Category Archives: Genome

Deep inside your cells, DNA provides the instructions to produce proteins, the essential molecules that grow and maintain your body.

RNA is the intermediary nucleic acid that carries these instructions from DNA to ribosomes, where proteins are produced within the cell. But in humans and in plants, only a tiny fraction of DNA produces the RNA that carries out protein-building instructions. In humans, almost 98% of the genome does not encode proteins. However, it often gives rise to RNA that does not produce proteins, called noncoding RNA. So what does this portion of the genome do?

Over the years, studies have found that more than 80% of the genome may be involved in transcription, or producing noncoding RNA, said Andrzej Wierzbicki, a professor in the University of Michigan Department of Molecular, Cellular and Developmental Biology. So the dilemma was: Is all this noncoding RNA functional? Is it important for something? Or is it just noise of the process of transcription or an error of detection methods?

Now, research led by Wierzbicki shows that in plants, a portion of this noncoding RNA may play an essential role in protecting the integrity of the genome. This portion of noncoding RNA is produced from transposons, rogue pieces of genes that jump around within DNA, inserting themselves haphazardly and causing genetic diversity. Sometimes this diversity is beneficial, aiding evolution, says Wierzbicki, but sometimes it can trigger mutations that can lead to disease.

The noncoding RNA produced from transposons is thought to protect the genome by making sure that transposable elements are permanently turned off. But how are transposons selected for silencing in the first place? In a recent study, the research team found evidence that this noncoding RNA is produced throughout the entire genome, not just at or around transposons. Their results are published in the Proceedings of the National Academy of Sciences.

We are essentially proposing a new model. Our model says the entire genome is transcribed, and this pervasive transcription is functional, said Wierzbicki, also a member of the Center for RNA Biomedicine at U-M. This pervasive noncoding transcription acts as a surveillance system, catching and silencing new transposons as they appear. This speculative model will hopefully be able to be tested in more detail.

These results include two parts. First, the researchers had to determine that this noncoding RNA detected throughout the genome is real, not simply an error of detection methods. To do this, the researchers focused on an enzyme called an RNA polymerase. The role of RNA polymerases is to produce RNA using the sequence of DNA as a template, Wierzbicki said.

The researchers used a plant model called Arabidopsis thaliana, which has a specialized RNA polymerase dedicated to silencing transposons. The researchers could mutate this particular polymerase enzyme and create plants that were unable to produce an entire category of noncoding RNA. No other eukaryotic organism, including humans, would survive with an RNA polymerase mutated, which makes plants uniquely suited to studying the roles of noncoding RNA.

With the polymerase enzyme mutated, the researchers then compared the mutated plant to a wild-type planta plant that had not been altered. If they detected RNA in the wild-type plant but not in the mutant plant, they could confirm that the noncoding RNA was real. And they did.

Next, the researchers wanted to understand the role of this noncoding RNA. They expected to find that noncoding transcription was taking place on transposons, but nowhere else outside of the transposons. But what they found was that noncoding transcription was happening almost everywhere in the genome.

One of the researchers, Masayuki Tsuzuki, at the time a postdoctoral fellow in the Wierzbicki lab and now an assistant professor at the University of Tokyo, looked for this transcription by using high-throughput sequencing. This sequencing is an approach that produces a huge amount of data corresponding to noncoding transcription. In-depth analysis of these results allowed the group to prove where noncoding transcription is present.

They found evidence that noncoding RNA is produced across almost 50% of the plant genome, while transposons composed only 10%-20% of the genome. By comparing their data to previously published results they further found evidence that this noncoding RNA is needed for silencing of transposons that became reactivated.

So when the transposon is new, or it has been activated in a way that the cell forgot it was previously marked as a foreign object, how can it be recognized as being foreign? Wierzbicki said. Theres one common factor thats always needed, and thats this noncoding RNA that we are studying. No matter where the transposon was inserted in the gene, it could not be turned off if the noncoding RNA was not present.

Although the research team looked at Arabidopsis thaliana, a similar process may play out in other flowering plants as well as in fungi and animals. In fungi and animals, a similar process happens, except these two groups dont have the specialized RNA polymerase. Instead, they carry out a similar process using the same polymerase that contributes to protein production.

Wierzbicki and Tsuzukis fellow researchers include Shriya Sethuraman, a doctoral student in the Bioinformatics Graduate Program at Michigan Medicine; Adriana Coke, a research assistant in the U-M Department of Molecular, Cellular and Developmental Biology; M. Hafiz Rothi, a doctoral student in the U-M Department of Molecular, Cellular and Developmental Biology; and Alan Boyle, an associate professor of computational medicine and bioinformatics and of human genetics at Michigan Medicine.

