Category Archives: Transhuman News

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.

More here:
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

Irene Blat, a senior director at Genuity Science, discusses how the intersection of data, engineering, genetics and more will be crucial to the future of healthcare.

The future of healthcare will need the right mix of skills and cross-disciplinary collaboration. Irene Blat, senior director of data products and analytics at Genuity Science, is particularly familiar with that. Throughout her career, she has worked with clinicians, geneticists, software engineers and more to drive progress in genomics.

Here, she discusses her passion for problem solving and why mentors have been crucial to her journey.

One of the biggest surprises has been realising the value of collaborative teamwork in tackling these different spaces IRENE BLAT

I have had a passion for life sciences since my early years. I loved experimenting in science class and being able to test, learn and improve. What really solidified my path into life sciences was an undergraduate experience I had working in an immunology lab. We would modify genetic sequences to better understand how immune cells were able to adapt their responses depending on the invaders they were fighting.

The way we measured the response was by looking at thousands of cells with a laser to see how the markers they expressed on their surface had changed based on the genetic changes to their sequence. This generated a lot of data that we then had to analyse.

One of the best aspects of experimenting was recording the data and then looking for and identifying patterns. The thrill of gaining insights into one more piece of the puzzle was what really drove me to continue my career in exploring genetics to better understand and potentially treat diseases.

My interest in genetics was what led me to my first job working at the Broad Institute in Cambridge, Massachusetts. At the time, it was an early data revolution in the life sciences where the human genome had just been sequenced a few years earlier and we were learning a wealth of information about healthy and disease states.

My role was to generate thousands of gene expression profiles of cells that had been treated with different drugs and then look for patterns in the cells responses to the drugs. We were looking for ways to link these genetic patterns to diseases to match them to a potential therapeutic compound. Here, I learned that the human cell is a very complex system and requires combing through lots of data to better understand how all the subtle changes in a cell work together to produce altered states.

Working with these large datasets put me on a path to look for opportunities where I could leverage the power of data to better understand complex biological systems.

For me, my career path has not been linear. I have taken risks and explored new opportunities to expand my experience where I could be impactful. Since joining Genuity, I have been fortunate to contribute to the R&D, product management and commercial aspects of the business with, at times, steep learning curves that have taken me out of my comfort zone.

What I have learned about myself is that I enjoy the challenge of learning something new and being able to leverage previous experiences to bring an original perspective to the company needs. While the subject matter might change, the concepts and learnings are still applicable across the organisation.

One of the biggest surprises has been realising the value of collaborative teamwork in tackling these different spaces. In graduate school, my work was focused on a very specific topic and in my career Ive been hired into very specific roles. But what has enabled me to move between different fields has really been collaborating and learning from other people.

Ive learned not to be afraid to ask questions and really take the opportunity to learn from others in the field. Then I have to take time to synthesise all these learnings to put forward a hypothesis that I can share with my colleagues for feedback and input. Basically, its a team effort and the more diverse the team the better the ideas.

I have had the good fortune of having many outstanding mentors throughout my career who see potential in me through my work ethic and dedication. I am grateful for having mentors who have encouraged me to take on bigger risks by giving me their vote of confidence. In particular, I have had strong female mentors who are excellent leaders and have leaned in throughout their careers.

Being able to learn from their experiences and listening to their guidance has been valuable in helping me decide where to go next in my career. The best mentors are the ones that give the gift of their time and my career has been shaped by the time of several great mentors in my life.

I really enjoy problem solving. In this role, I spend a lot of time thinking of creative ways to solve new problems. I also enjoy working through these problems in collaboration with our talented team. I have a deep appreciation for the value of sharing ideas and approaches with others from different backgrounds.

At Genuity Science, I have worked in teams with clinicians, geneticists, software engineers, bioinformaticians and data scientists who each bring their own expertise to the table. These types of cross-functional teams enable problem solving in a way that would not be possible if we all worked in silos.

What is even more exciting is that our team grows when we engage in collaborations with our customers. Our customers bring strong experiences in drug development that nicely complement our internal expertise in genomics discovery to help advance new therapies to the clinic. There are so many people to learn from both internal and external to our organisation and thats what makes my job exciting Im always learning!

I am a passionate learner. As I look back on how I landed at Genuity Science, the common thread is that every role I have had provided me the opportunity to learn. In this role, we are working at the cutting edge of how to analyse large clinical and genomic datasets. We have to iterate and adapt our analytical tools to solve increasingly complex biological problems.

