Category Archives: Transhuman News

By Wyss Institute for Biologically Inspired Engineering at HarvardJanuary 24, 2022

A collaborative research team at Harvards Wyss Institute and the ETH Zurich in Switzerland has identified genomic safe harbors (GSHs) in the tumultuous sea of human genome sequence to land therapeutic genes in. As part of their validation, they inserted a fluorescent GFP reporter gene into candidate GSHs and followed its expression over time. The GSHs could enable safer and longer-lasting expression of genes in future gene and cellular therapies. This illustration won the team the cover of the Cell Reports Methods issue the study is published in. Credit: Erik Aznauryan

Researchers at Harvards Wyss Institute, Harvard Medical School, and the ETH Zurich predict and validate genomic safe harbors for therapeutic genes, enabling safer, more efficient, and predictable gene and cell therapies.

Many future gene and cell therapies to treat diseases like cancer, rare genetic and other conditions could be enhanced in their efficacy, persistence, and predictability by so-called genomic safe harbors (GSHs). These are landing sites in the human genome able to safely accommodate new therapeutic genes without causing other, unintended changes in a cells genome that could pose a risk to patients.

However, finding GSHs with potential for clinical translation has been as difficult as finding a lunar landing site for a spacecraft which has to be in smooth and approachable territory, not too steep and surrounded by large hills or cliffs, provide good visibility, and enable a safe return. A GSH, similarly, needs to be accessible by genome editing technologies, free of physical obstacles like genes and other functional sequences, and allow high, stable, and safe expression of a landed therapeutic gene.

Thus far, only few candidate GSHs have been explored and they all come with certain caveats. Either they are located in genomic regions that are relatively dense with genes, which means that one or several of them could be compromised in their function by a therapeutic gene inserted in their vicinity, or they contain genes with roles in cancer development that could be inadvertently activated. In addition, candidate GSHs have not been analyzed for the presence of regulatory elements that, although not being genes themselves, can regulate the expression of genes from afar, nor whether inserted genes change global gene expression patterns in cells across the entire genome.

Now, a collaboration of researchers at Harvards Wyss Institute for Biologically Inspired Engineering, Harvard Medical School (HMS), and the ETH Zurich in Switzerland, has developed a computational approach to identify GSH sites with significantly higher potential for the safe insertion of therapeutic genes and their durable expression across many cell types. For two out of 2,000 predicted GSH sites, the team provided an in-depth validation with adoptive T cell therapies and in vivo gene therapies for skin diseases in mind. By engineering the identified GSH sites to carry a reporter gene in T cells, and a therapeutic gene in skin cells, respectively, they demonstrated safe and long-lasting expression of the newly introduced genes. The study is published in Cell Reports Methods.

While GSHs could be utilized as universal landing platforms for gene targeting, and thus expedite the clinical development of gene and cell therapies, so far no site of the human genome has been fully validated and all of them are only acceptable for research applications, said Wyss Core Faculty member George Church, Ph.D., a senior author on the study. This makes the collaborative approach that we took toward highly-validated GSHs an important step forward. Together with more effective targeted gene integration tools that we develop in the lab, these GSHs could empower a variety of future clinical translation efforts. Church is a leader of the Wyss Institutes Synthetic Biology Platform, and also the Robert Winthrop Professor of Genetics at HMS and Professor of Health Sciences and Technology at Harvard University and the Massachusetts Institute of Technology (MIT).

The researchers first set up a computational pipeline that allowed them to predict regions in the genome with potential for use as GSHs by harnessing the wealth of available sequencing data from human cell lines and tissues. In this step-by-step whole-genome scan we computationally excluded regions encoding proteins, including proteins that have been involved in the formation of tumors, and regions encoding certain types of RNAs with functions in gene expression and other cellular processes. We also eliminated regions that contain so-called enhancer elements, which activate the expression of genes, often from afar, and regions that comprise the centers and ends of chromosomes to avoid mistakes in the replication and segregation of chromosomes during cell division, said first-author Erik Aznauryan, Ph.D. This left us with around 2,000 candidate loci all to be further investigated for clinical and biotechnological purposes.

Aznauryan started the project as a graduate student with other members of Sai Reddys lab at ETH Zurichs Department of Biosystems Science and Engineering before he visited the Church lab as part of his graduate work, where he teamed up with Wyss Technology Development Fellow Denitsa Milanova, Ph.D. He since has joined Churchs group as a Postdoctoral Fellow. Reddy, senior and lead author of the collaborative study, is an Associate Professor of Systems and Synthetic Immunology at ETH Zurich and focuses on developing new methods in systems and synthetic biology to engineer immune cells for diverse research and clinical applications.

Out of the 2,000 identified GSH sites, the team randomly selected five and investigated them in common human cell lines by inserting reporter genes into each of them using a rapid and efficient CRISPR-Cas9-based genome editing strategy. Two of the GSH sites allowed particularly high expression of the inserted reporter gene in fact, significantly higher than expression levels achieved by the team with the same reporter gene engineered into two earlier-generation GSHs. Importantly, the reporter genes harbored by the two GSH sites did not upregulate any cancer-related genes, said Aznauryan. This also can become possible because regions in the genome distant from one another in the linear DNA sequence of chromosomes, but near in the three-dimensional genome, in which different regions of folded chromosomes touch each other, can become jointly affected when an additional gene is inserted.

