Category Archives: Genome

Ask the average whiskey drinker to name the key ingredients in their favorite spirit, and theyll probably tell you which grains its made from. Of course, whats just as crucial to the final product as the grains its distilled from is the barreland the American-made barrels that both American distillers and many of their Scottish and Irish counterparts rely on are almost exclusively made from the noble white oak tree.

The whisk(e)y business is so reliant on this species that concerns are arising about what would happen if disease hit the species, something that gets increasingly likely as the climate changes. Thats why, not unlike the research we wrote about earlier this fall into drought resistance in barley, researchers from the University of Kentucky, University of Tennessee, Penn State, and the US Forest Service are partnering with Makers Mark and the Independent Stave Company to research the genome of the white oak.

This research is for the greater good of the industry and the entire Eastern forest, said Seth DeBolt, director of the University of Kentuckys James B. Beam Institute for Kentucky Spirits, in a prepared statement. Wed like to get a reference map for the white oak genome. Weve identified a tree at the Makers Mark Distillery on Star Hill Farm as a gorgeous representative specimen of the species.

This reference tree is hundreds of years oldwhite oak trees have been known to live four centuriesand researchers are collecting acorns and grafts from it. The team is approaching oak as an agricultural product, which, for the whiskey business, makes sense. They hope to identify some of the genetic variation that exists within the species.

The challenge here is to thoroughly understand a species, a really foundational, long-lived species that anchors the forest, said DeBolt. The goal is to answer questions such as: How does it live that long, in a single location? How does it maintain resistance to so many different diseases?

American white oak is a key ingredient in bourbon-making. The color, and much of the flavor, of bourbon come from white oak barrels, so its critically important that this precious natural resource be managed and preserved for generations to come, said Makers Marks Rob Samuels, chief distillery officer. At Makers Mark, were constantly stepping up our own environmental efforts, which have become a guiding principle for everything we do, and were proud to play a part in this research that will reach far beyond our home at Star Hill Farm and help this vital species thrive long into the future.

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The University of Kentucky is Researching the Genome of White Oak - The Whiskey Wash

A substantial proportion of oncologists in the United States are loath to broach the issue of cost if patients require genomic testing as part of their cancer care, a recent survey has found.

And whereas half of those surveyed did frequently bring up the issue of cost with their patients, approximately one quarter only sometimes raise the issue of cost if genomic testing was required, and the other quarter rarely or never discuss it, the same survey shows.

The survey involved 1220 oncologists who participated in the 2017 National Survey of Precision Medicine in Cancer Treatment.

This is a nationally representative survey of medical oncologists sponsored by the National Cancer Institute, National Human Genomic Research Institute, and the American Cancer Society, say the authors.

The results were published online November 1 in The Journal of the National Cancer Institute (JNCI)

"Use of genomic testing is increasing in the United States," note the authors. led by Robin Yabroff, PhD, an epidemiologist with the American Cancer Society.

More than 30 genomic tests associated with cancer drugs are now available in the US. Most often, these tests identify a genetic mutation and thus allow the use of a targeted agent instead of chemotherapy.

Testing can be expensive and not all tests and related treatments are covered by health insurance, the authors write, and even when those who have private health insurance can experience medical financial hardship.

"Oncologists may not be the providers best suited for all discussions about the expected costs of care," the authors acknowledge.

However, they can ensure that cost conversations do take place with someone from the medical team who is qualified to do so, they suggest.

The authors also point out that training materials and practice guides are available to help physicians overcome their discomfort about having discussions concerning the cost of care with patients as well as about how much genomic interventions may cost that patient.

"Even privately insured cancer survivors report problems paying medical bills, stress related to medical bills, or delaying or forgoing care because of cost," the authors warn.

"Thus, discussions about the expected costs of cancer care are important for all patients," they conclude.

These discussions can be difficult because of the nuances involved, suggests Richard Schilsky, MD, chief medical officer of the American Society of Clinical Oncology (ASCO), writing in an accompanying editorial.

"The biggest challenge may be explaining to a patient the nuances of context of use and clinical utility that define the true value of a tumor biomarker test. Patients need to know not just what the test will cost but how it will inform their care, impact their options, affect their outcomes and whether, in the long run, it might even guide them to better treatments and/or lower their overall costs of care," he explains.

Further research on how best to convey these complex issues in the course of a clinical encounter is desperately needed before we can effectively 'talk the talk' about tumor genomic testing," Schilsky concludes.

The findings are based on answers that were obtained to this question in the survey: 'In the past 12 months, when you or your staff discussed any form of genomic testing with your cancer patients or their families, how often did you discuss the likely costs of the testing and related treatment?'

Results showed that the frequency of cost discussions differed by the type of cancer that physicians treated.

For example, some 60.1% of oncologists who treated only solid tumors frequently discussed the cost of genomic testing with patients compared with 50.4% of those who treated both hematologic cancers and solid tumors, and 27.9% of oncologists who treated only hematologic cancers (P < .001)

In fact, oncologists who treated both solid and hematologic cancers were almost three times more likely to often have cost discussions with patients compared with oncologists who only treated hematologic malignancies (odds ratio [OR], 2.82).

