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Dennis OConnor

A unified genealogy of modern and ancient genomes - 0 views

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    "Genomics and human ancestral genealogy Hundreds of thousands of modern human genomes and thousands of ancient human genomes have been generated to date. However, different methods and data quality can make comparisons among them difficult. Furthermore, every human genome contains segments from ancestries of varying ages. Wohns et al. applied a tree recording method to ancient and modern human genomes to generate a unified human genealogy (see the Perspective by Rees and Andrés). This method allows for missing and erroneous data and uses ancient genomes to calibrate genomic coalescent times. This permits us to determine how our genomes have changed over time and between populations, informing upon the evolution of our species. -LMZ"
Dennis OConnor

Genes, Blood Type Tied to Risk of Severe COVID-19 - NIH Director's Blog - 0 views

  • Many people who contract COVID-19 have only a mild illness, or sometimes no symptoms at all. But others develop respiratory failure that requires oxygen support or even a ventilator to help them recover [1]. It’s clear that this happens more often in men than in women, as well as in people who are older or who have chronic health conditions. But why does respiratory failure also sometimes occur in people who are young and seemingly healthy? A new study suggests that part of the answer to this question may be found in the genes that each one of us carries [2]. While more research is needed to pinpoint the precise underlying genes and mechanisms responsible, a recent genome-wide association (GWAS) study, just published in the New England Journal of Medicine, finds that gene variants in two regions of the human genome are associated with severe COVID-19 and correspondingly carry a greater risk of COVID-19-related death.
  • the findings suggest that people with blood type A face a 50 percent greater risk of needing oxygen support or a ventilator should they become infected with the novel coronavirus.
  • Their study included 1,980 people undergoing treatment for severe COVID-19 and respiratory failure at seven medical centers in Italy and Spain.
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  • the researchers compared SNPs in people with severe COVID-19 to those in more than 1,200 healthy blood donors from the same population groups.
  • he researchers did find evidence suggesting a relationship between blood type and COVID-19 risk. They noted that this area also includes a genetic variant associated with increased levels of interleukin-6, which plays a role in inflammation and may have implications for COVID-19 as well.
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  • Franke, Karlsen, and many of their colleagues are part of the COVID-19 Host Genetics Initiative, an ongoing international collaborative effort to learn the genetic determinants of COVID-19 susceptibility, severity, and outcomes
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    "Many people who contract COVID-19 have only a mild illness, or sometimes no symptoms at all. But others develop respiratory failure that requires oxygen support or even a ventilator to help them recover [1]. It's clear that this happens more often in men than in women, as well as in people who are older or who have chronic health conditions. But why does respiratory failure also sometimes occur in people who are young and seemingly healthy? A new study suggests that part of the answer to this question may be found in the genes that each one of us carries [2]. While more research is needed to pinpoint the precise underlying genes and mechanisms responsible, a recent genome-wide association (GWAS) study, just published in the New England Journal of Medicine, finds that gene variants in two regions of the human genome are associated with severe COVID-19 and correspondingly carry a greater risk of COVID-19-related death."
Dennis OConnor

iHope Genetic Health - 0 views

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    "iHopeTM Genetic Health (iGH) will eliminate the barriers to genomic insights for tens of thousands of individuals across the globe each year by addressing access to high-quality clinical whole genome sequencing (cWGS) as well as education and support. Leveraging contributions of genomic sequencing technology from Illumina and donations from philanthropists and technology and logistics partners, iGH will provide awards of reagents and, where necessary, sequencers and software to enable genomic testing across the globe. iGH will provide cWGS and patient support services for undiagnosed individuals in low and middle income countries1 (LMICs) and low-to-moderate income2 (LMI) households across the globe and in the United States (US) respectively. Over time iGH will develop in-country, sustainable solutions for communities with little to no access to genomic care."
Dennis OConnor