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Researchers find that a type of RNA monitors the genome to help ensure its integrity - University of Michigan News

Africa is the cradle of humankind. All humans are descendants from this common pool of ancestors. Africa and its multitude of ethnolinguistic groups are therefore fundamental to learning more about humankind and our origins.

A human genome refers to the complete set of genetic information found in a human cell. We inherit our genomes from our parents. Studying the variations in different peoples genomes gives important clues to how genetic information influences peoples appearance and health. It can also tell us about our ancestry. To date, very few African individuals have been included in studies looking at genetic variation. Studying African genomes not only fills a gap in the current understanding of human genetic variation, but also reveals new insights into the history of African populations.

My colleagues and I, who are all members of the Human Heredity and Health (H3Africa) consortium, contributed to a landmark genetics study. This study focused on 426 individuals from 13 African countries. More than 50 different ethnolinguistic groups were represented in the study one of the most diverse groups of Africans ever to be included in such an investigation. We sequenced the whole genome of each of these individuals this means we could read every part of the genome to look for variation.

This study contributes a major, new source of African genomic data, which showcases the complex and vast diversity of African genetic variation. And it will support research for decades to come.

Our findings have broad relevance, from learning more about African history and migration, to clinical research into the impact of specific variants on health outcomes.

One of the key outcomes was the discovery of more than three million new genetic variants. This is significant because we are learning more about human genetic diversity in general, and discovering more differences that could be linked to disease or traits in the future.

This study also adds details to what is known about the migration and expansion of groups across the continent. We were able to show that Zambia was most probably an intermediate site on the likely route of migration from west Africa to east and south Africa. Evidence supporting movement from east Africa to central Nigeria between 1,500 and 2,000 years ago was also revealed, through the identification of a substantial amount of east African ancestry in a central Nigerian ethnolinguistic group, the Berom.

The study also enabled us to reclassify certain variants that were previously suspected to cause disease. Variants that cause serious genetic diseases are often rare in the general population, mostly because their effect is so severe that a person with such a variant often does not reach adulthood. But we observed many of these variants at quite common levels in the studied populations. One wouldnt expect that these types of disease-causing variants would be this common in healthy adults. This finding helps to reclassify these variants for clinical interpretation.

Finally, we found a surprising number of regions with signatures of natural selection that have not been previously reported. Selection means that when individuals are exposed to environmental factors like a viral infection, or a drastic new dietary component, some gene variants may confer an added adaptive advantage to the humans that bear them in their genome.

Our best interpretation of these findings is that as humans across Africa were exposed to different environments sometimes as a result of migration these variants were likely important to surviving in those new conditions. This has left an imprint on the genome and contributes to genomic diversity across the continent.

Our data has shown that we have not yet found all the variation in the human genome. There is more to learn by adding new, unstudied population groups. We know that less than a quarter of participants in genomics research are of non-European ancestry. Most available genetic data come from just three countries the UK (40%), the US (19%) and Iceland (12%).

It is essential to keep adding more genomic data from all global populations including Africa. This will ensure that everyone can benefit from the advances in health that precision medicine offers. Precision medicine refers to the customisation of healthcare to fit the individual. Including personal genetic information could radically change the nature and scope of healthcare options that would work best for that individual.

The Human Heredity and Health consortium is now in its eighth year of existence, and supports more than 51 diverse projects. These include studies focusing on diseases like diabetes, HIV and tuberculosis. The reference data generated through our study are already being put to use by many of the consortiums studies.

Read more: What we've learnt from building Africa's biggest genome library

Next, we are planning to take an even deeper look at the data to better understand what other types of genetic variation exist. We are also hoping to add further unstudied populations to grow and enrich this data set.

Building capacity for genomics research on the African continent is a key goal of Human Heredity and Health. An important aspect of this study is that it was driven and conducted by researchers and scientists from the African continent. Researchers from 24 institutions across Africa participated and led this investigation. This study showcases the availability of both infrastructure and skills for large-scale genomics research on the continent. It also highlights the prospect of future world-class research on this topic from Africa.

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Major new study unveils complexity and vast diversity of Africa's genetic variation - The Conversation CA

In the past few years, people have become fascinated with using their DNA to learn more about themselves, their origins, family trees, predisposition to health conditions and quirky traits. This has been enabled by the rise in popularity and the relative affordability of direct-to-consumer ancestry testing in places like the US. This testing allows people to swab their mouths to collect cells containing DNA, which are then sent off to companies for testing and analysis.

Today sites like AncestryDNA, 23andMe, MyHeritage and FTDNA dominate the European and US markets. But until recently, this service has been inaccessible to most South Africans. Thats because testing using overseas companies can be expensive, and there are logistical hurdles to shipping sample collection kits into and out of South Africa.