Oncologists who only treated solid tumors were four times more likely to have frequent cost discussions (OR, 4.01) compared with those who only managed blood cancers, researchers add.

Oncologists who had graduated from medical school at least 15 years before taking the survey were also more likely to have frequent discussions about the cost of genomic testing and related treatment costs, compared with those who had graduated less than 15 years ago.

Just over half (54%) of physicians who had used next-generation sequencing gene panel tests in the past 12 months reported often discussing the cost of genomic testing compared with almost 38% of those who did not (P < .001), the authors add.

"Oncologists with formal training in genomic testing were more likely than those without this training to report discussing costs often," the investigators continue at 54.6% vs 44.1%, respectively (P =.001).

Similarly, oncologists who had electronic health record (EHR) alerts for genomic testing were at least twice as likely to have frequent cost discussions compared with oncologists who did not have EHR alerts (OR, 2.22).

Higher patient volumes also prompted more frequent discussions about genomic testing costs, as did a having a higher percentage of patients either insured by Medicaid, or who were self-pay or uninsured, as was practicing in lower income areas.

In 2009, the American Society of Clinical Oncology highlighted the important role that oncologists have in discussions about potential out-of-pocket costs that patients may incur in the course of their cancer care.

The Institute of Medicine later categorized these discussions as being a critical element in high-quality care.

The study authors have disclosed no relevant financial relationships.

JNCI. Published online November 1, 2019. Abstract, Editorial

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Cost of Genomic Tests Often Not Discussed With Patients - Medscape

Identification of melanoma-specific Dark Antigens to be presented at The Society for Immunotherapy of Cancer 34thAnnual Meeting (SITC)

LONDON, Nov. 6, 2019 /PRNewswire/ -- Ervaxx, a biotechnology company pioneering the use of Dark Antigens to developoff-the-shelf cancer vaccines and T-cell receptor-based immunotherapies, formally announces its launch following two years in incubation by SV Health Investors.

Ervaxx coincides its launch with the presentation of new research to identify novel melanoma-specific Dark Antigens by application of its novel EDAPT platform at The Society for Immunotherapy of Cancer 34th Annual Meeting (SITC) (9 November 2019, National Harbor, MD, USA). Details of the poster can be found below.

Ervaxx' founding idea is that the 'dark matter' of the human genome (i.e. the 98% of the genome that does not encode known proteins) contains antigen-coding sequences that are uniquely expressed by cancer cells and shared across patients. These sequences, which are normally silenced in healthy cells, represent a large potential repertoire of novel antigens that Ervaxx aims to develop as targets for new immunotherapies.

Ervaxx has developed its proprietary EDAPT platform to explore this new and expanding Dark Antigen repertoire, and to identify and assess its tumor-specific and immunogenic potential to combat cancer. EDAPT combines bioinformatics, transcriptomics, immunopeptidomics and state-of-the-art immunology to discover and validate novel Dark Antigens with which to deliver a pipeline of off-the-shelf tumor-specific therapeutic cancer vaccines and T cell receptor (TCR)-based therapies. The platform is built upon pioneering research from the company's founders at the Francis Crick Institute (London, UK) and developed by Ervaxx in partnership with other leading academic collaborators.

Initially, Ervaxx has focused on the discovery and development of off-the-shelf cancer vaccines based on Dark Antigens derived from endogenous retroviral (ERV) related DNA sequences where significant and compelling research by its founders has been conducted. Retroviral DNA is a component of genomic dark matter and makes up about 8% of the entire genome. Ervaxx and its collaborators have identified thousands of novel ERV-related sequences, with enriched expression in over 30 tumor types.

This work has been further advanced by Ervaxx, which is progressing its lead cancer vaccine programme targeting melanoma, for which highly immunogenic target antigens have been identified. The research being presented at SITC describes the application of EDAPT to identify over 2,000 potential melanoma-specific Dark Antigens encoded by the cancer genomes of melanoma patients using ERV markers to search for aberrantly expressed and highly immunogenic target antigens.

The presentation and tumor specificity of these Dark Antigens were validated, and immunogenicity and lack of central tolerance in normal donor CD8+ T-cells were also confirmed. Constructs encoding multiple Dark Antigens with high immunogenicity that are conserved across patients and across HLA subtypes have been selected to create a therapeutic, off-the-shelf cancer vaccine.

The company is utilizing the EDAPT platform to expand its discovery focus beyond ERV-related sequences and is also advancing into additional indications, including non-small cell lung cancer, ovarian cancer and other solid tumor indications with high unmet medical need.

Ervaxx has raised $17.5m in seed/Series A funding from SV Health Investors and a leading (undisclosed) global pharmaceutical company, with which it also has a strategic R&D partnership. The company is headquartered in London and operates R&D from its laboratory in the Bioescalator Building at Oxford University.

