large DNA segments. Nowadays, microarray-based investigations are very popular for assessment of large genomic rearrangements.MC: Why is a targeted test more suitable in the diagnostics space?LQ: Targeted NGS is most commonly used for routine diagnostics because:

MC: NGS is becoming increasingly easier for patients to access and costs are rapidly declining. In your opinion, will we reach a stage where a genetic test is as common as, say, having a blood test when you visit your healthcare provider?LQ: While the price of NGS, meaning reagents related costs to perform the test, is undoubtedly going down, one should not forget that the largest fraction of NGS cost is generated by the human labor necessary to carry out the analysis. Thus, any technological approach that will reduce human intervention in the process will be the most effective in compressing the overall sequencing cost to enable true democratization of NGS.At Thermo Fisher Scientific, we recently made a significant step in this direction with the launch of the Ion Torrent Genexus System, the first research NGS solution that automates the entire specimen to report workflow in a single day with only two touch points.Having said that, there is no doubt that sequencing will eventually become as common as performing a classical blood check. The question is, rather, when will it happen?

In my opinion, that will largely depend not exclusively on the reduction of the overall NGS cost, but rather our ability to expand our understanding of the genomic variants clinical implications. As for now, only a limited fraction of variants can be clearly classified and associated with either a clinical condition or a drug treatment benefit. In my view, it is rather a matter of knowledge than merely a problem of costs. We use blood testing not only because it is easy and cheap, but because we can generate valuable and meaningful information through it.MC: The number of individuals undergoing direct-to-consumer genetic testing at home is on the rise. In your opinion, what impact is this having on the use of genetic testing in the clinical spaceLQ: Direct-to-consumer (DTC) genetic testing is an interesting recent phenomenon that in my view poses several questions, mainly regarding the quality of the results it provides. Several regulatory agencies have expressed concerns and are now acting with the aim of monitoring this market. In this initial and still immature phase of DTC, I strongly advocate for the implementation of a regulatory framework that should be considered not a barrier to wide genomic testing access but rather a safeguard.Should that framework be implemented, then DTC market expansion will have a positive effect on the use of genetic testing in the clinical space, as an audience of genetic-educated patients will also inevitably push physicians toward the adoption of genomics in medicine.

Should the DTC genetic market be given complete freedom, I am concerned that it would negatively impact genetic testing in the clinical space, as people might be easily convinced that managing this kind of data is simplistic, and thus the value of a controlled and professionally regulated testing approach will lose value. I think of this in relation to the "Dr Google self-medication" phenomenon.MC: What challenges still exist in the use of NGS in diagnostics?LQ: Overall NGS data generation and interpretation is still perceived as being extremely complex. Furthermore, while we are witnessing an increase in policy coverage for NGS testing, reimbursement remains a practical issue as well as NGS results being restricted to very specific indications. Finally, limited medical education and awareness regarding the value of genetic testing remains high in the healthcare community, with a substantial knowledge gap between physicians working at large academic centres and those working in the community setting. It will take a shared collective effort to remove the above-mentioned barriers to allow broad adoption of NGS in routine diagnostics. No single company, as large as it could be, can achieve such results.

We at Thermo Fisher Scientific are on the front-line supporting precision medicine through partnering with a variety of major stakeholders in the field, from patient advocacy groups to medical associations and Pharma.

Luca Quagliata, Ph.D., Global Director of Medical Affairs for Thermo Fisher Scientific, was speaking to Molly Campbell, Science Writer, Technology Networks.References:

1. Clinical Exome Studies Have Inconsistent Coverage, Clinical Chemistry, Volume 66, Issue 1, January 2020, Pages 199206.

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Rapid genetic testing becomes available to Calgary medical community – CTV News

March 10th, 2020 7:45 pm

CALGARY -- When Madden Ellis Garraway was just under two-years-old, he became very sick.

His skin was so dry it bled and he couldnt hold down food, causing his weight dropped to within ounces of his birth weight of seven pounds, six ounces.

Doctors struggled to figure out what was wrong.

We had a large list of things that we were thinking of, and our immunology team and my colleagues who are working with Madden were having trouble arriving at the right one," said Dr. Francois Bernier, head of the Department of Medical Genetics and a professor in the Department of Paediatrics at the University of Calgary's Cumming School of Medicine.

"In fact, we made some attempts to arrive at a diagnosis but we're still unsure. It took a while.

Doctors often struggle with diagnosing unusual health issues, especially those that may require genetic testing.

They often must rely on genome sequencing tests to determine the root cause of a disease and until now, large-scale genome sequencing tests were often sent to labs in the United States for analysis.

Bernier calls it "the diagnostic odyssey," a long, difficult, journey for families waiting while cliniciansfigure out what is causing the underlying health issues.

Madden Garraway in hospital at the age of two. (Photo courtesy the Garraway family)

Maddens family can attest to that.

It was months of waiting, wondering and worrying before Madden's blood was sent to a U.S. lab for genome analysis, where it was learned he suffered from a rare genetic condition called immune dysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome.

IPEX is a rare genetic disorder that can be life threatening.

"If we could have learned about that instantly, or within the several weeks that we can do now, that will save a lot of time," said Maddens father, Patrick Garraway.

"We could have got on with his bone marrow transplant sooner."

Madden received a bone marrow transplant from his sister. Now five-years-old, the playful youngster has made a full recovery and no longer requires medication.

"There are so many families waiting for answers to serious medical conditions," said Bernier.

"Access to gene sequencing early in the medical journey can pinpoint the best treatment approaches and therapies to target the illness."