My flexibility in adapting with the needs of the problem has also helped me in looking at problems in different ways. Since my early days in the lab, I recognised I had a lot of perseverance and grit. Sometimes you have to try multiple approaches before you find a path forward, but it is incredibly rewarding when you gain a new insight into a problem that was unsolved. Thats what keeps me motivated to continue trying.

At Genuity Science, the leadership team has encouraged me to explore the commercial boundaries which are well outside my original scientific training. Being able to inform commercial engagements with my deep scientific understanding has significantly broadened my skillset and resulted in exciting partnerships for the company.

Genuity has supported me in attending trainings and conferences where I was able to learn more about the commercial space as well as gain the opportunity to observe others in action. This has been a great development opportunity for me.

If you enjoy a challenge and like to learn, then a career in data analytics will not disappoint you. You have to be willing to take risks and fail but also learn from the failures and apply the lessons to the next challenge. The greatest reward is seeing how this work can ultimately have an impact on patient lives.

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The role of a data-analytics director in genomic discovery - Siliconrepublic.com

This article was originally published here

Sci Rep. 2020 Nov 20;10(1):20243. doi: 10.1038/s41598-020-76791-y.

ABSTRACT

Lung cancer is the leading causes of cancer-related death worldwide. Precise treatment based on next-generation sequencing technology has shown advantages in the diagnosis and treatment of lung cancer. This cohort study included 371 lung cancer patients. The lung cancer subtype was related to the smoking status and sex of the patients. The most common mutated genes were TP53 (62%), EGFR (55%), and KRAS (11%). The mutation frequencies of EGFR, TP53, PIK3CA, NFE2L2, KMT2D, FGFR1, CCND1, and CDKN2A were significantly different between lung adenocarcinoma and lung squamous cell carcinoma. We identified the age-associated mutations in ALK, ERBB2, KMT2D, RBM10, NRAS, NF1, PIK3CA, MET, PBRM1, LRP2, and CDKN2B; smoking-associated mutations in CDKN2A, FAT1, FGFR1, NFE2L2, CCNE1, CCND1, SMARCA4, KEAP1, KMT2C, and STK11; tumor stage-associated mutations in ARFRP1, AURKA, and CBFB; and sex-associated mutations in EGFR. Tumor mutational burden (TMB) is associated with tumor subtype, age, sex, and smoking status. TMB-associated mutations included CDKN2A, LRP1B, LRP2, TP53, and EGFR. EGFR amplification was commonly detected in patients with acquired lcotinib/gefitinib resistance. DNMT3A and NOTCH4 mutations may be associated with the benefit of icotinib/gefitinib treatment.

PMID:33219256 | DOI:10.1038/s41598-020-76791-y

Continue reading here:
Comprehensive genomic profile of Chinese lung cancer patients and mutation characteristics of individuals resistant to icotinib/gefitinib - DocWire...

Dublin, Nov. 19, 2020 (GLOBE NEWSWIRE) -- The "Genomic Cancer Panel and Profiling Markets by Cancer and Germline/Somatic Type with Screening Potential Market Size, Customized Forecasting/Analysis, and Executive and Consultant Guides 2021-2025" report has been added to ResearchAndMarkets.com's offering.

This report provides data that analysts and planners can use. Hundreds of pages of information including a complete list of Current 2020 United States Medicare Fee Payment Schedules to help understand test pricing in detail.

Forecast demand for new testing regimes or technologies. Make research investment decisions. Existing laboratories and hospitals can use the information directly to forecast and plan for clinical facilities growth.

Cancer Gene Panels and Genomic Profiling are quickly changing the diagnosis and treatment of cancers. The market is moving out of a specialized niche and going mainstream as Oncologists begin routinely using information on the hundreds of genes related to cancer. The market is exploding as physicians use all the information they can get in the battle against cancer. And there is a lot of information to be had. But the COVID-19 Pandemic has impacted the market.

Comprehensive panels, genomic profiling, high-risk breast cancer panels. Learn all about how players are jockeying for position in a market that is being created from scratch. And some players are already taking the lead. It is a dynamic market situation with enormous opportunity where the right diagnostic with the right support can command premium pricing. And the science is developing at the same time creating new opportunities with regularity. And the cost of sequencing continues to fall.

The report includes detailed breakouts for 18 Countries and 4 Regions.