The company has established an experienced board of directors chaired by Houman Ashrafian (Ervaxx co-founder, Managing Partner at SV Health Investors) and including Kate Bingham (Managing Partner at SV Health Investors), Tim Edwards (Karus Therapeutics, AstronauTx, Storm Therapeutics and others); Veronique Birault (Director of Translation at the Francis Crick Institute) and Kevin Pojasek (Ervaxx President & CEO and Venture Partner at SV Health Investors).

Kevin Pojasek, CEO of Ervaxx, said:

"We are delighted to announce our formal launch today and to bring forward our exciting and innovative science. Our Dark Antigens have the potential to bring new and effective cancer treatments to patients by providing a completely new set of targets, which can be combined to maximise population coverage and immunogenic response. We believe we are the first company with an integrated platform designed to explore the dark matter of the genome for novel cancer targets. Our hope is that this pioneering approach will generate a new wave of effective immunotherapies for a wide range of cancers."

Houman Ashrafian, Chairperson and Co-founder of Ervaxx, added:

"The science behind Ervaxx is truly ground-breaking and opens up exciting possibilities for the development of new and multiple modalities of tumor-specific cancer therapies based on Dark Antigens. We are delighted with the progress the company has made during its incubation phase. An excellent team has been brought together with new R&D capabilities to rapidly drive the translation of this research into the clinic. We look forward to supporting its progress as a pioneer in this new cancer immunotherapy approach."

SITC Poster details

Abstract title: Discovery of immunogenic ERV-derived antigens as targets for melanoma immunotherapy

Abstract number:P680

Authors:Jupp, R. et al

Date/time:Saturday, 9 November, 07:00am - 08:30pm

About Ervaxx

Ervaxx is pioneering the use of Dark Antigens to deliver targeted off-the-shelf cancer vaccines and other immunotherapies for treating and preventing cancer. Ervaxx Dark Antigens derive from vast untapped expanses of genetic 'dark matter' beyond the normal coding regions of the genome, which are generally silenced in normal tissue but can become selectively activated in cancer.

Ervaxx' powerful, proprietary EDAPT platform has been developed to discover and validate Dark Antigens providing an in-depth assessment of candidate antigens on primary tumor cells along with their immunogenic potential. The EDAPT platform has identified proprietary antigens that map to multiple solid tumor types and generate robust, antigen-specific T-cell responses. Ervaxx is advancing a pipeline of off-the-shelf cancer vaccines and T cell receptor (TCR)-based therapies leveraging these insights into the role of Dark Antigens in cancer.

Ervaxx was co-founded by SV Health Investors and is based on pioneering research at the Francis Crick Institute (London, UK). The company has offices in London, UK and a laboratory in the Bioescalator Building at Oxford University, UK. Ervaxx also has a strategic partnership with a global pharmaceutical company.

For more information visit: http://www.ervaxx.com

Ervaxx, Dark Antigen and EDAPT are trademarks of Ervaxx Limited

FOR MORE INFORMATIONErvaxx LimitedKevin Pojasek, CEOTel: +44-(0)-1865618828Email: info@ervaxx.com

Citigate Dewe RogersonMark Swallow, Frazer Hall, Nathaniel DahanTel: +44-(0)-20-7638-9571Email: ervaxx@citigatedewerogerson.com

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Ervaxx Launches to Pioneer the Use of Dark Antigens for the Development of Off-the-Shelf Cancer Vaccines and T-cell Receptor-based Immunotherapies -...

ABBOTT PARK, Ill., Nov. 6, 2019 /PRNewswire/ -- Abbott (NYSE: ABT) announced today that a team of its scientists identified a new subtype of the human immunodeficiency virus (HIV), called HIV-1 Group M, subtype L.1 The findings, published today in the Journal of Acquired Immune Deficiency Syndromes (JAIDS), show the role next-generation genome sequencing is playing in helping researchers stay one step ahead of mutating viruses and avoiding new pandemics.

Since the beginning of the global AIDS pandemic, 75 million people have been infected with HIV and 37.9 million people today are living with the virus.2 Thanks to the work done by the global health community over the past few decades, the goal of ending the HIV pandemic is becoming feasible. Yet researchers must remain vigilant to monitor for new strains to make sure testing and treatments continue to work.

"In an increasingly connected world, we can no longer think of viruses being contained to one location," said Carole McArthur, Ph.D., M.D., professor in the departments of oral and craniofacial sciences, University of Missouri Kansas City, and one of the study authors. "This discovery reminds us that to end the HIV pandemic, we must continue to outthink this continuously changing virus and use the latest advancements in technology and resources to monitor its evolution."

This research marks the first time a new subtype of "Group M" HIV virus has been identified since guidelines for classifying new strains of HIV were established in 2000. Group M viruses are responsible for the global pandemic, which can be traced back to the Democratic Republic of Congo (DRC) in Sub-Saharan Africa.3,4

The science behind genetic sequencing to discover new viruses

To determine whether an unusual virus is in fact a new HIV subtype, three cases must be discovered independently.5 The first two samples of this subtype were discovered in DRC in the 1980s and the 1990s. The third, collected in 2001, was difficult to sequence at that time because of the amount of virus in the sample and the existing technology.

