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Researchers find genetic variations linked to Covid-19 severity

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BOSTON: A new study led by researchers from Beth Israel Deaconess Medical Center (BIDMC) sheds light on the genetic risk factors that make individuals more or less susceptible to severe Covid-19. Thousands of people test positive for the virus each day, and the reason behind people experiencing mild to no symptoms while others becoming critically ill is still under the shadow of a doubt. According to a new study published in the New England Journal of Medicine (NEJM), research led by Robert E. Gerszten, MD, Chief of the Division of Cardiovascular Medicine at BIDMC irradiate the key process of Covid-19 which can open new possibilities for the treatment of this disease. Gerszten, Professor of Medicine at Harvard Medical School shared that different patients effected by COVID-19 display different symptoms and different degrees of severity, “Pre-existing conditions, particularly cardiovascular and metabolic disease, are risk factors for disease severity and outcomes, the underlying reasons that some people develop the life-threatening disease while others remain asymptomatic are not well understood.” Findings published in the NEJM describes the link of COVID-19 outcomes to variations in two regions of the human genome on the basis of genetic evidence from patients in China, Europe and the United States. But, to find about the difference occurring due to the disease, scientists need to understand the role of the proteins carried by the genome in the context of disease. The database generated by Gerszten and colleagues of all the proteins and metabolites associated with various regions of the …

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Wheat’s genetic potential unlocked through global collaboration at K-State

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MANHATTAN, Kan. (WIBW) – The genetic potential of wheat has been unlocked through global collaboration at Kansas State University.Kansas State University says in a paper published on Wednesday, Nov. 25, in Nature, researchers in collaboration with the international 10+ Genome Project led by the University of Saskatchewan, announced the complete genome sequencing of 15 varieties of wheat representing breeding programs around the world, which is an invaluable resource to improve global wheat production. K-State said the effort gained momentum in 2018 when its team, in collaboration with the International Wheat Genome Sequencing Consortium, published the genome assembly of Chinese Spring, which was the first complete reference genome of bread wheat. It said with advances in DNA sequencing technology and the experience from assembling the first wheat genome, the 10+ Genome Project brought together the expertise and resources of over 95 scientists from universities and institutes in Canada, Switzerland, Germany, Japan, the U.K., Saudi Arabia, Mexico, Israel, Australia and the U.S.According to K-State, the study represents the start of a bigger effort to generate thousands of genome sequences of wheat, including genetic material brought in from the wild relatives of wheat. “It’s like finding the missing pieces for your favorite puzzle that you have been working on for decades,” said project leader Curtis Pozniak, wheat breeder and director of the University of Saskatchewan Crop Development Centre. “By having many complete gene assemblies available, we can now help solve the huge puzzle that is the massive wheat pan-genome and usher in a new …

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Doctoral student Ken Smith searches for patterns in genetic data for Alzheimer’s detection

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Data science and statistics doctoral student Ken Smith creates software that graphs connections among the DNA of individuals with Alzheimer’s as part of Assistant Professor Sharlee Climer’s lab. (Photo by August Jennewein).
Ken Smith didn’t get a yes when he first approached Assistant Professor Sharlee Climer about joining her lab. It might have struck her as an odd fit to bring on the PhD student in data science and statistics because Climer is a computer scientist.
But Smith was so intrigued by her research identifying patterns in genetic data that he persisted.
“I kept bugging her and bugging her until she said yes,” Smith says. “I really liked that she was working on a problem I could see – I’ve known people with Alzheimer’s or dementia.”
Climer’s lab turned out to be a great match. Since joining in 2018, Smith has completed software for identifying clusters of related data in large sets, which he presented at the Genetic and Evolutionary Computation Conference in 2019, and has embarked on a project developing an Alzheimer’s diagnostic technique in collaboration with Washington University School of Medicine genomicist Carlos Cruchaga.
The problem-solving elements of his University of Missouri–St. Louis research play into Smith’s background. After earning his bachelor’s in physics and a master’s in electric engineering, he’d started at Boeing. A few years in, he’d wanted to brush up and enrolled at UMSL part-time.
A little over a year later, he decided to go …

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Clinical and genetic features of cardiomyopathy reported from multiple large familial cases in India

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Hypertrophic cardiomyopathy (HCM) affects the health of the heart muscle. The genetic cause of 40-50% of HCM is not known. The mutations responsible for HCM often localized to genes encoding sarcomeric proteins.
In a study published in the journal Nature Scientific Reports, Scientists from MedGenome, Bangalore, India and Amrita Institute of Medical Science and Research, Cochin, India report a rare form of HCM where they have identified mutation in a non-sarcomeric protein PRKAG2.
This study was the first of its kind from India that analysed the inheritance pattern of the mutation in a large number of multigenerational affected members from three unrelated families.