Genome Medical has Partnered with LunaDNA | LunaDNA - 0 views

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    "Our partner, Genome Medical, makes it easy for you to speak with a clinical professional about your DNA information. Interested in DNA testing but don't know where to begin? The experts at Genome Medical can help with that, too. Access your data files directly from your LunaDNA dashboard to support proactive health discussions. Help you better understand your genetic test results or help you determine if testing is right for you Explain your health risks based on your family and personal health history Offer guidance on how you can integrate your results into your health care Assess whether family members should consider genetic testing Within days from scheduling your phone or video appointment, speak with a board-certified genetic counselor who can: Genome Medical's genetic counselors do not analyze raw data from various DNA vendors, such as 23andme and AncestryDNA. However, they can answer any of your specific medical questions and determine if additional genetic testing is right for you and your family. SCHEDULE YOUR SESSIONASK A QUESTION SELF-PAY $99 AS LOW AS $50 With qualified insurance the cost for genetic counseling may be as low as $50 if the consultation is a covered service under your plan. © 2020 LunaPBC. All rights reserved. ABOUT US   LunaDNA was created by the Public Benefit Corporation, LunaPBC™, a team of passionate genomics and technology veterans. 2019 Technology Pioneers World Economic Forum SELF-PAY $99 AS LOW AS $50 With qualified insurance the cost for genetic counseling may be as low as $50 if the consultation is a covered service under your plan. SCHEDULE YOUR SESSIONASK A QUESTION HOW IT WORKSRESOURCES 2020 Most Innovative Companies Fast Company "
Dennis OConnor

The Genomic Kitchen - 0 views

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    "The Genomic Kitchen combines genomics, nutrition and culinary skills so you can leverage the power of your genes with food-for a lifetime of great health. The Genomic Kitchen is a system of cooking and eating that directly connects the food you eat with the behavior of your genes. Beyond determining the color of your eyes, genes play an active role throughout life, converting the food you eat into the biochemical reactions that keep you living, breathing and growing"
Dennis OConnor

(The Genomics of Obesity with Sharon Hausman-Cohen, MD - YouTube - 0 views

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    American Nutrition Association The Genomics of Obesity Sharon Hausman-Cohen, MD The modernization of our society has contributed to higher rates of obesity through an environment that promotes increased caloric intake and decreased physical activity. However, recent studies suggest that genetics may contribute to 40-70% of obesity with the discovery of more than 50 genes that are strongly associated with obesity. Changes in the environment have significantly increased obesity rates over the last 20 years, and the presence or absence of genetic factors can protect us from or predispose us to obesity in conjunction with diet and lifestyle factors that support healthy weight. In this webinar, Dr. Hausman-Cohen will * Describe how the leptin pathway is interrelated to the functions of genes in the hypothalamus, as well as how inflammation, fat absorption and insulin can contribute to obesity. * Discuss how specific food intake can be linked to obesity risk and how weight loss can be individualized based on a patient's genomics. * Attain practical ways of discussing various obesity interventions and patterns with patients - whether or not practitioners have access to patient genomic data. Category"
Dennis OConnor

Patient Information | Center for Applied Genomics & Precision Medicine - 1 views

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    Recommended by: DeAunne Denmark, MD, PhD "It's important for the public to be aware of what's available to them in the world of genomics and precision medicine. Various resources are available that provide general and disease-specific information about genomics and precision medicine. A list of some resources available to the public is provided below, but additional resources are likely available through your health provider or other groups such as the US National Institutes of Health."
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    The resource index in this article is incredible.
Dennis OConnor

EDNA - 0 views

shared by Dennis OConnor on 07 Feb 21 - No Cached
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    Discovered by Tyler Orion: "EDNA is the first Genetic Sequencing Service Provider to go far beyond hereditary or ancestral related reporting. EDNA allows individuals from anywhere in the world to own their personal encrypted whole genome sequence, and sell and/or donate their personal genome to accredited medical research teams from around the globe who share their personal ambitions of finding a cure for many of life's most debilitating and too often fatal disease"
Dennis OConnor

Sequencing whole genomes helps diagnose more rare diseases - 0 views

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    "Researchers hope that building out sequencing data from more people in tandem with reviewing their clinical information can help steer them to more connections between genetic variants and disease. And with new technology, scientists are getting better at whittling down all the genetic noise produced by looking at someone's whole genome to home in on what's causing these conditions."
Dennis OConnor

About Arivale: Our Team - 0 views

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    Dr. K's mentor "Lee Hood, MD, PhD, is a pioneer in the systems approach to biology and medicine. His research has focused on molecular immunology, biotechnology, and genomics. Dr. Hood began his career at Caltech, where he and his colleagues developed the DNA gene sequencer and synthesizer and the protein synthesizer and sequencer, which paved the way for mapping the human genome. A pillar in the biotechnology field, Dr. Hood has played a role in founding more than fourteen biotechnology companies, including Amgen, Applied Biosystems, Darwin, and Integrated Diagnostics."
Dennis OConnor