Today, next-generation sequencing technology allows researchers to build an entire genome at higher speeds and lower costs. In order to utilize this technology, Abbott scientists had to develop and apply new techniques to help narrow in on the virus portion of the sample to fully sequence and complete the genome.6

"Identifying new viruses such as this one is like searching for a needle in a haystack," said Mary Rodgers, Ph.D., a principal scientist and head of the Global Viral Surveillance Program, Diagnostics, Abbott, and one of the study authors. "By advancing our techniques and using next generation sequencing technology, we are pulling the needle out with a magnet. This scientific discovery can help us ensure we are stopping new pandemics in their tracks."

Twenty-five years of tracking mutating viruses around the world

As a leader in blood screening and infectious disease testing, Abbott created its Global Viral Surveillance Program 25 years ago to monitor HIV and hepatitis viruses and identify mutations to ensure the company's diagnostic tests remain up to date. As part of this research, Abbott scientists confirmed that its core and molecular laboratory diagnostic tests can detect this new HIV strain.

In partnership with blood centers, hospitals and academic institutions around the world, Abbott has collected more than 78,000 samples containing HIV and hepatitis viruses from 45 countries, identified and characterized more than 5,000 strains, and published 125 research papers to date to help the scientific community learn more about these viruses. The study published today, "Complete genome sequence of CG-0018a-01 establishes HIV-1 subtype L," is now available online.

To learn more about Abbott's virus hunting efforts, visit http://www.abbott.com/virushunters.

About Abbott:Abbott is a global healthcare leader that helps people live more fully at all stages of life. Our portfolio of life-changing technologies spans the spectrum of healthcare, with leading businesses and products in diagnostics, medical devices, nutritionals and branded generic medicines. Our 103,000 colleagues serve people in more than 160 countries.

Connect with us atwww.abbott.com, on LinkedIn at http://www.linkedin.com/company/abbott-/, on Facebook atwww.facebook.com/Abbottand on Twitter @AbbottNews and @AbbottGlobal.

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Abbott Announces Discovery of New Strain of HIV, Keeping Global Health Community a Step Ahead of the Virus - BioSpace

(The Conversation is an independent and nonprofit source of news, analysis and commentary from academic experts.)

Jessica M. Velez, University of Tennessee; Alison Gerken, Kansas State University, and Amey Redkar, Universidad de Crdoba

(THE CONVERSATION) Humans, the latest tally suggests, have approximately 21,000 genes in our genome, the set of genetic information in an organism. But do we really need every gene we have? What if we lost three or four? What if we lost 3,000 or 4,000? Could we still function? Humans have variation in their genomes, but the overall size does not vary dramatically among individuals, with the exception of certain genetic disorders like Downs syndrome, which is caused by an extra copy of chromosome 21 and all the genes that it carries.

Each gene in a genome provides the code for a protein which affects our lives, from the growth of our hair to allowing us to digest certain foods. Most of the genes found in the human genome are probably safe for now, but there are some organisms which, over time, have cut down their genome to live in various habitats.

Scientists previously thought that every gene in an organisms genome was essential for survival because humans have little variation in our genome sizes from person to person. However, studies using animals with smaller, streamlined genomes have proven this untrue.

What does it take to streamline a genome? Does the organism just cut genes over time and hope for the best, or are there a series of processes that compensate for the loss of these genes? If researchers can understand how some of these small genomes work so efficiently, we can better understand how human genomes function as well. We, Amey Redkar, Alison Gerken and Jessica Velez, are a team of biologists with diverse backgrounds, all associated with the Genetics Society of America. We are interested in understanding how diverse genetic processes work in a variety of organisms and strive to communicate these exciting facts about genetics to a broad audience.

Genome structural rearrangement through evolutionary processes

Genomes can change in a variety of ways. Changes can be slight, involving just a single DNA building block, or large-scale, such as the duplication or loss of a large chunk of DNA. It is even possible to lose entire gene pathways groups of genes acting together. Large losses in DNA over time are known as genome streamlining.

Every organism is adapted to their environment, and some have achieved this through the process of genome streamlining. During this process the genome is rearranged as the species adapt to their environment. Genome streamlining enables organisms to thrive in challenging environments, such as low-nutrient ocean sites, or adapt to unique evolutionary challenges, such as those posed by flight.

Researchers explore these adaptations by studying the streamlined genomes of specific species, known as model species, to uncover what genetic material is excessive and if there is an optimum number of genes needed for an organism to survive.

Birds and plants undergo genome streamlining

A striking example of genome streamlining is seen in hummingbirds, in which the main drivers of genome size adaptations are thought to be flight and metabolic demands. These birds developed the ability to fly as well as a high-energy lifestyle, which are both reflected in their genetic code. Hummingbirds possess the smallest and least variable genome within bird species at around 900,000,000 units of DNA. The genes that encode proteins are, on average, between 27% and 50% shorter than those in mammalian genomes. These adaptations arose through the process of genome streamlining. DNA and genes which did not actively contribute to hummingbirds living at higher altitudes and having an extremely active, high-energy lifestyle were lost through adaptive mutations.