Madden Garraway today at the age of five. (Photo courtesy the Garraway family)

A new partnership struck between the University of Calgary, University of Alberta, and Alberta Precision Laboratorieswill help families and medical professionalsanswer to those diagnostic puzzles sooner.

The partnership is funded by Genome Canada, the Alberta Childrens Hospital Foundation, and other partners. Four other centres in Canada are also undertaking similar programs through Genome Canadas funding, one in B.C., two in Ontario and one in Quebec.

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Patients turn to Stanford’s center of excellence for treatment of hereditary hemorrhagic telangiectasia – Stanford Medical Center Report

March 10th, 2020 7:45 pm

Jennifer Cook has dealt with migraine headaches and nosebleeds since she was in junior high school, but it wasnt until much later in life, after two small strokes in her 40s, that she discovered these seemingly disconnected ailments including strange, little red dots on her hands and face were all symptoms of a genetic disorder running rampant through three generations of her family.

We all started to connect the dots, said Cook, 48, of Sacramento, referring to about a decade ago, when her father was the first in the family diagnosed with hereditary hemorrhagic telangiectasia, or HHT, a little-known disorder causing malformed blood vessels that can affect the skin and other organs. Since then, her aunt, sister, two of her brothers and two of her daughters also have been diagnosed.

It was so shocking to find out, said her daughter Nina Murphy-Cook, 23, also of Sacramento, who was diagnosed four years ago. Bloody noses, headaches and strokes in really young people. Literally, we had no idea. We all got those little red spots on the skin. My mom just called them Irish moles and said it was just something our family gets.

Cook and her daughter, now patients at Stanford Health Cares recently designatedHHT Center of Excellence, are under the care of a multidisciplinary team of specialists that includes interventional radiologists, neurosurgeons, pulmonologists, otolaryngologists, hematologists, gastroenterologists and a genetic counselor. The team members diagnose, prevent and, if necessary, treat the disparate problems that can result from this often undiagnosed and misdiagnosed disease.

If people get diagnosed and treated, they can have a normal life expectancy with this disease, said Edda Spiekerkoetter, MD, associate professor of pulmonary and critical care medicine and director of the Stanford HHT center. Otherwise, theyre susceptible to chronic, dangerous illnesses without even knowing there are treatments that can prevent them from happening. Key to solving this problem is better educating the public, including doctors, on how to recognize the symptoms. Shes educating primary care physicians, otolaryngologists and dentists, in particular, to serve as frontline screeners: They can keep an eye out for the hallmark red dots, called teleangiectasia, in the oral cavity and on lips and ask about nosebleeds, which are extremely common in patients.

HHTcauses abnormal connections, called arteriovenous malformations, to develop between arteries and veins. They can cause all sorts of problems. These deformed vessels growmost commonly in the nose, lungs, brain, gut and liver andcan cause brain bleeds, nosebleeds, strokes, gastrointestinal bleeding and heart failure. Themalformationsgrow in place of smaller vessels called capillaries, which normally connect arteries and veins. Capillaries are responsible for oxygen uptake into the blood and filter small particles circulating in the blood. Bypassing the capillary bed, these larger, malformed vessels allow small blood clots, bacteria and air bubbles to circulate throughout the body unfiltered. This can lead to strokes or a reduction of oxygen in the blood, which can lead to shortness of breath and exhaustion.

To prevent complications from these deformed vessels in the lungs, you need an interventional radiologist to step in; to prevent brain bleeds, you need a neurosurgeon;abdominal bleeds and anemia can be controlled by a gastroenterologist and hematologist; andotolaryngologists can help prevent severe nosebleeds, Spiekerkoetter said. While HHT is rare affecting an estimated 1 in 5,000 people 90% of cases go undiagnosed, Spiekerkoetter said. Patients often dont get diagnosed until after a serious event, such as a stroke.

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This is why you always skip the gym, according to scientists – Ladders

March 10th, 2020 7:45 pm

There are plenty of possible choices, but perhaps the most obnoxious type of Instagram selfie is the gym snapshot. In the world of social media, did you really visit the gym if you didnt post about it? These images and their captions usually make exercise seem like a breeze; a daily ritual that the fitness influencers of the world seem to be able to accomplish without the slightest bit of hesitation. For the rest of us, though, visiting the gym can feel like a struggle.

If youve ever felt like an entirely different species than the people who smile their way through 6 AMgym sessions four days per week, a new study finds that may not be as outlandish as it initially sounds. No, those people arent aliens, but researchers from Kings College London have discovered a connection between ones genes and their ability to exercise.

More specifically, theyve found a genetic mutation that appears to seriously hinder an individuals capacity to exercise efficiently. This mutation affects ones cellular oxygen sensing. Basically, this means that people with this genetic variation run out of breath faster and find it harder to partake in aerobic exercises.

These findings could seriously come in handy the next time your co-worker signs you up for that 5K run next month. Sorry, I totally would but my genes just wont cooperate!

To come to their conclusions, the studys authors examined a local patient who exhibited a particularly slow rate of physical growth, constant low blood sugar, a limited ability to exercise, and a large amount of red blood cells.

Over the course of that examination, the patient was placed in a simulated high altitude environment, had their exercise capacity formally measured, and underwent a series of metabolic tests.

This analysis allowed them to zero in on the specific gene that is influenced by this mutation: thevon Hippel-Lindau (VHL) gene. This gene is actually incredibly important for all us whenever our oxygen availability is reduced.