Recently, local companies like DNAnalysis and Be Happy To Be You have started to offer genetic testing, ranging from ancestry to nutrigenetics (what your genes say you should and should not eat) and health screenings.

Many potential clients are, however, sceptical about using these services. They view them as sub-standard and more expensive than some of the larger, overseas competitors. There are also concerns regarding privacy.

So, is supporting local businesses and getting your DNA analysed worth it? My opinion, as a human population geneticist who has researched the role that extensive genetic testing can play in mapping diseases, is yes. As more clients choose a local service provider for direct-to-consumer testing, the accuracy of the service will increase, the costs will decrease and the resulting data generation can be used to boost medical research efforts.

The process of completing a direct-to-consumer ancestry test is fairly simple. When you visit a site and request a test, you will be required to sign a consent form, fill in your personal information (contact details and address) and then wait for your test kit to be couriered to you. This kit is used to swab the inside of your mouth. The swabs are then sent back to the company for further processing, which involves extraction of your DNA and then computational analysis. An ancestry report is generated by comparing your genetic data to data of other worldwide populations.

But what of peoples concerns around accuracy, cost and privacy?

Firstly, there is no evidence that the services offered by local companies are sub-par. In fact, they should be more accurate because of the context in which the data is analysed. Local companies will have databases of South African data that other overseas companies do not. For example, instead of containing two different southern African populations (in line with overseas companies), local companies might have 10 and therefore be able to provide more detailed, granular reports.

Furthermore, scientists who work in local companies have acquired local knowledge and are therefore able to work with South Africas unique genetic diversity better than anyone else.

Secondly, testing in South Africa is for the most part not more expensive than overseas. If South Africans use an overseas company, theyll generally have to pay for courier fees to get a sample collection kit delivered and sent back to the company as well as potentially paying import taxes. Theres also a risk that the sample collection kit might get held up or even lost in either direction of the courier process. This may add to the overall cost.

Typically the price for direct-to-consumer ancestry testing in the US is between $69 and $99. Adding approximately R800 (around $50) for courier charges brings the cost for an international test to between R1,900 and R2,400, compared to between R1,000 and R2,499 locally (courier fees included). And, as more and more people start using local resources, the products and services will become cheaper over time.

Read more: What we've learnt from building Africa's biggest genome library

With regard to data privacy, confidentiality and anonymity, South Africa has some of the strictest laws that govern personal data, particularly the Protection of Personal Information Act. All local companies are required to adhere to this.

There is another aspect South Africans should consider when theyre thinking about using local services for genomic testing: the importance of creating a genomic citizenship movement.

When you send your DNA to a direct-to-consumer genetic testing company, you are investing in a product and service that benefits others. By making your de-identified genetic data available for use in local companies databases and for research purposes, you directly contribute to scientific development by increasing the accuracy of these services for other clients and in some cases, for yourself and for your family members.

Scientific researchers can use that de-identified data to investigate, for instance, why some individuals get sick and others dont. An example of this has been seen during the COVID-19 pandemic. Genetic data from direct-to-consumer genetic testing has been used to investigate how the disease progresses and why some patients are asymptomatic while others succumb to the disease. This was made possible by individuals who allowed researchers to use their genetic data for this purpose.

Over time, with an expansion of genetic data, it will be possible to diagnose patients with genetic diseases that would not have been diagnosed otherwise. Scientists will be able to answer questions regarding the efficacy of medications in some patients and speed up the development of gene therapies that could save countless lives.

The rise of direct-to-consumer services is an opportunity for South Africans to contribute, in their own way, to a greater genomic future.

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How South Africans can use their DNA to be good genomic citizens - The Conversation CA

COVID-19 Coronavirus molecule, March 24, 2020.

CDC | API | Gamma-Rapho via Getty Images

A team of CRISPR scientists at the New York Genome Center, New York University and Icahn School of Medicine at Mount Sinai said they have identified the genes that can protect human cells against Covid-19, a disease that has infected over 40 million and led to 1 million deaths worldwide.

The discovery comes after an eight-month screen of all 20,000 genes in the human genome led by Dr. Neville Sanjana at the New York Genome Center. Leading virologist at Mount Sinai, Dr. Benjamin tenOever, developed a series of human lung cell models for the coronavirus screening to better understand immune responses to the disease and co-authored the study.

Their study, published online last month by Cell, will appear in the scientific peer-reviewed journal's Jan. 7 print issue.

The goal was two-fold: to identify the genes that make human cells more resistant to SARS-CoV-2 virus; and test existing drugs on the market that may help stop the spread of the disease.