The proximal origin of SARS-CoV-2 | Nature Medicine - 1 views

  • Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data
  • Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.
  • The receptor-binding domain (RBD) in the spike protein is the most variable part of the coronavirus genome1,2. Six RBD amino acids have been shown to be critical for binding to ACE2 receptors and for determining the host range of SARS-CoV-like viruses7.
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  • Theories of SARS-CoV-2 originsIt is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus.
  • the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone
  • we propose two scenarios that can plausibly explain the origin of SARS-CoV-2: (i) natural selection in an animal host before zoonotic transfer; and (ii) natural selection in humans following zoonotic transfer.
  • COVID-19 were linked to the Huanan market in Wuhan
  • it is likely that bats serve as reservoir hosts for its progenitor
  • Malayan pangolins (Manis javanica) illegally imported into Guangdong province contain coronaviruses similar to SARS-CoV-221
  • Although no animal coronavirus has been identified that is sufficiently similar to have served as the direct progenitor of SARS-CoV-2, the diversity of coronaviruses in bats and other species is massively undersampled
  • Detailed understanding of how an animal virus jumped species boundaries to infect humans so productively will help in the prevention of future zoonotic events.
  • It is possible that a progenitor of SARS-CoV-2 jumped into humans, acquiring the genomic features described above through adaptation during undetected human-to-human transmission.
  • All SARS-CoV-2 genomes sequenced so
  • are thus derived from a common ancestor that had them too
  • Estimates of the timing of the most recent common ancestor of SARS-CoV-2 made with current sequence data point to emergence of the virus in late November 2019 to early December 201923,
  • compatible with the earliest retrospectively confirmed cases
  • Basic research involving passage of bat SARS-CoV-like coronaviruses in cell culture and/or animal models has been ongoing for many years in biosafety level 2 laboratories across the world27, and there are documented instances of laboratory escapes of SARS-CoV28. We must therefore examine the possibility of an inadvertent laboratory release of SARS-CoV-2.
  • The finding of SARS-CoV-like coronaviruses from pangolins with nearly identical RBDs, however, provides a much stronger and more parsimonious explanation of how SARS-CoV-2 acquired these via recombination or mutation1
  • it is reasonable to wonder why the origins of the pandemic matter
  • For a precursor virus to acquire both the polybasic cleavage site and mutations in the spike protein suitable for binding to human ACE2, an animal host would probably have to have a high population density (to allow natural selection to proceed efficiently) and an ACE2-encoding gene that is similar to the human ortholog
  • More scientific data could swing the balance of evidence to favor one hypothesis over another.
Dennis OConnor

Cas9-mediated gene editing in the black-legged tick, Ixodes scapularis, by embryo injec... - 0 views

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    "Despite their capacity to acquire and pass on an array of debilitating pathogens, research on ticks has lagged behind other arthropod vectors, such as mosquitoes, largely because of challenges in applying available genetic and molecular tools. CRISPR-Cas9 is transforming non-model organism research; however, successful gene editing has not yet been reported in ticks. Technical challenges for injecting tick embryos to attempt gene editing have further slowed research progress. Currently, no embryo injection protocol exists for any chelicerate species, including ticks. Herein, we report a successful embryo injection protocol for the black-legged tick, Ixodes scapularis, and the use of this protocol for genome editing with CRISPR-Cas9. We also demonstrate that the ReMOT Control technique could be successfully used to generate genome mutations outside Insecta. Our results provide innovative tools to the tick research community that are essential for advancing our understanding of the molecular mechanisms governing pathogen transmission by tick vectors and the underlying biology of host-vector-pathogen interactions."
Dennis OConnor

Knight Lab - 0 views

  • The Knight Lab uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. We subscribe to an open-access scientific model, providing free, open-source software tools and making all protocols and data publicly available in order to increase general interest in and understanding of microbial ecology, and to further public involvement in scientific endeavors more generally.
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    Rob Knight PHD, Embriette Hyde PHD, Sandrine Miller Montgomery PharmD PHD The Knight Lab uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. We subscribe to an open-access scientific model, providing free, open-source software tools and making all protocols and data publicly available in order to increase general interest in and understanding of microbial ecology, and to further public involvement in scientific endeavors more generally.
Dennis OConnor

Xconomy: LunaDNA Health Data Platform to Merge with Genetic Alliance Database - 0 views

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    "Xconomy San Diego -  LunaDNA, a startup that is offering individuals company stock in exchange for personal genomic and health information in a bid to build a database that could help advance scientific research, is merging its research platform with the Genetic Alliance's Platform for Engaging Everyone Responsibly (PEER)."
Dennis OConnor