Upon closely analyzing the patients VHL gene, researchers noted that the mutation appears to cause impaired functionality in the mitochondria, the cellular powerhouse that uses oxygen to produce fuel. This hampered mitochondrial function is what causes people with this mutation to have an especially hard time with aerobic exercises.

So, the average persons cells are fully equipped to deal with a lack of oxygen, but those with this mutation dont share the same luxury.

The discovery of this mutation and the associated phenotype is exciting because it enables a deeper understanding of human physiology, especially in terms of how the human body senses and responds to reduced oxygen availability, comments study author Dr Federico Formenti, from KCLs School of Basic & Medical Biosciences, in a press release.

Before you go and cancel your gym membership while citing medical reasons, keep in mind this was an initial observation in one patient. Some days, we would all love an extra excuse to skip the gym and stay on the couch, but these findings are very, very preliminary. As of now, researchers are unsure just how prevalent this gene mutation is, as well as the full extent to which it can impact a persons life.

Regardless, this study is very noteworthy due to the simple fact that it has proven that some people are indeed genetically disinclined to exercising.

The full study can be found here, published in the New England Journal of Medicine.

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The biology of coronaviruses: From the lab to the spotlight – Penn: Office of University Communications

March 10th, 2020 7:45 pm

Things change fast. Even just a few months ago, most of us who arent virologists, microbiologists, or veterinarianshad probably never heard of coronaviruses. Yet last week, the Centers for Disease Control and Prevention advised that its not a question of whether the outbreak of a coronavirus known as SARS-CoV-2 (and its associated disease, COVID-19) would spread in U.S. communities, but whenand we should be prepared for potential disruptions in our daily lives as a result.

But this change didnt come out of nowhere. Even though this particular viral strain only recently emerged as a new human disease, coronaviruses have been around for a very long time. Likewise,Susan Weiss,a professor of microbiology at the Perelman School of Medicine, is newly quite busy launching research projects to help respond to the threat of the novel coronavirusbut coronaviruses generally have been a major focus of her research for four decades.

Coronaviruses first became better known among non-scientists in early 2003 thanks to the virus familys first famous human disease: Severe Acute Respiratory Syndrome (SARS). The agent, called SARS-CoV, started to cause illness in southern China before spreading to North America, South America, Europe, and Asia. It was really scary because there was a high mortality rate, but compared to whats going on now, it was fairly contained and small, Weiss says. Ultimately SARS dissipated within about eight months. Since 2004 there have been no more known cases. But SARS was a warning shotmore viruses like it could be out there, on the verge of transforming into strains that cause serious human illness. Based on analyses of the SARS virus and searches for related genetic sequences in the environment where it emerged, scientists determined that the human virus evolved from a bat coronavirus that infected a civet, from which it mutated again and jumped to humans.

After SARS, people started looking for human coronaviruses, and two others were identified, Weiss says. These new strains caused some more severe symptoms than a typical cold but were still rarely fatal.

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Prefer tea over coffee? It could be your genes, study finds – CNN

March 10th, 2020 7:45 pm

To examine genetic associations with food preferences, researchers from the Riken Center for Integrative Medical Sciences (IMS) and Osaka University in Japan studied the genetic data and food preferences of more than 160,000 people in Japan.

The research, published in the journal Nature Human Behavior, found genetic links for 13 dietary habits including consumption of alcohol, other beverages and foods, and also complex human diseases such as cancer and diabetes.

"We know that what we eat defines what we are, but we found that what we are also defines what we eat," said Yukinori Okada, Senior Visiting Scientist at Riken IMS and professor at Osaka University, in a press release.

This involves grouping thousands of people together depending on whether they have a disease and looking at DNA markers called single nucleotide polymorphisms, or SNPs, which can be used to predict the presence of that disease. If researchers find a SNP that is repeatedly associated with the disease group, they can assume that people with that genetic variation might be at risk for the disease.

Rather than looking at diseases, the Riken team examined dietary habits to find out if there were any markers that made people "at risk" for typically eating certain foods.

The researchers used data of more than 160,000 Japanese people from the BioBank Japan Project, launched in 2003 with a goal to provide evidence for the implementation of personalized medicine. The project collects DNA and clinical information, including items related to participants' lifestyles such as dietary habits, which were recorded through interviews and questionnaires.

They found nine genetic locations that were associated with consuming coffee, tea, alcohol, yogurt, cheese, natto (fermented soy beans), tofu, fish, vegetables and meat.

Variants responsible for the ability to taste bitter flavors were also observed. This association was found among people who liked to eat tofu; while those without the variant consumed less alcohol or none at all.

Those who ate more fish, natto, tofu and vegetables had a genetic variant that made them more sensitive to umami tastes, best described as savory or "meaty" flavors.

The main ingredients of the foods mattered, too -- for example, there were positive genetic correlations between eating yogurt and eating cheese, both milk-based foods.

In order to find whether any of these genetic markers associated with food were also linked with disease, the researchers conducted a phenome study.

The phenome comprises all the possible observable traits of DNA, known as phenotypes. Six of the genetic markers associated with food were also related to at least one disease phenotype, including several types of cancer as well as type 2 diabetes.

Nature vs. nurture: Food edition

Since the research studied only people native to Japan, the same genetic variations associated with food preferences are likely not applicable to populations across the globe. However, similar links have been discovered in different groups.

The study authored by Okada also didn't measure environmental factors. Our environment, demographics, socioeconomic status and culture -- such as whether we eat food from work or home; our age; how much money we make; and what our families eat -- are some of the biggest drivers of our food choices.