The breakthrough comes at a time when drug makers such as Pfizer, Oxford-AstraZeneca and Moderna are fast-forwarding vaccine and therapeutics to treat Covid-19. On Friday, Pfizer and BioNTech requested emergency authorization from the FDA for their Covid vaccine that contains genetic material called messenger RNA, which scientists expect provokes the immune system to fight the virus.

In order to better understand the complex relationships between host and virus genetic dependencies, the team used a broad range of analytical and experimental methods to validate their results. This integrative approach included genome editing, single-cell sequencing, confocal imaging and computational analyses of gene expression and proteomic datasets.

After intensive research, the scientists and doctors claim they have found 30 genes that block the virus from infecting human cells including RAB7A, a gene that seems to regulate the ACE-2 receptor that the virus binds to and uses to enter the cell. The spike protein's first contact with a human cell is through ACE-2 receptor.

"Our findings confirmed what scientists believe to be true about ACE-2 receptor's role in infection; it holds the key to unlocking the virus," said Dr. tenOever. "It also revealed the virus needs a toolbox of components to infect human cells. Everything must be in alignment for the virus to enter human cells."

The team discovered that the top-ranked genes those whose loss reduces viral infection substantially clustered into a handful of protein complexes, including vacuolar ATPases, Retromer, Commander, Arp2/3, and PI3K. Many of these protein complexes are involved in trafficking proteins to and from the cell membrane.

"We were very pleased to see multiple genes within the same family as top-ranked hits in our genome-wide screen. This gave us a high degree of confidence that these protein families were crucial to the virus lifecycle, either for getting into human cells or successful viral replication," said Dr. Zharko Daniloski, a postdoctoral fellow in the Sanjana Lab and co-first author of the study.

Using proteomic data, they found that several of the top-ranked host genes directly interact with the virus's own proteins, highlighting their central role in the viral lifecycle. The team also analyzed common host genes required for other viral pathogens, such as Zika or H1N1 pandemic influenza.

The research team also identified drugs that are currently on the market for different diseases that they claim block the entry of Covid-19 into human cells by increasing cellular cholesterol. In particular, they found three drugs currently on the market were more than 100-fold more effective in stopping viral entry in human lung cells:

The other five drugs that were tested called PIK-111, Compound 19, SAR 405, Autophinib, ALLN -- are used in research but are not yet branded and used in clinical trials for existing diseases.

Our findings confirmed what scientists believe to be true about ACE-2 receptor's role in infection; it holds the key to unlocking the virus.

Their findings offer insight into novel therapies that may be effective in treating Covid-19 and reveal the underlying molecular targets of those therapies.

The bioengineers in New York were working on other projects with gene-editing technology from CRISPR but quickly pivoted to studying the coronavirus when it swept through the metropolitan area last March. "Seeing the tragic impact of Covid-19 here in New York and across the world, we felt that we could use the high-throughput CRISPR gene editing tools that we have applied to other diseases to understand what are the key human genes required by the SARS-CoV-2 virus," said Dr. Sanjana.

Dr. Neville Sanjana and his team at the New York Genome Center used CRISPR to identify the genes that can protect human cells against Covid-19.

New York Genome Center

As he explained, "current treatments for SARS-CoV-2 infection currently go after the virus itself, but this study offers a better understanding of how host genes influence viral entry and will enable new avenues for therapeutic discovery."

Previously, Dr. Sanjana has applied genome-wide CRISPR screens to identify the genetic drivers of diverse diseases, including drug resistance in melanoma, immunotherapy failure, lung cancer metastasis, innate immunity, inborn metabolic disorders and muscular dystrophy.

"The hope is that the data from this study which pinpoints required genes for SARS-CoV-2 infection could in the future work be combined with human genome sequencing data to identify individuals that might be either more susceptible or more resistant to Covid-19," Dr. Sanjana said.

The New York team is not the first to use CRISPR gene editing techniques to fight Covid-19. Other bioengineering groups at MIT and Stanford have been using CRISPR to develop ways to fight the SARS-CoV-2 and develop diagnostic tools for Covid-19.

The potential for using CRISPR to eliminate viruses has already generated some enthusiasm in the research community. Last year, for example, Excision BioTherapeuticslicenseda technology from Temple University that uses CRISPR, combined with antiretroviral therapy, to eliminate HIV, the virus that causes AIDS.

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Gene experts claim they identified human genes that can protect against Covid-19 - CNBC

In 2003, biologists created the first ever human genome sequence. The 3 billion DNA letter sequence, called the reference genome, was mostly made up of DNA donated from people in the city of Buffalo, New York. So far, when clinicians and researchers study an individuals genome, they compare it to the reference genome to identify differences. But can you compare all of humanity to one genome? No, because one reference genome does not convey the genomic diversity of the human species. We need many reference genomes a pangenome. This monumental undertaking is already taking place and is poised to redefine the future of genomic research and human health.