EMPOWEREDPATIENTPODCAST.COM - 0 views

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    Welcome to the Empowered Patient Podcast with Karen Jagoda. This show is a window into the latest innovations in digital health and the changing dynamic between doctors and patients. Topics on the show include the emergence of personalized medicine and breakthroughs in genomics advances for aging in place using big data from wearables and sensors transparency in the medical marketplace challenges for connected health entrepreneurs The audience includes researchers, medical professionals, patient advocates, entrepreneurs, patients, caregivers, solution providers, students, journalists, and investors.
Dennis OConnor

Milasen: The drug that went from idea to injection in 10 months - 0 views

  • itting in freezer at Boston Children’s Hospital is a drug you won’t find anywhere else. It’s called milasen, and the 18 g that the hospital custom-ordered nearly 2 years ago should last for decades. That’s because milasen was designed to treat a single patient—a now 8-year-old girl named Mila Makovec. Milasen was built on decades of work on a class of drugs called antisense oligonucleotides. But after Boston Children’s Hospital scientist Timothy Yu diagnosed Mila with a never-before-seen genetic mutation, he took only 10 months to go from idea to injection. It’s a record-shattering sprint in the typical drug-development marathon, and an unprecedented degree of personalization for a chemical drug.
  • While the story of milasen could be seen as a template for other highly personalized drugs—what the field has come to call n-of-1 therapies—it also raises questions: Who should get these treatments? How will they be funded? And how will the US Food and Drug Administration regulate these projects?
  • Yu was intrigued. He reached out and offered to do whole-genome sequencing on Mila, her parents, and her younger brother.
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  • Mila’s mom, Julia Vitarello, had started a group called Mila’s Miracle Foundation to raise money to develop a gene therapy for her daughter.
  • Julia Vitarello, Mila's mother In March, Yu’s team found that a piece of DNA called a retrotransposon—the genetic remnants of viruses scattered throughout all of our genomes—had spontaneously inserted itself in the middle of a noncoding region of Mila’s CLN7 gene.
  • Black told Yu to renegotiate with the FDA. The 3-month safety study in rats, followed by another couple months to report the data, would take too long. After a letter from Vitarello outlining Mila’s decline, the FDA made a concession: Mila could get the drug after just 1 month of testing, so long as the rat studies continued to 3 months to understand any long-term toxicity.
  • Today, Mila continues to get injections of her drug approximately every 2 months. She used to have up to 30 seizures a day, each lasting more than a minute. Now, she only has a few a day, and they don’t last long,
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    "Sitting in freezer at Boston Children's Hospital is a drug you won't find anywhere else. It's called milasen, and the 18 g that the hospital custom-ordered nearly 2 years ago should last for decades. That's because milasen was designed to treat a single patient-a now 8-year-old girl named Mila Makovec. Milasen was built on decades of work on a class of drugs called antisense oligonucleotides. But after Boston Children's Hospital scientist Timothy Yu diagnosed Mila with a never-before-seen genetic mutation, he took only 10 months to go from idea to injection. It's a record-shattering sprint in the typical drug-development marathon, and an unprecedented degree of personalization for a chemical drug."
Dennis OConnor

Empowered Patient Podcast: When the Patient is a Medical Mystery with Cathy Miller - 0 views

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    "Welcome to the Empowered Patient Podcast with Karen Jagoda.  This show is a window into the latest innovations in digital health and the changing dynamic between doctors and patients. Topics on the show include the emergence of personalized medicine and breakthroughs in genomics advances for aging in place using big data from wearables and sensors transparency in the medical marketplace challenges for connected health entrepreneurs The audience includes researchers, medical professionals, patient advocates, entrepreneurs, patients, caregivers, solution providers, students, journalists, and investors."
Dennis OConnor

Ben Brown | Biosciences | Berkeley Lab - 0 views

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    "Department Head, Molecular Eco-Systems Biology, EGSB Computational Biologist Staff Scientist Environmental Genomics and Systems Biology Molecular Eco-Systems Biology Secondary Affiliation: Biological Systems and Engineering BioEngineering & BioMedical Sciences"
Dennis OConnor

Small Data, Where N = Me | April 2014 | Communications of the ACM - 0 views

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    "We hear a lot about how big data, smart devices, and all the '-omics' (for example, genomics, proteomics, metabolomics, and so forth) are going to transform medicine-and they will. But there is another force that is going to change the way we think about and practice health, and that is our small data-small data derived from our individual digital traces."
Dennis OConnor

COVID-19 Testing Project - Pre-print manuscript - 0 views

  • April 24, 2020: Read our pre-print manuscript. This is a preliminary report of work that has not been certified by peer review. This should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information.
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    "We are a multidisciplinary team of researchers and physicians at UCSF, UC Berkeley, Chan Zuckerberg Biohub, and Innovative Genomics Institute."
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