"These factors would weigh more than the genetics in some cases," said Dr. Jos Ordovs, director of Nutrition and Genomics at Tufts University in Massachusetts, who was not involved in the study.

"Something that sometimes we have felt is that the nutrition field has been focusing too much on nutrients rather than on foods," Ordovs said.

"Previous studies have been looking at genes that were associating with higher protein intake or higher fat intake or higher carbohydrate intake," Ordovs said. "But this study is more aligned with the fact that people eat foods. They don't just eat proteins, carbohydrates and fats. People tend to eat within a specific pattern."

Further research is needed to explain an exact balance between genetic predisposition and volition when it comes to food choices in different groups of people, but Okada suggests that by "estimating individual differences in dietary habits from genetics, especially the 'risk' of being an alcohol drinker, we can help create a healthier society."

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Repurposed drugs may help scientists fight the new coronavirus – Science News

March 10th, 2020 7:45 pm

As the new coronavirus makes its way around the world, doctors and researchers are searching for drugs to treat the ill and stop the spread of the disease, which has already killed more than 3,800 people since its introduction in Wuhan, China, in December.

The culprit virus is in the same family as the coronavirusesthat caused two other outbreaks, severe acute respiratory syndrome and MiddleEast respiratory syndrome. But the new coronavirus may be more infectious. Inearly March, the number of confirmed cases of the new disease, called COVID-19,had exceeded 100,000, far surpassing the more than 10,600 combined total casesof SARS and MERS.

Health officials are mainly relying on quarantines to try tocontain the virus spread. Such low-tech public health measures were effectiveat stopping SARS in 2004, Anthony Fauci, director of the U.S. NationalInstitute of Allergy and Infectious Diseases, said January 29 in Arlington,Va., at the annual American Society for Microbiologys Biothreats meeting.

But stopping the new virus may require a more aggressive approach. In China alone, about 300 clinical trials are in the works to treat sick patients with standard antiviral therapies, such as interferons, as well as stem cells, traditional Chinese medicines including acupuncture, and blood plasma from people who have already recovered from the virus.

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Researchers are not stopping there. They also are working to develop drugs to treat infections and vaccines to prevent them (SN: 3/14/20, p. 6). But creating therapies against new diseases often takes years, if not decades. With this new coronavirus, now known as SARS-CoV-2, nobody wants to wait that long. Thanks to their experience developing treatments against the MERS coronavirus, as well as other diseases, such as HIV, hepatitis C, influenza, Ebola and malaria, researchers are moving quickly to see what they can borrow to help patients sooner.

Finding new uses for old drugs is a good strategy,especially when racing to fight a fast-moving disease for which there is notreatment, says Karla Satchell, a microbiologist and immunologist atNorthwestern University Feinberg School of Medicine in Chicago.

Repurposing drugs is absolutely the best thing that could happen right now, Satchell says. Potentially, drugs that combat HIV or hepatitis C might be able to put the new coronavirus in check, too. Those drugs exist. Theyve been produced. Theyve been tested in patients, she says. Although these drugs arent approved to treat the new coronavirus disease, theyre a great place to start. One of the most promising candidates, however, hasnt yet been approved for any disease.

Scientists have been quick to reveal the new coronavirussecrets. When SARS emerged in 2002, researchers took about five months to get acomplete picture of the viruss genetic makeup, or genome. With the new virus,Chinese health officials first reported a cluster of mysterious pneumonia casesin Wuhan to the World Health Organization on December 31. By January 10, thenew coronaviruss full genome was made available to researchers worldwide inpublic databases.

A viruss genome is one of the most valuable toolsscientists have for understanding where the pathogen came from, how it worksand how to fight it. The first thing that coronaviruses have in common is thattheir genetic material is RNA, a chemical cousin to DNA.

Researchers immediately began comparing the newcoronaviruss genome with SARS and MERS viruses and other RNA viruses todetermine whether drugs developed to combat those disease-causing organismswould work against the new threat. As a result, some potential Achilles heelsof SARS-CoV-2 have already come to light.

One target is the viruss main protein-cutting enzyme,called M protease. RNA viruses often make one long string of proteins thatlater get cut into individual proteins to form various parts of the virus. Inthe new coronavirus, the M protease is one of 16 proteins that are linked likebeads on a string, says Stephen Burley, an oncologist and structural biologistat Rutgers University in Piscataway, N.J.

The virus can mature and infect new cells only if M proteasecan snip the string of proteins free, he says. Stop the protease from cuttingand the virus cant reproduce, or replicate.

Existing drugs might be able to stop the viruss M protease, two research groups proposed online January 29 at bioRxiv.org. One group suggested four drugs, including one used to treat hepatitis C and two aimed at HIV. A second group named 10candidates, including an anti-nausea medication, an antifungal drug and some cancer-fighting drugs.

HIV and hepatitis C are both RNA viruses that need aprotease to cut proteins free from long chains. Drugs that inhibit thoseproteases can reduce levels of the HIV and hepatitis C viruses to undetectable.Some of those drugs are now being tested against the new coronavirus inclinical trials in China.

The HIV drug Kaletra, also called Aluvia, is a combination of two protease inhibitors, lopinavir and ritonavir. Kaletras maker, the global pharmaceutical company AbbVie, announced on January 26 that it is donating the drug to be tested in COVID-19 patients in China. Kaletra will be tested alone or in combination with other drugs. For instance, researchers may combine Kaletra with Arbidol, a drug that prevents some viruses from fusing with and infecting human cells. Arbidol may be tested on its own as well.