This video was co-produced by Massive Science and NIH/NHGRI.

Presented by the National Human Genome Research InstituteDirection and animation by Rosanna WanNarration by Dr Shawntel OkonkwoSound + music by SkillbardScript by Harriet Bailey and Prabarna GangulyProducer Harriet BaileySenior producer Nadja OerteltExecutive producer Prabarna GangulyProduced for and supported by the National Human Genome Research Institute

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Video: The Ambitious Project To Prepare a Library of Genomes of the Human Species - The Wire Science

In the ultimate game of genetic hide and seek, scientists at Virginia Tech have identified several instances in which they found giant virus genomes embeddedsome in their entiretyin the genomes of their hosts. The results, published today (November 18) in Nature, suggest that such integration by giant viruses may be more common than previously believed and that these viruses are likely an underappreciated source of genetic diversity in eukaryotes.

We always assumed that [giant viruses] that can integrate into host genomes were not common, Karen Weynberg, a virologist at the University of Queensland in Australia who was not involved in the work, tells The Scientist. Now theyve shown that these viruses are able to integrate on a much wider scope than we ever really perceived. Its going to be groundbreaking, and I think people will be looking more into where these viruses are popping up.

Giant viruses, so named because they tend to be about 10 times larger than the average virus, have challenged traditional ideas in virology since their discovery in 2003. In addition to their unusually large size, their genomes sometimes include genetic contributions from bacteria and eukaryotes, including metabolic genes. Because of this, they dont necessarily look viral at the genomic level, says Frank Aylward, a virologist at Virginia Tech and a coauthor of the study.

Towards the beginning of his postdoc in Aylwards lab, Mohammad Monir Moniruzzaman went searching for a handful of giant virus marker genes in all genomes accessible through the National Center for Biotechnology Informations many databasesan exploratory exercise to see what came back. While most of the genes appeared in genomes labeled as viruses, Moniruzzaman says he was surprised by how many of these giant virus genes appeared in genomes labeled as belonging to microscopic marine phytoplankton.

Aylward and Moniruzzaman first thought they might be picking up contamination. But when they looked more closely, they noticed genetic signals suggesting parts of the viruses had been incorporated into the genomes of their hosts. Following up on this hypothesis, the team went looking for systematic evidence of this integration in 65 publicly available green algae genomes, some of which are known to be hosts to giant viruses.

The giant virus Ostreococcus tauri virus (OtV-1) can insert large portions of its roughly 200,000 base pair genome into the genome of its host Ostreococcus tauri,the smallest known free-living eukaryote.The arrow points to the attachment site for host cell absorption.

karen weynberg

Moniruzzaman and his colleagues developed a bioinformatics tool, called ViralRecall, to identify regions in algal genomes suspected of having a viral origin based on several cues. For example, they used the tool to scan for certain viral hallmark genes, clear demarcations between the two genomes, shared genes between virus and host, and the presence of noncoding introns and large duplications within the integrated viral sequences thought to be caused by the hosts molecular machinery.

The researchers identified 18 examples of giant endogenous viral elements (GEVEs) within a dozen host genomes, meaning that some hosts had more than one of these GEVEs integrated into their genetic code. In some cases, the viral contributions were fragmented, representing only a small fraction of the virus genome. But in two samples, the entire viral genome appears to have made the jump into the phytoplankton, making up as much as 10 percent of the hosts genes. Overall, these GEVEs contributed between 78 and 1,782 genes.

This essentially opens up a large conduit of horizontal gene transfer from viruses into eukaryotes, Aylward says. All sorts of possibilities open up once you see these huge cases of endogenization.

Using a phylogenetic analysis, Moniruzzaman was able to trace the GEVEs back to members of the Phycodnaviridaeand Mimiviridaefamilies, two diverse groups that have informed much of what is known about giant viruses. The first discovery alerting scientists to their existence, for example, was of a mimivirus isolated from a cooling tower in England.

Taken together, the results suggest that endogenization by giant viruses may be more common than previously thought. The idea that they built this new tool and then saw so many cases of this, even with just that first, somewhat limited scan, is pretty surprising, says Nels Elde, an evolutionary geneticist at the University of Utah who was not involved in the current work. Theyve built a somewhat circumstantial case, but with several lines of complementary evidence that look pretty strong.

Elde urges caution in accepting the teams analysis of duplications in the integrated viral genome as evidence of endogenization. Previous work, including his own on poxviruses (whose status as a giant virus is debated), has shown that viruses are capable of carrying out rapid, large-scale gene duplications themselves without a host. In the paper, the authors stress that they found many more duplications in endogenized viruses than in free-living comparisons.