The genetic data obtained helped refine the clinical diagnosis providing a template for personalized treatment applying genomics in the clinic. The families in the study were followed longitudinally for over 7 years to understand the natural history and clinical outcomes of the affected individuals adding to our knowledge of the disease and interventions needed.
Dr Sameer Phalke, Senior Scientist, MedGenome and senior study co-author said, “Genetic testing for HCM diagnosis and screening for risk can now be used routinely for overall disease management.”
He added, “The unique population structure of India makes studies such as this possible.  Familial disease studies in India will create a wealth of knowledge and opportunity to understand many diseases beyond HCM.”
“As far as inherited cardiovascular disease is concerned, it is quite clear that we are now in the era of leveraging the potential of cardiovascular genetic testing for the prompt recognition of …

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Research inspired by COVID-19: UW work on genetic sequencing traces community spread

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David O’Connor, left, and Thomas Friedrich are pictured in a lab at the University of Wisconsin–Madison in March.

Jeff Miller, UW-Madison

Yvonne Kim | The Capital Times

This is the first in a series of stories about research at UW-Madison inspired by the COVID-19 pandemic.Genetic sequencing of SARS-CoV-2 — the novel coronavirus that causes COVID-19 — reveals that the virus, which was once distinct between Dane and Milwaukee Counties, now reflects patterns of geographic mixing across the state, according to a paper published by University of Wisconsin-Madison researchers this month.In a study published Nov. 3 in Nature Journal, researchers in Thomas Friedrich and David O’Connor’s labs examined the spread of COVID-19 in Dane and Milwaukee counties, which are not only the state’s most populous, but had the most COVID-19 cases early in the pandemic. Data showed that the two counties had largely distinct epidemics through April with limited genetic mixing and that both saw lower rates of spread after Wisconsin’s Safer at Home executive order in March.“The Safer at Home orders in the spring really did seem to keep viruses in Milwaukee and Dane counties from mixing with each other,” Friedrich said. “That compartmentalization has stopped and now, in fact, we see the opposite … Now we’re trying to understand what are the patterns of behavior? What are the things that affect this mixing?”The virus mutates about once every two weeks, or every second transmission between people, like a game of telephone, although these …

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Targeting high-risk cancer patients with genetics

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Adventist Health for several years has been rolling out a genetic testing and cancer risk-assessment program to sites across the Roseville, Calif.-based system. Now, the program is playing a part in Adventist’s efforts to get patients in need of cancer screenings back into its facilities despite fears over COVID-19.
In the wake of the pandemic, patients have deferred or canceled preventive care appointments out of concern they’ll be exposed to the virus. That could have long-term consequences for cancer care, since fewer patients screened could make it harder to catch cancer cases at an early stage.
Staff at Adventist hope to avoid that by proactively reaching out to patients at high risk for cancer.
Dr. Candace Westgate, an obstetrician-gynecologist and now medical director of the cancer risk-assessment program at the system, began developing the Adventist Health Early All-Around Detection program—abbreviated as AHEAD—in 2016 for OB-GYN services. It’s since expanded to more than two dozen primary-care and specialty sites across Adventist.
Front desk staff ask patients to fill out an online questionnaire from software company CancerIQ about their family history. The software program determines whether the patient might benefit from genetic testing, based on guidelines from medical societies.
Information from family history and the genetic tests is used to stratify patients as low-, medium- or high-risk for various cancers. That informs subsequent care plans, such as more frequent screenings, referrals to specialists or even risk-reducing surgery for some patients.
That risk stratification also can identify patients …

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Idaho police to use grant to examine cold cases using genetic genealogy