But the HIV drugs may not work against the new virus because of two differences in the proteases. The coronavirus protease cuts proteins in different spots than the HIV protease does, say Guangdi Li of the Xiangya School of Public Health of Central South University in Changsha, China, and Erik De Clercq, a pioneer in HIV therapy at KU Leuven in Belgium. Secondly, the HIV drugs were designed to fit a pocket in HIVs protease that doesnt exist in the new coronaviruss protease, the researchers reported February 10 in Nature Reviews Drug Discovery.

Yet a few anecdotal accounts suggest the HIV drugs may help people with COVID-19 recover. Doctors at Rajavithi Hospital in Bangkok reported in a news briefing February 2 that they had treated a severely ill 70-year-old woman with high doses of a combination of lopinavir and ritonavir and the anti-influenza drug oseltamivir, which is sold as Tamiflu. Within 48 hours of treatment, the woman tested negative for the virus.

Her recovery may be due more to the HIV drugs than to oseltamivir. In 124 patients treated with oseltamivir at Zhongnan Hospital of Wuhan University, no effective outcomes were observed, doctors reported on February 7 in JAMA. Clinical trials in which these drugs are given to more people in carefully controlled conditions are needed to determine what to make of those isolated reports.

Researchers may be able to exploit a second weakness in thevirus: its copying process, specifically the enzymes known as RNA-dependent RNApolymerases that the virus uses to make copies of its RNA. Those enzymes areabsolutely essential, says Mark Denison, an evolutionary biologist atVanderbilt University School of Medicine in Nashville. If the enzyme doesntwork, you cant make new virus.

Denison and colleagues have been testing molecules that muckwith the copying machinery of RNA viruses. The molecules mimic the nucleotidesthat RNA polymerases string together to make viral genomes. Researchers havetested chemically altered versions of two RNA nucleotides adenosine andcytidine against a wide variety of RNA viruses in test tubes and in animals.The molecules get incorporated into the viral RNA and either stop it fromgrowing or they damage it by introducing mutations, Denison says.

One of the molecules that researchers are most excited aboutis an experimental drug called remdesivir. The drug is being tested in peoplewith COVID-19 because it can stop the MERS virus in the lab and in animalstudies. The drug has also been used in patients with Ebola, another RNA virus.

Remdesivir has been given to hundreds of people infected with Ebola, without causing serious side effects, but the drug hasnt been as effective as scientists had hoped, virologist Timothy Sheahan of the University of North Carolina at Chapel Hill said January 29 at the Biothreats meeting. In a clinical trial in Congo, for example, about 53 percent of Ebola patients treated with remdesivir died, researchers reported November 27 in the New England Journal of Medicine. Thats better than the 66 percent of infected people killed in the ongoing Ebola outbreak, but other drugs in the trial were more effective.

Several tests of remdesivir in lab animals infected with MERS have researchers still hopeful when it comes to the new coronavirus. In studies in both rhesus macaques and mice, remdesivir protected animals from lung damage whether the drug was given before or after infection. Molecular pathologist Emmie de Wit of NIAIDs Laboratory of Virology in Hamilton, Mont., and colleagues reported the monkey results February 13 in the Proceedings of the National Academy of Sciences.

Remdesivir appears to be one of the most promisingantiviral treatments tested in a nonhuman primate model to date, the teamwrote. The results also suggest remdesivir given before infection might helpprotect health care workers and family members of infected people from gettingsevere forms of the disease, Sheahan says.

Denison, Sheahan and colleagues tested remdesivir on infected human lung cells in the lab and in mice infected with MERS. Remdesivir was more potent at stopping the MERS virus than HIV drugs and interferon-beta, the researchers reported January 10 in Nature Communications.

But the question is still open about whether remdesivir canstop the new coronavirus.

In lab tests, it can. Both remdesivir and the antimalaria drug chloroquine inhibited the new viruss ability to infect and grow in monkey cells, virologist Manli Wang of the Wuhan Institute of Virology of the Chinese Academy of Sciences and colleagues reported February 4 in Cell Research. Remdesivir also stopped the virus from growing in human cells. Chloroquine can block infections by interfering with the ability of some viruses including coronaviruses to enter cells. Wang and colleagues found that the drug could also limit growth of the new coronavirus if given after entry. Chloroquine also may help the immune system fight the virus without the kind of overreaction that can lead to organ failure, the researchers propose.

In China, remdesivir is already being tested in patients. And NIAID announced February 25 that it had launched a clinical trial of remdesivir at the University of Nebraska Medical Center in Omaha. The first enrolled patient was an American evacuated from the Diamond Princess cruise ship in Japan that had been quarantined in February because of a COVID-19 outbreak.

Ultimately, nearly 400 sick people at 50 centers around theworld will participate in the NIAID trial, which will compare remdesivir with aplacebo. The trial may be stopped or altered to add other drugs depending onresults from the first 100 or so patients, says Andre Kalil, an infectiousdisease physician at the University of Nebraska Medical Center.

Researchers considered many potential therapies, but basedon results from the animal and lab studies, remdesivir seemed to be the onethat was more promising, Kalil says.

In the early patient studies, figuring out when to give remdesivirto patients might not be easy, Sheahan says. Often drugs are tested on thesickest patients. For example, those in the NIAID trial must have pneumonia toparticipate. By the time someone lands in the intensive care unit withCOVID-19, it may be too late for remdesivir to combat the virus, Sheahan says.It may turn out that the drug works best earlier in the disease, before viralreplication peaks.