Key Topics Covered:

Cancer Panel Market - Strategic Situation Analysis & COVID Update

1. Introduction and Market Definition 1.1 What are Cancer Gene Panels and Profiling? 1.2 The Sequencing Revolution 1.3 Market Definition 1.4 Methodology 1.5 A Spending Perspective on Clinical Laboratory Testing 1.5.1 An Historical Look at Clinical Testing

2. Market Overview 2.1 Players in a Dynamic Market 2.1.1 Academic Research Lab 2.1.2 Diagnostic Test Developer2.1.3 Instrumentation Supplier 2.1.4 Distributor and Reagent Supplier 2.1.5 Independent Testing Lab2.1.6 Public National/regional lab 2.1.7 Hospital lab 2.1.8 Physician Office Labs 2.1.9 Audit Body 2.1.10 Certification Body2.2 Oncogenomics2.2.1 Carcinogenesis2.2.2 Chromosomes, Genes and Epigenetics 2.2.2.1 Chromosomes 2.2.2.2 Genes 2.2.2.3 Epigenetics 2.2.3 Cancer Genes 2.2.4 Germline vs Somatic 2.2.5 Gene Panels, Single Gene Assays and Multiplexing 2.2.6 Genomic Profiling 2.2.7 The Comprehensive Assay 2.2.8 Changing Clinical Role 2.2.9 The Cancer Screening Market Opportunity2.3 Cancer Management vs. Diagnosis 2.3.1 The Role of Risk Assessment 2.3.2 Diagnosis 2.3.3 Managing 2.3.4 Monitoring 2.4 Phases of Adoption - Looking into The Future 2.5 Structure of Industry Plays a Part 2.5.1 Hospital Testing Share 2.5.2 Economies of Scale2.5.2.1 Hospital vs. Central Lab 2.5.3 Physician Office Lab's 2.5.4 Physician's and POCT

3. Market Trends3.1 Factors Driving Growth3.1.1 Level of Care 3.1.2 Companion Dx 3.1.3 Immuno-oncology 3.1.4 Liability3.1.5 Aging Population3.2 Factors Limiting Growth3.2.1 State of knowledge3.2.2 Genetic Blizzard. 3.2.3 Protocol Resistance3.2.4 Regulation and coverage 3.3 Instrumentation and Automation 3.3.1 Instruments Key to Market Share 3.3.2 Bioinformatics Plays a Role 3.4 Diagnostic Technology Development3.4.1 Next Generation Sequencing Fuels a Revolution 3.4.2 Single Cell Genomics Changes the Picture 3.4.3 Pharmacogenomics Blurs Diagnosis and Treatment3.4.4 CGES Testing, A Brave New World 3.4.5 Biochips/Giant magnetoresistance based assay

4. Cancer Panels & Profiles Recent Developments 4.1 Recent Developments - Importance and How to Use This Section 4.1.1 Importance of These Developments 4.1.2 How to Use This Section

5. Profiles of Key Players

6. The Global Market for Cancer Gene Panels and Profiles

7. Global Cancer Gene Panels & Profiles Markets - By Type of Cancer 7.1 Comprehensive Panels & Profiles 7.2 Breast Cancer Gene Testing 7.3 Colorectal Cancer Gene Testing7.4 Gynecological Cancer Gene Testing 7.5 Blood Cancer Gene Testing 7.6 Prostate Cancer Gene Testing 7.7 Lung Cancer Gene Testing7.8 Other Cancer Gene Testing

8. Global Cancer Gene Testing Markets - Germline and Somatic 8.1 Global Market Somatic 7.3 Global Market Germline

9. Potential Market Opportunity Sizes 9.1 Potential Cancer Screening by Country: Lung, Breast & Colorectal 9.2 Potential Cancer Screening by Country: Prostate, Other Cancer & All Cancer 9.3 Potential Market Size - Cancer Diagnosis 9.4 Potential Market Size - Therapy Selection

Appendices

For more information about this report visit https://www.researchandmarkets.com/r/5bx3ai

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

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Global Genomic Cancer Panel and Profiling Markets Report 2021-2025: The Market is Moving Out of a Specialized Niche and Going Mainstream -...

Hidden in plain sight, a group of scientists in Porirua some wearing lab coats, some more at home in jeans carry out some of the most important work in the fight against Covid-19.

Genomic sequencing is at the heart of contact tracing, although most New Zealanders hadnt heard those words until after the first wave.

ESR Bioinformatics lead Dr Joep de Ligt and his team, Dr Una Ren and Matt Storey, work around the clock to map the chain of transmission for every single case of Covid-19 in New Zealand.

Their building is straight out of the 1980s, a warren of corridors and stairwells. There are drawings by de Ligts kids on the bookshelf, a small 3D model of a coronavirus molecule on the next shelf.