To evaluate the two most compelling GSH sites in human cell types with interest for cell and gene therapies, the team investigated them in immune T cells and skin cells, respectively. T cells are used in a number of adoptive cell therapies for the treatment of cancer and autoimmune diseases that could be safer if the receptor-encoding gene was stably inserted into a GSH. Also, skin diseases caused by harmful mutations in genes controlling the function of cells in different skin layers could potentially be cured by insertion and long-term expression of a healthy copy of the mutated gene into a GSH of dividing skin cells that replenish those layers.

We introduced a fluorescent reporter gene into two new GSHs in primary human T cells obtained from blood, and a fully functional LAMB3 gene, an extracellular protein in the skin, into the same GSHs in primary human dermal fibroblasts, and observed long-lasting activity, said Milanova. While these GSHs are uniquely positioned to improve on levels and persistence of gene expression in parent and daughter cells for therapeutics, I am particularly excited about emerging gain-of-function cellular enhancements that could augment the normal function of cells and organs. The safety aspect is then of paramount importance. With an entrepreneurial team at the Wyss, Milanova is developing a platform for genetic rejuvenation and enhancements with a focus on skin rejuvenation.

An extensive sequencing analysis that we undertook in GSH-engineered primary human T cells clearly demonstrated that the insertion has minimal potential for causing tumor-promoting effects, which always is a main concern when genetically modifying cells for therapeutic use, said Reddy. The identification of multiple GSH sites, as we have done here, also supports the potential to build more advanced cellular therapies that use multiple transgenes to program sophisticated cellular responses, this is especially relevant in T cell engineering for cancer immunotherapy.

This collaborative interdisciplinary effort demonstrates the power of integrating computational approaches with genome engineering while maintaining a focus on clinical translation. The identification of GSHs in the human genome will greatly augment future developmental therapeutics efforts focused on the engineering of more effective and safer gene and cellular therapies, said Wyss Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and Boston Childrens Hospital, and Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences.

Reference: Discovery and validation of human genomic safe harbor sites for gene and cell therapies by Erik Aznauryan, Alexander Yermanos, Elvira Kinzina, Anna Devaux, Edo Kapetanovic, Denitsa Milanova, George M. Church and Sai T.Reddy, 14 January 2022, Cell Reports Methods.DOI: 10.1016/j.crmeth.2021.100154

Additional authors on the study are Alexander Yermanos, Ph.D, and Edo Kapetanovic, members of Reddys group; Anna Devaux at the University of Basel, Switzerland; and, Elvira Kinzina at the McGovern Institute for Brain Research at MIT. The study was supported by ETH Research Grants, the Helmut Horten Stiftung and Aging and Longevity-Related Research Fund at HMS, as well as a Genome Engineer Innovation Grant 2019 from Synthego to Aznauryan.

Go here to read the rest:
Landing Therapeutic Genes Safely in the Human Genome Improving Gene and Cell Therapies - SciTechDaily

The Earth Biogenome Project, a global consortium that aims to sequence the genomes of all complex life on Earth (some 1.8 million described species) in 10 years, is ramping up.

The projects origins, aims, and progress are detailed in two multi-authored papers published this week. Once complete, it will forever change the way biological research is done.

Specifically, researchers will no longer be limited to a few model species and will be able to mine the DNA sequence database of any organism that shows interesting characteristics. This new information will help us understand how complex life evolved, how it functions, and how biodiversity can be protected.

The project was first proposed in 2016, and I was privileged to speak at its launch in London in 2018. It is currently in the process of moving from its startup phase to full-scale production.

The aim of phase one is to sequence one genome from every taxonomic family on Earth, some 9,400 of them. By the end of 2022, one-third of these species should be done. Phase two will see the sequencing of a representative from all 180,000 genera, and phase three will mark the completion of all the species.

The grand aim of the Earth Biogenome Project is to sequence the genomes of all 1.8 million described species of complex life on Earth. This includes all plants, animals, fungi, and single-celled organisms with true nuclei (that is, all eukaryotes).

While model organisms like mice, rock cress, fruit flies, and nematodes have been tremendously important in our understanding of gene functions, its a huge advantage to be able to study other species that may work a bit differently.

Many important biological principles came from studying obscure organisms. For instance, genes were famously discovered by Gregor Mendel in peas, and the rules that govern them were discovered in red bread mold.

DNA was discovered first in salmon sperm, and our knowledge of some systems that keep it secure came from research on tardigrades. Chromosomes were first seen in mealworms and sex chromosomes in a beetle (sex chromosome action and evolution has also been explored in fish and platypus). And telomeres, which cap the ends of chromosomes, were discovered in pond scum.

Comparing closely and distantly related species provides tremendous power to discover what genes do and how they are regulated. For instance, in another PNAS paper, coincidentally also published this week, my University of Canberra colleagues and I discovered Australian dragon lizards regulate sex by the chromosome neighborhood of a sex gene, rather than the DNA sequence itself.