Fast-moving birds are only one of the more energetically complex species which have undergone genome streamlining. In the plant kingdom, the tiny, rootless aquatic bladderwort plant, Utricularia gibba, captures insect prey in miniature traps using vacuum suction. This plant is adapted to a predatory lifestyle through evolutionary selection of genes that allow the bladderwort to break down complex molecules using special enzymes and retain the plants structural integrity in water environments. Redundant, less important and unnecessary genes were lost.

Extreme streamlining: The smallest genome

The previous examples of reduced genome sizes raise a fundamental question: Just how streamlined can a genome be? As the genome of a species shrinks, scientists can explore how many genes a species can lose before an organism can no longer survive.

One such organism used in these studies, Prochlorococcus marinus, is a single-celled cyanobacterium living in the open ocean. At 1,800,000 units of DNA, P. marinus is known for having the smallest genome of any known photosynthetic organism.

These cyanobacteria can no longer create many essential molecules needed for survival. They have lost entire gene pathways used for the creation of amino acids, which are necessary to build proteins. As a result, P. marinus is no longer able to survive in its natural environment without the assistance of symbiotic or beneficial species which provide the amino acids P. marinus needs. In a laboratory, researchers cannot grow P. marinus without the presence of these helper species, or by directly adding the necessary amino acids P. marinus needs.

Reliance upon another species

Similar symbiotic relationships exist inside of insects. Some species of the bacterial pathogen Nardonella have undergone genome streamlining to a genome size as small as 230,000 units of DNA, shedding all genes except those necessary for DNA synthesis and the gene pathway for manufacturing tyrosine, an amino acid for building proteins.

These bacteria derive almost all of their metabolic requirements from the weevil in which they live. The bacteria, in turn, provide the final building block for the pathway in order for the weevil to generate the amino acid tyrosine that builds a darker, harder exoskeleton for the weevil which protects the insect from predators and from drying out. As a result, Nardonella both relies on and provides a benefit to the host weevil in exchange for this reliance.

Like humans, these species all have structured genetic information, but studies in these animals, plants, and bacteria have revealed that not every gene was essential to survive in their environments. As researchers continue to explore genome streamlining, we move closer to understanding how genetic adaptations arise, how the loss of genetic information affects the genomes of species, and just how few genes a species must have in order to survive in unique, challenging environments.

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This article is republished from The Conversation under a Creative Commons license. Read the original article here: http://theconversation.com/not-all-genes-are-necessary-for-survival-these-species-dropped-extra-genetic-baggage-121673.

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Not all genes are necessary for survival these species dropped extra genetic baggage - Thehour.com

It is a huge leap forward for global medicine and especially relevant right now as we live longer, healthier lives.

According to the chief medical officer of Sydney health information company, Genome.One, Dr Leslie Burnett, genome sequencing is the holy grail of medicine. It underpins precision healthcare and for the first time it offers the potential for preventing or lessening the impacts of avoidable illnesses in an individual rather than just waiting until the condition appears and only then providing treatment.

For Australia's ageing population it is a heartening breakthrough, especially as many older Australians start to struggle with chronic diseases. Yet before precision healthcare becomes a reality, there are still a few hurdles to overcome, the major one being moving it from the laboratory into your local GP's surgery.

"The gap at present is how we connect genomics into healthcare," Genome.One chief scientific officer and founding CEO, Associate Professor Marcel Dinger says.

"At the moment there is an enormous limitation in terms of how accessible the information is and how it's actually translated into the population. The transition that needs to happen is ensuring genomic medicine has mainstream access so your local GP for example, has access to genomic information to guide their practice."

Bearing this in mind, Dinger says genomic medicine's future lies with a more connected healthcare system and "enabling digital healthcare is fundamental to genomics".

"If it remains constrained within existing clinical and laboratory processes, its promise will never come to bear," he says.

The scale of the challenge is clear for the Garvan Institute-backed start-up, which is undergoing a restructure.

Genome.One's Burnett and Dinger were speaking after a recent joint research study undertaken by Fairfax Media, publisher of The Australian Financial Review, in partnership with the Commonwealth Bank of Australia, which examined ways in which innovation can underpin the nation's economic future.

Sam Bowen, Commonwealth Bank of Australia, executive director, healthcare, institutional banking and markets, says a major focus of the survey of AFR readers was whether or not Australia's health system is fit-for-purpose considering the nation's ageing population. The research found that 71 per cent of study respondents lack confidence in Australia's preparedness.

To address these shortcomings, respondents highlighted three key initiatives.

Firstly, 49 per cent suggested the community should be encouraged to invest in, and improve, their long-term health. Secondly, more than 40 per cent of respondents recommended helping people of a working age to fund their own long-term healthcare and finally, 39 per cent of respondents indicated there needs to be more investment in technological innovations that assist with home healthcare.

Chief executive officer of aged care provider Estia Health, Norah Barlow bridles at terms like "ageing tsunami" and suggests we should stop thinking of it as a negative.

Barlow acknowledges our ageing population is a challenge and we need to work out how to ensure we have the resources and people available to deal with the coming change.