READ MORE:* Covid-19: Covid Tracer app is a form of protection, expert says* Covid-19: How Auckland's 'mystery' coronavirus case was genome sequenced* Covid-19: Non-stop late nights, public pressure for genome sequencing team tracing coronavirus cases

ROSA WOODS/Stuff

ESR bioinformatics lead Dr Joep de Ligt demonstrates the software which maps the chains of transmission of local cases, just like a complex family tree.

These scientists knew from the beginning this work would be important. During the first lockdown they tested samples, mapped chains of transmission, and added to their database, funding it all themselves.

Then they laid all their data on the table at the Ministry of Health, and explained how they could help.

The ministry now relies on this work, and funds it jointly with the Ministry of Business, Innovation and Employments Covid-19 Innovation Acceleration Fund.

At the moment, ESR in Wellington is the main player in this field. Samples can be sequenced elsewhere, but the results are usually sent to Wellington for analysis and mapping.

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The robot responsible for pipetting and mixing solutions with the inert virus capable of doing 84 at a time at the ESR lab in Porirua.

Equipment is easy to obtain, but the people with expertise are invaluable, and scarce.

New Zealand can say weve sequenced nearly every case, de Ligt said. That meant a near-conclusive map of cases, with every chain of transmission shown as a line on a diagram, like a family tree.

Other countries around the world were doing this too. Australia and some smaller Pacific islands were also able to track every case and map them.

But for countries overwhelmed with thousands of cases a day, it wasnt a priority. The United Kingdom was sequencing about 30 per cent of its cases, de Ligt said impressive considering its volume of daily cases could reach more than 20,000.

New Zealand was in a sweet spot; a manageable amount of cases, with real value to be gained by knowing where they came from.

Dom Thomas/Getty Images

Joep de Ligt talks to Prime Minister Jacinda Ardern about the different Covid-19 genomes in New Zealand, during an ESR tour in August. (File photo)

The first sequence was produced on March 9. Since then, ESR had done the bulk of the work 1289 of a total 1296 sequences with one other by Otago University, and sic by Massey University.

The case of the Auckland AUT student who tested positive on November 12 was the fastest turnaround so far in New Zealand and, according to de Ligt, likely the fastest in the world.

Overseas, a sample could take anywhere from 24 to 48 hours to sequence. In New Zealand, with the pedal to the floor, it took around 10 hours.

Since samples often travelled from around the country to the lab in Wellington, ESR is planning to equip and train the teams in its Christchurch and Auckland centres to perform the same service, to shorten delivery times even further.

This would also provide alternatives if something happened to the Wellington base, be it disastrous like an earthquake or fire, or simple as a power outage.

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A Covid-19 molecule, shown here as an enlarged 3D replica, has spikes on the outside which attach themselves to a human cell, and transfer their contents RNA.

When a coronavirus sample lands in the hands of ESR scientists, taken by swabbing the nose and throat of a person with symptoms, it has already tested positive for Covid-19.

The person it came from should already be in self-isolation, and perhaps there is already some indication of whom they caught it from.

Or perhaps everyone is scratching their heads, workplaces thrust into lockdown, and staff at the Ministry of Health are calling hushed, hurried meetings.

RNA, like DNA, is a long ladder of chemical compounds; adenine (A), uracil (U), guanine (G) and cytosine (C). They pair up to form a double helix structure, A always joining with U, and C with G.

These letters change due to mutation. Because of the way Covid-19 RNA mutates, scientists know they can expect a change in the code once every two weeks.

The closer one persons virus resembles another known case, the more likely it is they caught it from that person.

Last week, the AUT students sample was identical to another known case.

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De Ligt and his team spend most of their time in the office rather than the lab, comparing one sequence to the next.

A positive sample begins its quest for an answer by being turned from a live form of the virus, into one which cannot infect people.

According to ESR chief scientist Dr Brett Cowan, we explode it, and then we cook it. Simple, when you put it like that.

Cowan spends a lot of his time explaining things in layman's terms. While it can be interesting to the public, more importantly, it helps if those co-ordinating health responses and contact tracing understand the process.

The membrane around the outside of the virus is burst open, spilling the genetic data. The spikes on the membranes surface are the parts that latch onto human cells, and allow the RNA, the code of the virus, to transfer and infect. Without the membrane, the RNA cant enter a cell.

The sample is then heated to a temperature that will damage everything but the RNA a second line of defence.

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ESR chief scientist Dr Brett Cowan, holding a 3D printed replica of the virus Covid-19, is well-versed in explaining the science of viruses to the public.

Once the sample is no longer infectious, the RNA is isolated from the other junk collected in a sample pollen, dust, or bacteria in the nose of the test subject.

The only part of the sample they were interested in, said de Ligt, was the RNA. We dont want to learn about the person.