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MERIDIAN — Recent grant funding awarded to the Idaho State Police’s Forensic Services will allow the agency to examine over 50 cold cases in hopes of finally bringing justice and closure to victims.The money, which totals more than $750,000, was allocated by the Bureau of Justice Assistance, part of the U.S. Department of Justice’s Office of Justice Programs, to help enhance forensic services in Idaho. Roughly $150,000 of it will go toward helping to solve these crimes using a new technique called forensic molecular genetic genealogy. Matthew Gamette, director of ISP’s Forensic Services, said an investigative team — comprised of lab technicians, law enforcement and other personnel — determined specific cases that could possibly benefit from this approach, where DNA has been collected from crime scenes but not yet matched to a suspect in existing databases, like the FBI’s Combined DNA Index System, or CODIS. “We don’t want it to stop at just identifying a potential perpetrator. We want these to result in successful prosecutions, or in some instances, it might result in exonerations,” said Gamette, who was unable to comment on specific cases, since the investigations remain ongoing.The team will work with professional genealogists, who use the molecular biology information in “public opt-in genealogy DNA databases,” such as Ancestry.com, GEDMatch or 23andMe, to hopefully narrow in on a suspect. They have already started contacting local police agencies and county prosecutors to partner on the chosen cases so far, he added. All of the cold cases they are examining involve serious …

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Genetic research reveals Neanderthals could tolerate smoke, plant toxins

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Comparison of Modern Human and Neanderthal skulls from the Cleveland Museum of Natural History. Credit: DrMikeBaxter/Wikipedia

The idea that modern humans displaced Neanderthals because they were better protected against toxins from smoke is now under fire. An earlier study that put forward this suggestion has now been refuted by genetic research by scientists from Leiden and Wageningen. This new research was published in Molecular Biology and Evolution on 24 November.

Making and using fire is regarded as one of the most significant innovations in man’s evolution. Fire brought with it such benefits as warmth, for example, protection against predators and a broader diet because it made it possible to cook raw, inedible foods. Traces of fire do not preserve well, so it is far from clear when fire-making skills developed and whether Neanderthals have have already had these skills for a long time.
Contradictory research
A disadvantage of fire is that it exposes people to the toxic substances in smoke. In 2016, two contradictory genetic studies appeared on whether modern humans or Neanderthals were better able to tolerate the toxins produced by smoke. A group of Amerian scientists studied a receptor protein (the aryl hydrocarbon receptor or Ah receptor) that is sensitive to toxins found in smoke and is different in the two hominids. They concluded that Neanderthals were up to a thousand times more sensitive to these toxins than modern humans.
The other group comprised Leiden researchers including Professor of Archaeology Wil Roebroeks and molecular biologist/toxicologist Jac Aarts. Together …

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Disliking Brussels sprouts at Christmas could be down to your genetics

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Disliking Brussels sprouts could be down to the genetics you were born with, according to research.The leafy green vegetable often sparks debate when it comes to Christmas dinner as people either love or loathe them. However, two third of the nation could have a gene variation, known as a “supertaster”, that makes them more sensitive to bitter tastes, according to genetics company 23andMe. The gene variant means the bitter chemical called PTC – found in Brussels sprouts and broccoli – is more easily detected.

The UK produces 82,000 tons of Brussels sprouts a year
(Image: Getty Images/iStockphoto)

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Previous research had identified that several variations of the supertaster gene affect other bitter tastes such as dark chocolate, coffee and even beer. Researchers found that a quarter of the UK populations doesn’t enjoy eating the leafy green vegetable. In Scotland, the two biggest cities are split – with 76% of people in Glasgow loving Brussels sprouts compared to 17% in Edinburgh. The UK produces 82,000 tons of Brussels sprouts a year – enough to fill 3,200 football pitches. Spokeswoman and senior product scientist Alisa Lehman said: “Brussels sprouts have a high level of sulphur compounds which are responsible for the bitter flavour. “People with certain genetic variants in the TAS2R38 gene can detect bitter taste more than others and therefore may be more likely to dislike sprouts. “But just because you can detect bitterness, it doesn’t automatically mean an instant dislike – as the research shows, …

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