"In Australia we are not as well prepared as we should be and while there are lots of reviews going on around the aged care set-up, the big question is someone has to think about whether the aged care system is a universal system or is it a subsidised system? It's a hard political question and difficult to answer but when you're well prepared you know how you're going to fund it and what it's going to look like," she says.

Barlow believes Australians are a little ageist when it comes to looking after our elderly. She suggests our view has to change, especially as the aged care sector will generate about 20 per cent of new jobs in the future healthcare economy.

She recommends changing the structure of the aged-care model with more of a focus on rehabilitation. Rather than keeping people in residential care, they should be allowed to return home after a period of rehabilitation and hopefully access reliable and flexible home care services.

As for the future of medicine, Barlow says we have to get digital health right first and foremost. Beyond that immediate challenge, there will be much greater use of technology, with innovations like the virtual doctor, more telehealth and remote monitoring of chronic conditions.

But Barlow warns we can go too far with technology because there is a danger of losing the human interaction in medicine. "We believe that the amazing technology that is emerging will support rather than replace humans in the provision of care."

AFR readers agree. In response to a question about what technological advances are most likely to help with the ageing population, 41 per cent of respondents said that human care is most likely to help.

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Digital the right medicine for healthy nation - The Australian Financial Review

Clinical exome sequencing has revolutionized genetic testing for children with inherited disorders, and Baylor College of Medicine researchers have led efforts to apply these DNA methods in the clinic. Nevertheless, in more than two-thirds of cases, the underlying genetic changes in children who undergo sequencing are unknown. Researchers everywhere are looking to new methods to analyze exome sequencing data to look for new associations between specific genes and those rare genetic diseases called Mendelian disorders. Investigators at theHuman Genome Sequencing Centerhave developed new approaches for large-scale analysis of Mendelian disorders, published today in theAmerican Journal of Human Genetics.

The investigators used an Apache Hadoop data lake, a data management platform, to aggregate the exome sequencing data from approximately 19,000 individuals from different sources. Using information from previously solved disease cases, they established methods to rapidly select candidates for Mendelian disease. They found 154 candidate disease-associating genes, which previously had no known association between mutation and rare genetic disease, according toAdam Hansen, lead author of the study and graduate student inmolecular and human geneticsat Baylor.

We found at least five people for each of these 154 genes that have very rare genetic mutations that we suspect might be causing disease, Hansen said. This shows the power of big data approaches toward accelerating the rate of discovery of associations between genes and rare diseases.

These computational methods solve the dual problems of large-scale data management and careful management of data access permission. saidDr. Richard Gibbs, study author and professor of molecular and human genetics and director of the Human Genome Sequencing Center at Baylor. They are perfect for outward display of data from the Baylor College of Medicine programs.

Exome sequencing currently only diagnoses 30 to 40% of patients, Hansen said. He hopes that diagnosis rate will increase with the discovery of new associations between mutations in certain genes and rare diseases.

The genetics community can now focus on genetic mutations in these genes when they see undiagnosed patients, Hansen said. Since our initial analysis, 19 of these genes have already been confirmed as disease-associating by independent researchers. The collective effort of the genetics community will advance our understanding of these genes and provide further evidence for their potential role in disease.

Other researchers at the Human Genome Sequencing Center who were involved in the study included Mullai Muragan, Donna Muzny, Fritz Sedlazeck, Aniko Sabo, Shalini Jhangiani, Kim Andrews, Michael Khayat, and Liwen Wang.

This work was supported in part by grants UM1 HG008898 from the National Human Genome Research Institute (NHBLI) to the Baylor College of Medicine Center for Common Disease Genetics; UM1 HG006542 from the NHGRI/National Heart, Lung, and Blood Institute (NHLBI) to the Baylor Hopkins Center for Mendelian Genomics; R01 NS058529 and R35 NS105078 (J.R.L.) from the National Institute of Neurological Disorders and Stroke (NINDS); and P50 DK096415 (N.K.) from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK).

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Connecting gene mutations, rare genetic diseases - Baylor College of Medicine News

Predicting genetically complex traits from the DNA of cells taken from an IVF embryo (above) isn't easy.

By Jocelyn KaiserOct. 24, 2019 , 5:15 PM

HOUSTON, TEXASTwo years ago, news headlines began to appear about a development that made many human geneticists uneasy. A U.S. company planned to offer a test for embryos created through in vitro fertilization (IVF) that screened the entire genome for DNA variants linked to cognitive ability, in order to help couples avoid having children with intellectual impairment. Many ethicists fear such multigene analyses could one day be used to screen embryos for desirable traits as well, such as tall stature or high IQ.

For those disturbed by the prospect, a study reported here last week at the annual meeting of the American Society of Human Genetics (ASHG) may come as a relief: For now, the strategy would not work very well.

Researchers, led by statistical geneticist Shai Carmi of the Hebrew University of Jerusalem, calculated exactly how much of a boost in IQ or height could be expected by scanning for relevant DNA markers in a batch of embryos and choosing those with the highest scores. The result: The gains would be slight, and prospective parents might even end up discarding their tallest or smartest potential offspring.