We dont know because it hasnt really been evaluated inpeople how remdesivir will work, or if it will work at all, Sheahan cautions.

The drug seems to have helped a 35-year-old man in Snohomish County, Wash., researchers reported January 31 in the New England Journal of Medicine. The man had the first confirmed case of COVID-19 in the United States. He developed pneumonia, and doctors treated him with intravenous remdesivir. By the next day, he was feeling better and was taken off supplemental oxygen.

Thats just one case, and the company that makes remdesivirhas urged caution. Remdesivir is not yet licensed or approved anywhereglobally and has not been demonstrated to be safe or effective for any use,the drugs maker, biopharmaceutical company Gilead Sciences, headquartered inFoster City, Calif., said in a statement on January 31.

But global health officials are eager to see the drug testedin people. Theres only one drug right now that we think may have realefficacy, and thats remdesivir, WHOs assistant director-general BruceAylward said during a news briefing on February 24. But researchers in Chinaare having trouble recruiting patients into remdesivir studies, partly becausethe number of cases has been waning and partly because too many trials ofless-promising candidates are being offered. We have got to start prioritizingenrollment into those things that may save lives and save them faster, Aylwardsaid.

Another strategy for combating COVID-19 involves distracting the virus with decoys. Like the SARS virus, the new virus enters human cells by latching on to a protein called ACE2. The protein studs the surface of cells in the lungs and many other organs. A protein on the surface of the new virus binds to ACE2 10 to 20 times as tightly as the SARS protein does.

Researchers at Vienna-based Apeiron Biologics announced February 26 that they would use human ACE2 protein in a clinical trial against the new coronavirus. When released into the body, the extra ACE2 acts as a decoy, glomming on to the virus, preventing it from getting into cells.

ACE2 isnt just a viruss doorway to infection. Normally, it helps protect the lungs against damage, says Josef Penninger, an immunologist at the University of British Columbia in Vancouver and a cofounder of Apeiron. Penninger and colleagues reported the proteins protective qualities, based on studies with mice, in Nature in 2005.

During a viral infection, the protein is drawn away from thecell surface and cant offer protection. Penninger thinks that adding in extraACE2 may help shield the lungs from damage caused by the virus and by immunesystem overreactions. The protein is also made in many other organs. Penningerand colleagues are testing whether the new virus can enter other tissues, whichmight be how the virus leads to multiple organ failures in severely ill people.

The decoy protein drug, called APN01, has already beenthrough Phase I and Phase II clinical testing. We know its safe, Penningersays. Now researchers just need to determine whether it works.

No one knows whether any of these approaches can help stemthe spread of COVID-19.

Right now, we need lots of people working with lots ofideas, Satchell says. Similarities between the viruses that cause SARS andCOVID-19 may mean that some drugs could work against both. There is a hopethat several small molecules that were identified as inhibitors of the SARSprotease would represent reasonable starting points for trying to make a drugfor the 2019 coronavirus, Burley says.

The open questionis, can you produce a drug that is both safe and effective quickly enough tohave an impact? SARS was stopped by traditional infection-control measures in2004, before any virus-fighting drugs made it through the development pipeline.

But had a decision been made then to spend $1 billion tomake a safe and effective drug against SARS, Burley says, such a drug might beworking now against the new coronavirus, eliminating the need to spend hundredsof billions of dollars to contain this new infection.

An investment in SARS would not have paid off for peoplewith MERS, which is still a danger in the Middle East. The MERS virus is toodifferent from SARS at the RNA level for SARS drugs to work against it.

But a future coronavirus might emerge that is similar enough to SARS and SARS-CoV-2 to be worth the cost, Burley says. Even if the current outbreak dwindles and disappears, he says, governments and companies should keep investing in drugs that can stop coronaviruses.

Im quite certain that the economic impact of the epidemic is going to run into the hundreds of billions, he says. So you would only need a 1 percent chance of something that was treatable with the drug to show up in the future to have made a good investment.

The reliable science journalism you count on is expensive. It takes professional reporters, editors, fact checkers, designers and digital producers to make sureScience Newsreflects the depth and breadth of science.We need your financial support to make it happen every contribution makes a difference.

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Penn is fighting pancreatic cancer – Penn: Office of University Communications

March 10th, 2020 7:45 pm

Swept up in a pancreatic cancer diagnosis is inevitably a sense of fear and sadness.

But at Penn, researchers are bringing new hope to this disease. And with patients like Nick Pifani, its clear that theyre moving in the right direction.

Pifani, from Delran, New Jersey, first noticed some lingering stomach upset in February 2017. He called his family doctor, concernedespecially given that he was an otherwise healthy marathon runner who was only 42. He was sent to a gastrointestinal specialist. A few weeks later, some crippling stomach pain sent him back to the emergency room and he received an MRI that showed a mass on his pancreasStage Three, inoperable, he was told.

He was treated with chemotherapy, along with radiation and, eventually, and after receiving advice from doctors at Penn, his tumor was removed. Thereafter, he realized he had a PALB2 mutationa cousin of the BRCA gene mutation. At that moment, his long-term needs changed and he found himself seeking specialized care at Penn, where he met Kim Reiss Binder, assistant professor of medicine at the Hospital of the University of Pennsylvania (HUP).

Im a planner; I want to understand what [my] potential options are, Pifani says. [Reiss Binder] asked why I was there to see her and I explained and quickly I could tell she wasoutside of her being remarkably intelligenta great listener and a compassionate doctor.