A next step could involve looking more broadly across the tree of life. Scientists are unsure exactly how many different organisms these viruses can infect, but the green algae targeted in this study, in the phylum Chlorophyta, share a common ancestor with modern land plants.

Another step, both Weynberg and Elde say, should be studies into whether these introduced viral genes bring functional changes to the hosts. Roughly 10 percent of the human genome, for example, is thought to be derived from endogenous retroviruses, and some of their genes have been coopted in reproduction and brain function.

I like the fact that this paper really focuses on the influence of viruses in shaping their hosts genomes that then spills into the evolution of the host as well, Weynberg says. Once these viruses become integrated into host genomes and persist across generations, it starts to confer benefits as well. That really highlights this intimacy that viruses have with their hosts.

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Giant Viruses Can Integrate into the Genomes of Their Hosts - The Scientist

From gulls to grouse to grackles, more than 10,000 bird species live on this planet. Now, scientists are one step closer to understanding the evolution of all of this feathered diversity.

An international team of researchers has released the genetic instruction books of 363 species of birds, including 267 genomes assembled for the first time. Comparing all of that genetic data can help scientists figure out how the varied traits of birds from their diverse, spellbinding songs and courtship displays to their adaptations for flight have evolved, the team says in the Nov. 12 Nature.

Birds have long received scientific attention, says ornithologist Michael Braun of the Smithsonian National Museum of Natural History in Washington, D.C., one of the researchers involved in the project. Thats partly because birds are relatively easy to see out in nature, he says.

To compile some of the newly assembled genomes, the team took DNA from bird tissue samples in 17 scientific collections from around the world. Overall, the data cover roughly 92 percent of all modern bird families. Some species, such as chickens, are familiar; others are rare, such as the Henderson crake (Zapornia atra), found only on remote Henderson Island in the South Pacific.

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Scientists are just starting to uncover the secrets of avian evolution hidden in the genomes. Braun says that the data can be used better understand everything from the parallel evolution of flightlessness in ratites like emus and kiwis (SN: 4/4/19) to the evolution of vision and song learning in birds overall.

Already, the researchers have found peculiarities in the genomes of passerines the order of songbirds that includes over half of all modern bird species, though the origin of this diversity is poorly understood. These alterations include the loss of a gene involved in the development of the vocal tract, possibly influencing passerines songs.

This new information is the latest from the Bird 10,000 Genomes Project, but it wont be the last. The international research collaboration doesnt plan to stop assembling and releasing avian genomes until every last bird species on the planet is included.

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Hundreds of new genomes help fill the bird tree of life - Science News

As a nationwide telehealth medical practice, Genome Medical has assembled an extensive team of clinical genetic experts, including board-certified genetic counselors, medical geneticists and other specialists. This team delivers education, risk assessment, access to genetic testing and specialty care referrals -- all through virtual visits. During the COVID-19 pandemic, when two out of five Americans have avoided or delayed medical care1, access to safe virtual services is essential to ensure people at greatest risk are receiving the care they need. Genetic services support the diagnosis and care management of hereditary conditions and the identification of patients at an elevated risk for disease.

Some of the largest payers in the United States are recognizing the critical role geneticists and genetic counselors play. Their members can now self-refer and get in-network access to Genome Medical's genetic experts, and the payer's contracted providers can also make in-network referrals for their patients.

The 90 million covered lives are across multiple payers, including (in part):

"Genome Medical brings together telemedicine and genomics to tackle the rising need for genetic experts to guide patients and providers in making appropriate decisions around 1) who should get genetic testing, 2) which test is optimal and 3) how clinical care should be changed based on test results," said Steven B. Bleyl, M.D., Ph.D., chief medical officer of Genome Medical. "Patients can be seen sooner, and through telehealth, we extend the reach of genetic services to rural communities and underserved areas that have less access to in-person care. Genome Medical is a flexible and cost-effective solution for payers and their members."

Genome Medical can see 85% of cancer patients more quickly than in a traditional clinic setting.2 And in areas like pediatric genetics, where wait times of six months or more for an appointment are common, Genome Medical's growing clinical team can often see patients within a few days. The company's genetic experts are licensed in all 50 states and provide clinical genetics expertise across six major specialty areas: cancer, reproductive health, proactive health, pediatrics/rare disease, pharmacogenomics and cardiovascular genetics. Genome Medical's innovative services are trusted and utilized by health systems, hospitals, testing labs, payors, providers and employers.