The work "is the first to empirically test the viability of screening embryos" for traits that are influenced by many genes, says sociologist and demographer Melinda Mills of the University of Oxford in the United Kingdom. Such embryo screening goes beyond today's testing for single-gene disorders and currently "isn't plausible," she concludes.

Such tests are based on a polygenic risk score, a tool for evaluating a person's likelihood of a disease or trait that has emerged over the past decade from genomic studies combing through variable DNA markers in many thousands of people. Although having any one DNA variant may barely raise the risk of, say, heart disease, adding up the effects from hundreds or thousands of these markers can generate a score that helps identify people at relatively high risk of common diseases. Some direct-to-consumer DNA testing companies have begun to give customers polygenic risk scores for diseases such as heart disease, breast cancer, and diabetes.

Testing embryos, however, is hugely controversial, because of both the scientific limitations of such polygenic scores and the prospect of designer babies. Undeterred, a company called Genomic Prediction last year began to offer to test cells plucked from an IVF embryo for millions of DNA markers to produce risk scores for some common diseases and for "intellectual disability" or low IQ. Co-founder Stephen Hsu, a physicist at Michigan State University in East Lansing who has branched into genomics, says that for now, the company is not returning genetic scores predicting high IQ because "society is not ready for it."

Still, testing embryos for desirable traits could be coming soon. Most people agree it's not a good idea, but there are no data, Carmi said at the ASHG meeting. To find out whether the strategy could work, his team created virtual genomes for potential embryos by combining the DNA profiles of "parents." One parental group included actual and randomly chosen pairs of men and women from 102 Ashkenazi Jewish couples with recorded heights and the other 919 randomly paired Greek men who had cognitive test scores. The team then calculated polygenic scores for the synthetic genomes to predict height or cognitive ability. For the five embryos typically generated in an IVF cycle, the theoretical height gain from selecting an Ashkenazi couple's embryo with the highest "tallness" score was about 2.5 centimeters (with a range of 1 to 6 centimeters). Selecting for the Greek virtual embryo with the highest IQ-favorable score brought a similarly limited gain in cognitive ability, just 2.5 IQ points (in a range from one to seven points), Carmi said.

His team also looked at the actual genomes of adult offspring in 28 large families (about 10 children on average). They found that for height, unknown environmental influences, which could include factors such as diet, and genes not represented in the polygenic score apparently overpowered the assessed genetic markers: In only seven of the 28 families was the sibling with the top score for height the tallest; in five families, the best scoring child was shorter than all siblings' average height. Although Carmi's team didn't have similar real-life data for IQ, University of Edinburgh population geneticist Peter Joshi expects that any intelligence polygenic score would be even more unreliable. "You might be wrong almost as often as you're right," Joshi says. (Carmi declined to discuss his study, which is online as a preprint and in press at a journal.)

An embryo screening test that uses a polygenic score to predict low IQ is likely to face the same limitations, says Joshi, who views such testing as unethical. Hsu, however, emphasizes that Genomic Prediction doesn't use its risk scores to screen for subtle IQ distinctions, but rather to avoid embryos with rare "outlier" DNA profiles for which scores predict a high risk of an IQ below 75, indicating intellectual disability.

Carmi's embryo study comes on top of other problems with polygenic tests. Most such scores have been derived from scanning DNA of people of European ancestry, making them of limited use for other ancestry groups. And recent studies have found they often aren't as predictive for older people, men, or people living in a certain location. Scores predicting behavioral traits such as a person's level of education are even more problematic, because these traits are strongly shaped by the family environment in which a child is raised.

But such polygenic scores, for IQ as well as diseases, are sure to improve as researchers look at genetic markers in larger, more diverse groups of people. "What about when they do become predictive?" an audience member asked during an ASHG discussion, wondering whether that would justify use of the scores. "That equation can change," responded Oxford statistical geneticist Alexander Young. The ethical debate over this brave new expansion of embryo screening is just beginning.

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Screening embryos for IQ and other complex traits is premature, study concludes - Science Magazine

After nine years of work, an international consortium of scientists has released gene sequences for more than 1100 plant species.

The massive undertaking described in a paper in the journal Nature is part of the One Thousand Plant Transcriptomes Initiative (1KP), a global collaboration to examine the diversification of plant species, genes and genomes back to the ancestors of flowering plants and green algae.

It reveals the timing of whole genome duplications and the origins, expansions and contractions of gene families contributing to fundamental genetic innovations enabling the evolution of algae, mosses, ferns, conifer trees, flowering plants and all other green plant lineages.

"In the tree of life, everything is interrelated, and if we want to understand how the tree of life works we need to examine the relationships between species," says lead investigator Gane Ka-Shu Wong, from the University of Alberta, Canada. That's where genetic sequencing comes in."

By sequencing and analysing genes from a broad sampling of species, the researchers say, they are better able to reconstruct gene content in the ancestors of all crops, model plant species, and gain a more complete picture of the gene and genome duplications that enabled evolutionary innovations.