I have a feeling she worries about me more than I do, he laughs.

Pifani has now been in remission for two years and four months; he sees Reiss-Binder every three months for checkups. His survival story is inspiring and a sign of momentum, even if a world without pancreatic cancer is still frustratingly out of reach.

Pancreatic cancer is the third-leading cause of cancer-related death in the United States, outmatched only by lung cancer (No. 1) and colorectal cancer (No. 2). A person diagnosed with pancreatic cancer is still unlikely to survive past five yearsonly 9%of survivors do, giving it the highest mortality rate among every major cancer.

In short, pancreatic cancer seldom paves the way for optimistic narratives. Some of the hope that has surfaced, though, is thanks to some talent, dedication to the cause, and hard work at Penn.

A key point of progress in the battle against the disease was made in 2002, when former Assistant Professor of Medicine David Tuveson established a standard model for examining human development of this disease in mice. This model has allowed for a reliable way to study the disease and has influenced progress made here at Penn and elsewhere since.

Theres been a burst of activity in translational research, from bench to bedside, explains Ben Stanger, the Hanna Wise Professor in cancer research and director of the Penn Pancreatic Research Center (PCRC).

And theres a lot of momentum with community building, a dramatic increase in patient volumes, and a dramatic increase in what we know about the cancer, he says of the status of pancreatic cancer today.

Reiss Binder, meanwhile, explains that one mark of progress at Penn and beyond has been learning about people like Pifani, who have the PALB2 gene, and why they respond differently to treatments than those without it. Platinum-based chemotherapies, for example, are especially effective for people with the PALB2 gene who are battling pancreatic cancer. An ongoing trial at Penn has tested and found some success with using PARP inhibitorstaken orally as an enzyme that fixes single-stranded breaks of DNAas a maintenance therapy in that same PALB2 demographic after theyve had chemotherapy. These are less toxic than chemotherapy for patients with the same mutations.

Its all been slow progress toward better treatments, but there has been progress.

This is the tip of the iceberg for a disease that we historically have treated with perpetual chemotherapy,Reiss Binder says. We owe it to patients to find better options to suppress the cancer but not ruin their quality of life.

The consensus on why pancreatic cancer is so deadly? It just cant be spotted fast enough.

Pancreatic cancer often presents well after it has developed and metastasized, and does so in a way that is not easy to recognize as cancer. Common symptoms include, for example, stomach upset and back pain. And by the time a harder-to-ignore symptom of the cancer surfaces, a sort of yellowing of the skin (a result of a bile duct blockage), its likely too late to stop the cancer in its tracks.

One approach to improved detection being tested at Penn, by Research Assistant Professor of Medicine Erica Carpenter, is a liquid biopsydrawn from a standard blood test. Current means to test for pancreatic cancerimaging through an endoscopic tubeare invasive and expensive, meaning a common liquid test could transform how many cases are detected early.

Carpenter explains that circulating tumor cells (CTCs) can shed from a tumor thats adjacent to the wall of a blood vessel; whats shed then shows up in a blood test. The cells, if detected, can explain more about the nature of the tumor, giving doctors an opportunity to examine characteristics of cancerous cells and decide how to effectively treat a tumor if it cant be surgically removed. It also allows interpretations of disease burden and the effectiveness of medicationsthrough genome sequencingthat imaging does not.

Ultimately, this gives doctors the potential to track the growth of a tumor before its fully developed, all through one tube of blooddetected through an innovative use of technology.

David Issadore, associate professor of bioengineering and electrical and systems engineering in the School of Engineering and Applied Science, has worked since 2017 to develop a chip that detects cancer in the blood, using machine learning to sort through literally hundreds of billions of vesicles and cells, looking for these CTCs. The chip retrieves data and the machine learning developed interprets that data, attempting to make a diagnosis that not only finds pancreatic cancer but also provides information about its progressionand, importantly, whether a patient might benefit from surgery.

Right now, that test has a 24-hour turnaround, he says, but could eventually advance to having a one-hour turnaround. That would be a remarkable mark of progress for discovering the disease earlier when the chip enters a commercial stage.

Pancreatic cancer is a tough disease, and catching it early is hard, Issadore acknowledges. So, we think optimistically but also very cautiously, knowing what a challenging disease its been to make progress on, which is what drew us to the disease in the first place.

Im not an oncologist, he adds, but Im a bioengineer, and people like us who have a different perspective, the hope is we can do something truly [novel] to shift the [state of the disease].

He would eventually like to test the chip in people with other types of cancers, like lung, bladder, and liver.

For now, Penn still uses imaging as the standard of care but Carpenter is confident that blood testing is where were heading, starting with at-risk patients with diabetes and other risk factors.

The most important thing with this would be that when you put a patient on therapy, its good to know as early as possible how likely it is theyre going to respond, she explains. Tumor markers are increasingly valuable because you can avoid toxicity of the therapy, the expense of it, and most importantly you then have the opportunity to put the patient on something that might have more of an effect for them.

The challenge, she adds, is in pancreatic cancer we dont have that many effective therapies.

Another challenge, she adds, is to find the presence of exosomes, small pieces of tumor cells released into the blood stream, which she says are found in abundance among people with pancreatic cancer and could particularly be targeted among people living with diabetes or an intraductal papillary mucinous neoplasm (IPMN). So, at-risk candidates who may not present with the disease currently but are at risk. Several clinical studies and trials are currently taking place at Penn evaluating this.