Genome Medical is also committed to leveraging advanced technology-enabled solutions to transform the delivery of standard-of-care genetic health services. Beyond wider and accelerated access, the company's technology delivers a 5.5X return on investment in genetic services, while also reducing the cost of care by up to 75 percent.3,4 Its Genome Care DeliveryTM platform creates an efficient and comprehensive experience, including patient engagement and care navigation, risk assessment, self-directed education and informed consent through the Genome Care NavigatorTM, multi-modality patient support, and peer-to-peer provider consultations.

"We are pleased to see health plan partners continue to expand in-network coverage for our genetic health services," said Lisa Alderson, co-founder and CEO of Genome Medical. "It is estimated that tens of millions of patients in the United States meet medical management guidelines for referral to genetics, but most are still being missed. These patients could benefit from the advancements made in utilizing genomics for prevention, diagnosis and treatment. Giving their members access to Genome Medical and telegenetics is a significant step payers are taking in removing historical barriers."

About Genome MedicalGenome Medical is a national telegenomics technology, services and strategy company bringing genomic medicine to everyday care. Through our nationwide network of genetic specialists and efficient Genome Care DeliveryTM technology platform, we provide expert virtual genetic care for individuals and their families to improve health and well-being. We also help health care providers and their patients navigate the rapidly expanding field of genetics and utilize test results to understand the risk for disease, accelerate disease diagnosis, make informed treatment decisions and lower the cost of care. We are shepherding in a new era of genomic medicine by creating easy, efficient access to top genetic experts. Genome Medical is headquartered in South San Francisco. To learn more, visit genomemedical.com and follow @GenomeMed.

References

SOURCE Genome Medical

Genetic Counseling & Services from Anywhere | Genome Medical

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Genome Medical Reaches 90 Million Covered Lives in US - PRNewswire

As a large multinational corporation, Eli Lilly has their hands in boundless projects, from cancer and immuno-oncology to diabetes, psoriasis and Crohns disease.But Friday they signaled a shift in their R&D focus toward genome editing, leaping into a cutting-edge field CEO Dave Ricks had shied away from as recently as January 2019.

The big pharma is ponying up $100 million upfront to partner with Precision BioSciences, focusing initially on Duchenne muscular dystrophy and two other undisclosed in vivo targets. Lilly is also acquiring $35 million worth of the biotechs stock, and has the option to develop three additional in vivo therapies.

By offering up to $420 million in R&D and commercialization milestones per product, Lilly could end up paying Precision as much as $2.655 billion when all is said and done. On top of that, the biotech is eligible for single-digit to low-teen royalties on successful therapies.

Precision $DTIL investors greeted the news warmly, sending shares up more than 12% in early trading Friday.

We feel like this is a strong statement from Lilly, Precision CEO Matthew Kane told Endpoints News. This is clearly a validating event for the company, but importantly it unlocks the potential for us to more aggressively go after some of these diseases.

At the heart of the deal is Precisions ARCUS genome editing platform, coming from a group of North Carolina scientists including CSO Derek Jantz who claim they have a better way to accomplish DNA hacking than the gene editing promoted by biotechs working on CRISPR/Cas9 technologies like CRISPR Therapeutics, Intellia and Editas.

ARCUS deals with whats known as the ARC nuclease, with the company saying it provides a simpler, more effective way of completing the gene editing process and allows for lower production costs when production eventually has to scale up. The enzyme itself is synthetic and comes from a homing endonuclease found in algae called I-CreI, with scientists re-engineering its editing abilities to knock in, knock out or repair cells as they see fit.

Weve spent the last 15 years getting good at modifying this natural enzyme from algae and bending it to our will, and making it have the ability to edit DNA sequences that were interested in, Jantz said.

He added that while Precision is looking at multiple delivery options, the biotech is fond of AAV technology because of its long track record in the clinic.

Precisions current lead program is an off-the-shelf CAR-T therapy acute lymphoblastic leukemia and non-Hodgkin lymphoma, aiming to target CD19, with Phase I data expected no earlier than the end of 2020. Such treatments and other ex vivo programs are not included in Fridays partnership, however, and Duchenne had not been one of the biotechs previous pipeline targets.

Kane said its too early to know when the DMD program could hit the clinic, but described the program as moving aggressively.

For Lilly, Ricks has stated his wariness of gene therapies in the past, despite several other big companies investing heavily in the area. Though the collaboration doesnt deal with the CAR-Ts Precision is developing internally, Friday marks an apparent course correction. Lilly will be jumping into a highly competitive DMD field where there are already multiple programs in the clinic, including those from Pfizer, Solid Biosciences, Vertex and Sarepta.