More than 100 taxonomic specialists contributed material from field and living collections, including Germanys Central Collection of Algal Cultures; the Royal Botanic Gardens in London and Edinburgh; Atlanta Botanical Garden, New York Botanical Garden and Florida Museum of Natural History in the US; Fairylake Botanical Garden in Shenzhen, China; and the University of British Columbia Botanical Garden and University of Alberta in Canada.

The size and scope of the project also required the development and refinement of new computational tools for sequence assembly and phylogenetic analysis.

The timing of 244 whole genome duplications across the green plant tree of life was of particular interest to the researchers.

"Perhaps the biggest surprise of our analyses was the near absence of whole genome duplications in the algae," says Mike Barker, from University of Arizona, US.

"Building on nearly 20 years of research on plant genomes, we found that the average flowering plant genome has nearly four rounds of ancestral genome duplication dating as far back as the common ancestor of all seed plants more than 300 million years ago.

We also find multiple rounds of genome duplication in fern lineages, but there is little evidence of genome doubling in algal lineages."

In addition to genome duplications, the expansion of key gene families has contributed to the evolution of multicellularity and complexity in green plants, adds co-author Marcel Quint, from Germanys Halle University.

"Gene family expansions through duplication events catalysed diversification of plant form and function across the green tree of life," he says.

"Such expansions unleashed during terrestrialisation or even before set the stage for evolutionary innovations including the origin of the seed and later the origin of the flower."

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The really big book of plants - Cosmos

A new way to modify DNA, prime editorcouples two enzymes, Cas9 (blue) and reverse transcriptase (red), to a guide RNA (green) that takes the complex to a specific place on DNAs double helix (yellow and purple) and also holds the code for an insertion of new DNA at that spot.

By Jon CohenOct. 21, 2019 , 11:00 AM

CRISPR, an extraordinarily powerful genome-editing tool invented in 2012, can still be clumsy. It sometimes changes genes it shouldnt, and it edits by hacking through both strands of DNAs double helix, leaving the cell to clean up the messshortcomings that limit its use in basic research and agriculture and pose safety risks in medicine. But a new entrant in the race to refine CRISPR promises to steer around some of its biggest faults. Its a huge step in the right direction, chemist George Church, a CRISPR pioneer at Harvard University, says about the work, which appears online today in Nature.

This newfangled CRISPR, dubbed prime editing, could make it possible to insert or delete specific sequences at genome targets with less collateral damage. Prime editors offer more targeting flexibility and greater editing precision, says David Liu, a chemist at the Broad Institute in Cambridge, Massachusetts, whose lab led the new study and earlier invented a popular CRISPR refinement called base editing.

Liu, his postdoc Andrew Anzalone, and co-workers tested variations of their prime editors on several human and mouse cells, performing more than 175 different edits. As a proof of principle, they created and then corrected the mutations that cause sickle cell anemia and Tay-Sachs disease, DNA aberrations that previous genome-editing systems either could not fix or only did so inefficiently. The edits occurred in a high percentage of cells and caused relatively few off-target changes. In its paper, the team claims the technology in principle can correct about 89% of known pathogenic human genetic variants.

Most CRISPR systems rely on a molecular complex that couples a guide RNAwhich homes in on a specific location in the genomewith an enzyme, Cas9, that cuts both strands of DNA. During the cells efforts to reconnect the DNA, its repair machinery can introduce or delete nucleotides. Researchers can take advantage of the botched repair to knock out genes that, say, cause a disease. They can also hijack the inefficient repair process to add DNAeven an entire gene.

But double-stranded breaks are genome vandalism, Church says. As the cell attempts to repair the break it introduces insertions and deletions willy-nilly, sometimes creating unwantedand even dangerousmutations.

Lius earlier handwork, base editing, does not cut the double-stranded DNA but instead uses the CRISPR targeting apparatus to shuttle an additional enzyme to a desired sequence, where it converts a single nucleotide into another. Many genetic traits and diseases are caused by a single nucleotide change, so base editing offers a powerful alternative for biotechnology and medicine. But the method has limitations, and it, too, often introduces off-target mutations.

Prime editing steers around shortcomings of both techniques by heavily modifying the Cas9 protein and the guide RNA. The altered Cas9 only nicks a single strand of the double helix, instead of cutting both. The new guide, called a pegRNA, contains an RNA template for a new DNA sequence, to be added to the genome at the target location. That requires a second protein, attached to Cas9: a reverse transcriptase enzyme, which can make a new DNA strand from the RNA template and insert it at the nicked site.

Liu, who has already formed a company around the new technology, Prime Medicine, stresses that to gain a place in the editing toolkit, it will have to prove robust and useful in many labs. Delivering the large construct of RNA and enzymes into living cells will also be difficult, and no one has yet shown it can work in an animal model.

Fyodor Urnov, scientific director at the Innovative Genomics Institute in Berkeley, California, reviewed the paper for Nature and says it brought one of those yay, science! kind of moments. Prime editing well may become the way that disease-causing mutations are repaired, he says. But, he adds, its too soon to be sure. The technique just showed up this year.

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New 'prime' genome editor could surpass CRISPR - Science Magazine