A related area of interest is determining if people with diabetes, in particular, are developing cancer as part of the diabetes, or developing diabetes from the cancer. Risk factorsdiabetes, genetic markers, etc.continue to be an important area of study with pancreatic cancer.

Immunotherapy is rapidly changing the way patients are treated. And interest in immunotherapy for pancreatic cancer is growing exponentially.

But, its complicated.

We are still learning about the immune system in pancreatic cancer, explains Gregory Beatty, assistant professor of medicine and director of the Pancreatic Cancer Clinical Trials Program within the PCRC.

On one hand, we know that inflammation in the pancreas is a driver of pancreatic cancer. But we also know that T cells in the immune system can attack pancreatic cancer, he says.

The challenge that has surfaced is that T cells in patients living with pancreatic cancer are often weakened or slowed down; they dont divide or proliferate very well; and they have a hard time finding the cancer. That makes harnessing them for therapy a challenge. One idea, though, is to engineer ones own T cells (as inCAR T therapy), while theyre still healthy, to detect and kill pancreatic cancer cells.

Penn recently completed a trial in ovarian cancer, mesothelioma, and pancreatic cancer, using CAR T cells engineered to recognize a protein called mesothelin, which is expressed by pancreatic cancer. The team found that the T cells, when injected into the blood of patients, were safe but had limited activity.

These CAR T cells can kill pancreatic cancer in the lab really well. But why they dont do so in patients still remains a mystery, Beatty says.

It does prove that pancreatic cancer evades the immune system extraordinarily well.

Penn investigators have also done work on CD40, a protein expressed in a wide range of immune cells, explains Bob Vonderheide, the John H. Glick Abramson Cancer Center Professor. Patients are responding to treatment with CD40a protein that activates T cells to work more steadfastly and seek out cancer cells.

It seems to make chemo work better, Beatty explains.

This is a very promising treatment for convincing the immune system to attack pancreatic cancer, Beatty adds, And in the lab, we are finding ways to make it work even better.

The larger idea is to build on a backbone of chemo and CD40 in the future to help coax T cells to work better. Overall, a major thrust of treatment for patients at the PCRC is focused on unraveling ways to use immunotherapy while developing the next-generation of strategies for patients with BRCA 1 and 2 genes who are receiving PARP inhibitors.

The stress of a pancreatic cancer diagnosis can be dizzying. It is, says Pancreatic Nurse Navigator Trish Gambino, a cause to act fast.

We really believe pancreas cancer is a medical emergency much like a heart attack, she says. As a nurse navigator, I try to get newly diagnosed patients with pancreatic cancer expeditiously to the correct provider for staging and treatment.

Because of that, she says, patients are often still digesting their diagnosis while also juggling appointments, choosing a doctor, making decisions about care, settling personal matters, and communicating with insurance companies. Gambino, one of eight nurse navigators hired to put organization and compassion on the frontlines, takes multiple incoming callsas many as fiveper day from people who have been diagnosed and sound shell-shocked.

I get so many of these calls per week saying, Trish, I just went to the doctor and they told me I have a pancreatic mass on my CAT scan. And I dont know what to do, she says. A lot of times patients dont know what they need.

Her job is one of compassion but also pragmatism. She listens and places their concerns in context and individualizes her approach to moving patients in the right direction, laying out all the options and giving them a sense of order and control over their narrative.

It really does take a village to try to get people through this, Gambino explains, noting how overwhelming the cancer experience can be. When you have pancreas cancer, its not just the medical oncologist, the radiation oncologist, the surgeon, the dietician, the social worker, the nurse navigator, the infusion nurses, the nurse practitionerstheyre all there and the response is often Who is everybody? They need someone who can lead the team for them.

She says that Penn is especially well-regarded for its interdisciplinary teamseven factoring in diet and financial wellnessand their ability to act swiftly. Penn, for instance, performs more than 150 pancreatic cancer surgeries per year and is practiced at itnot typical of every hospital and a draw for newly diagnosed patients who are eligible for resection.

Looking ahead, Stanger is optimistic about advances in screening and immunotherapy treatmentparticularly research funded by the Parker Institute for Cancer Immunotherapy, started by Sean Parker, a cofounder of Facebook. Penn is one of 10 sites of major investment for research and was the impetus for the investment in pancreatic cancer.

Hes also encouraged that the research community surrounding pancreatic cancer is collaborative, he says, with many doctors recognizing the enormous challenge of the disease and working together well.

Celebrity diagnoses, like that of Alex Trebek, als0lend some hope in the messaging of how the disease is presented to the world today.

I talk to people almost every day, and when we talk about pancreatic cancer they say, Oh, thats a really bad one, he says. One thing I respect about Alex is he came out and was very forthcoming and he spoke with a great deal of confidence and hope in the medical community and gave a positive message that said, Im going to do my best to beat this.

Pifani, meanwhile, more than two years out from his surgery, is feeling optimistic. Hes mostly resumed a normal lifewith occasional side effects that linger, of course, and scans every six months. He runs marathons and spends time with his wife and kids. And, a member of the Survivor Council at the Pancreatic Cancer Action Network and sponsorship chair for the Philadelphia affiliate, he shows up to community events built around raising awareness of the disease and advocating research and caregiver support.

At Penn, he says, he feels like hes in the right place with his carethat hes in the best hands if something does happen, and recognizing the diseases ongoing presence in his life.

I got a long way to go, he says, but were off to a good start.

Homepage photo: Gregory Beatty, assistant professor of medicine and director of the Pancreatic Cancer Clinical Trials Program within the Penn Pancreatic Cancer Research Center, examines a blood sample.

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