Almost everything I am aware of is single gene edit defects, which ultimately leads you to pretty ultra-rare conditions, which are not our area of interest, Ricks told Reuters in a Jan. 2019 interview, adding later, We dont need new areas to grow.

Kane said that while he cant speak for Lilly, he noted that genome editing is distinct from traditional gene therapies.

When we think of traditional gene therapy if you will, even though its still such a new and emerging field, there were typically inserting in or adding a gene thats missing from the body, but were not actually impacting the patients genome, Kane said. With gene editing, we actually do that. We have an opportunity to make a permanent change to the patients genome.

Originally posted here:
In an apparent R&D about-face, Eli Lilly partners with Precision BioSciences on genome editing in a deal worth up to nearly $2.7B - Endpoints News

Discovery of shape of the SARS-CoV-2 genome after infection could inform new COVID-19 treatments.

Scientists at the University of Cambridge, in collaboration with Justus-Liebig University, Germany, have uncovered how the genome of SARS-CoV-2 the coronavirus that causes COVID-19 uses genome origami to infect and replicate successfully inside host cells. This could inform the development of effective drugs that target specific parts of the virus genome, in the fight against COVID-19.

SARS-CoV-2 is one of many coronaviruses. All share the characteristic of having the largest single-stranded RNA genome in nature. This genome contains all the genetic code the virus needs to produce proteins, evade the immune system, and replicate inside the human body. Much of that information is contained in the 3D structure adopted by this RNA genome when it infects cells.

The researchers say most current work to find drugs and vaccines for COVID-19 is focused on targeting the proteins of the virus. Because the shape of the RNA molecule is critical to its function, targeting the RNA directly with drugs to disrupt its structure would block the lifecycle and stop the virus replicating.

In a study published recently in the journal Molecular Cell, the team uncovered the entire structure of the SARS-CoV-2 genome inside the host cell, revealing a network of RNA-RNA interactions spanning very long sections of the genome. Different functional parts along the genome need to work together despite the great distance between them, and the new structural data shows how this is accomplished to enable the coronavirus life cycle and cause disease.

The RNA genome of coronaviruses is about three times bigger than an average viral RNA genome its huge, said lead author Dr. Omer Ziv at the University of Cambridges Wellcome Trust/Cancer Research UK Gurdon Institute.

He added: Researchers previously proposed that long-distance interactions along coronavirus genomes are critical for their replication and for producing the viral proteins, but until recently we didnt have the right tools to map these interactions in full. Now that we understand this network of connectivity, we can start designing ways to target it effectively with therapeutics.

In all cells the genome holds the code for the production of specific proteins, which are made when a molecular machine called a ribosome runs along the RNA reading the code until a stop sign tells it to terminate. In coronaviruses, there is a special spot where the ribosome only stops 50% of the times in front of the stop sign. In the other 50% of cases, a unique RNA shape makes the ribosome jump over the stop sign and produce additional viral proteins. By mapping this RNA structure and the long-range interactions involved, the new research uncovers the strategies by which coronaviruses produce their proteins to manipulate our cells.

We show that interactions occur between sections of the SARS-CoV-2 RNA that are very long distances apart, and we can monitor these interactions as they occur during early SARS-CoV-2 replication, said Dr. Lyudmila Shalamova, a co-lead investigator at Justus-Liebig University, Germany.

Dr. Jon Price, a postdoctoral associate at the Gurdon Institute and co-lead of this study, has developed a free, open-access interactive website hosting the entire RNA structure of SARS-CoV-2. This will enable researchers world-wide to use the new data in the development of drugs to target specific regions of the viruss RNA genome.

The genome of most human viruses is made of RNA rather than DNA. Ziv developed methods to investigate such long-range interactions across viral RNA genomes inside the host cells, in work to understand the Zika virus genome. This has proved a valuable methodological basis for understanding SARS-CoV-2.

Reference: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 by Omer Ziv, Jonathan Price, Lyudmila Shalamova, Tsveta Kamenova, Ian Goodfellow, Friedemann Weber and Eric A. Miska, 5 November 2020, Molecular Cell.DOI: 10.1016/j.molcel.2020.11.004

This research is a collaborative study between the group of Professor Eric Miska at the University of Cambridges Gurdon Institute and Department of Genetics, and the group of Professor Friedemann Weber from the Institute for Virology, Justus-Liebig University, Gieen, Germany. The authors are grateful for the support of the Biochemistry Department at the University of Cambridge, who provided specialist laboratory facilities for performing part of this research.

The work was funded by Cancer Research UK, Wellcome, and Deutsche Forschungsgemeinschaft (DFG).

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SARS-CoV-2 Uses Genetic Origami to Infect and Replicate Inside Host Cells Discovery Could Lead to New COVID-19 Treatments - SciTechDaily