In any sample, there isnt enough RNA present to produce a result at this stage. The RNA needs to be replicated millions, if not billions of times.

Then a robot transfers the virus into a cocktail of chemicals. This machine, which costs around $30,000, can transfer up to 84 samples at a time thats a sample of inert Covid-19 RNA from 84 different people.

For a country like New Zealand, which rarely had more than a handful of positive cases a day, the robot was not intended to speed up the process.

Rather, it meant everything was done systematically, with no risk of mixed-up samples. Some samples are still pipetted by hand such as the single case of the AUT student.

The next stage is to run it through a machine called a GridION, which costs around $100,000, and can sequence the RNA into the string of As, Us, Cs, and Gs.

The machine spits out the code, and the scientists move in to analyse the results.

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Coding is a big part of the process. Here, de Ligt enters the data from the machine into the mapping program, to see the bigger picture of community transmission.

By comparing one sequence with every other on file, they can pinpoint the person it most closely resembles, and then the epidemiologists and contact tracing teams take over.

We take data, and turn it into actionable intelligence, Cowan said. We have the end of the chain, and sequencing gives us the beginning.

Link:
Covid-19: Behind the scenes of genomic sequencing in Wellington's own backyard - Stuff.co.nz

WASHINGTON, Nov. 17, 2020 /PRNewswire/ -- Seven leading diagnostics companies andlaboratory service providers have formed the Access to Comprehensive Genomic Profiling Coalition (ACGP). The goal of the organization is to collectively advocate for appropriate broad U.S. health insurance coverage of comprehensive genomic profiling (CGP) for patients living with advanced cancer. The current members of ACGP are Exact Sciences (NASDAQ: EXAS), Foundation Medicine, Illumina (NASDAQ: ILMN), LabCorp (NYSE: LH), QIAGEN (NYSE: QGEN), Roche Diagnostics (SIX: RO, ROG:OTCQX: RHHBY), and Thermo Fisher Scientific (NYSE: TMO).

CGP testingperformed soon after a diagnosis of advanced cancer betterinforms medical management, including treatment decisions and patient care, which can improve clinical outcomes. In advocating for coverage of CGP, ACGP will educate health insurers and other healthcare stakeholders about the clinical utility and economic value of CGP.

CGP tests assess the genomic alterations within a patient's cancer to help physicians make more informed decisions about personalized treatment approaches. Using next-generation sequencing (NGS) with a tissue biopsy or a blood sample, this testing method can detect the four main classes of alterations known to drive cancer growth: base substitutions, insertions and deletions, copy number alterations (CNAs), and rearrangements or fusions. These tests can reveal clinically relevant alterations and biomarkers in the tumor's DNA and RNA. This helps identify patients who could respond to specific targeted therapies and immunotherapy that can be more effective and may have fewer side effects.Healthcare professionals can use CGP to help predict patient benefit across multiple targeted therapies and cancer indications, with benefits in progression-free survival for patients with non-small cell lung cancer (NSCLC) as one example.1

"Cancer is a disease of the genome, not solely the tissue. Tumor profiling hasevolved tremendously in the last decade," said Jim Almas, MD, vice president and national medical director of clinical effectiveness atLabCorp, and the chairman of ACGP. "The manufacturers and laboratories forming the coalition have produced incredible assays to help identify the mutations driving advanced cancers, leading patients to better care through targeted cancer treatments."

Despite evidence of the benefits of this approach, some health insurers still use an outdated framework to evaluate coverage for CGP, creating a disparity in access across patient populations. Many commercial insurance plans do not cover this type of testing, while public or government plans like Medicare do.Limited insurance coverage options may prevent some treating physicians from ordering CGP for their patients.

"There is no question that obstacles to coverage have inhibited physicians from ordering comprehensive genomic profiling," said Almas."Additionally, we believe some clinicians are not aware of the advantages of a comprehensive testing approach and the benefits of one CGP test to provide genomic profiling, detect microsatellite instability and tumor mutational burden, and help physicians identify clinical trials for which patients may be candidates."

To learn more about ACGP, go to http://www.accesstoCGP.com

1: Singal G, Miller PG, Agarwala V, et al. Association of Patient Characteristics and Tumor Genomics With Clinical Outcomes Among Patients With Non-Small Cell Lung Cancer Using a Clinicogenomic Database.JAMA.2019;321(14):1391-1399.

SOURCE Access to Comprehensive Genomic Profiling

http://www.accesstoCGP.com

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Leading Diagnostics Companies Join Forces to Establish the Access to Comprehensive Genomic Profiling Coalition (ACGP) - PRNewswire