Scientists also use species comparisons to trace genes and regulatory systems back to their evolutionary origins, which can reveal astonishing conservation of gene function across nearly a billion years. For instance, the same genes are involved in retinal development in humans and in fruit fly photoreceptors. And the BRCA1 gene that is mutated in breast cancer is responsible for repairing DNA breaks in plants and animals.

The genome of animals is also far more conserved than has been supposed. For instance, several colleagues and I recently demonstrated that animal chromosomes are 684 million years old.

It will be exciting, too, to explore the dark matter of the genome, and reveal how DNA sequences that dont encode proteins can still play a role in genome function and evolution.

Another important aim of the Earth Biogenome Project is conservation genomics. This field uses DNA sequencing to identify threatened species, which includes about 28 percent of the worlds complex organisms, helping us monitor their genetic health and advise on management.

Until recently, sequencing large genomes took years and many millions of dollars. But there have been tremendous technical advances that now make it possible to sequence and assemble large genomes for a few thousand dollars. The entire Earth Biogenome Project will cost less in todays dollars than the Human Genome Project, which was worth about US$3 billion in total.

In the past, researchers would have to identify the order of the four bases chemically on millions of tiny DNA fragments, then paste the entire sequence together again. Today they can register different bases based on their physical properties, or by binding each of the four bases to a different dye. New sequencing methods can scan long molecules of DNA that are tethered in tiny tubes, or squeezed through tiny holes in a membrane.

But why not save time and money by sequencing just key representative species?

Well, the whole point of the Earth Biogenome Project is to exploit the variation between species to make comparisons, and also to capture remarkable innovations in outliers.

There is also the fear of missing out. For instance, if we sequence only 69,999 of the 70,000 species of nematode, we might miss the one that could divulge the secrets of how nematodes can cause diseases in animals and plants.

There are currently 44 affiliated institutions in 22 countries working on the Earth Biogenome Project. There are also 49 affiliated projects, including enormous projects such as the California Conservation Genomics Project, the Bird 10,000 Genomes Project, and UKs Darwin Tree of Life Project, as well as many projects on particular groups such as bats and butterflies.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Image Credit: paulbr75 / 2230 images

Visit link:
Scientists Are Sequencing the Genome of Every Complex Species on Earth - Singularity Hub

Genome Editing Market: Snapshot

Genome editing tools have come a long way from the mid-twentieth century. In 1970s and 1980s, gene targeting was done using largely homologous combination, but was only possible in mice. Since then, the expanding science of genetic analysis and manipulation extended to all types of cells and organisms. Advent of new tools helped scientists achieve targeted DNA double-strand break (DSB) in the chromosome, and is a key pivot on which revenue generation in the genome editing market prospered. New directions for programmable genome editing emerged in the decades of the twenty-first century, expanding the arena.

Request Brochure of Report - https://www.transparencymarketresearch.com/sample/sample.php?flag=B&rep_id=46494

Cutting-edge platforms at various points in time continue to enrich genome editing market. Various classes of nucleases emerged, most notable of which is CRISPR-Cas. Research labs around the world have extensively used the platforms in making DSBs at any target of choice. Aside from this, agricultural sciences and medical sectors make substantial use of zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) in genome editing. Strides made in stem cell therapies, particularly in rectifying an aberrant mutation, have boosted the growth of the genome editing market. Genetic diseases such as muscular dystrophy and sickle cell disease present an incredible revenue prospect in the genome editing market. Ongoing research on novel vectors and non-vector approaches are expected to bolster the outlook of the market.

Request for Analysis of COVID-19 Impact on Genome Editing Market

https://www.transparencymarketresearch.com/sample/sample.php?flag=covid19&rep_id=46494

Genomic editing refers to the strategies and techniques implemented for the modification of target genetic information of any living organism. Genome editing involves gene modification at specific areas through recombinant technology, which increases precision in insertion and decreases cell toxicity. Current advancement in genome editing is based on programmable nucleases. The genome editing market is presently witnessing significant growth due to increase in R&D expenditure, rise in government funding for genomic research, technological advancements, and growth in production of genetically modified crops. Companies have made significant investments in R&D in the past few years to develop cutting-edge technologies, such as, CRISPR and TALEN. For instance, Thermo Fisher Scientific is investing significantly in the development of its CRISPR technology for providing better efficiency and accuracy in research and also to fulfil the unmet demands in research and therapeutics. Cas9 protein and FokI protein have been combined to form a dimeric CRISPR/Cas9 RNA-guided FokI nucleases system, which is expected to have wide range of genome editing applications.

Pre book Genome Editing Market Report at

https://www.transparencymarketresearch.com/checkout.php?rep_id=46494&ltype=S

The genome editing market is growing rapidly due to its application in a large number of areas, such as mutation, therapeutics, and agriculture biotechnology. Genome editing techniques offer large opportunities in crop improvement. However, the real potential of homologous recombination for crop improvement in targeted gene replacement therapy is yet to be realized. Homologous recombination is expected to be used as an effective methodology for crop improvement, which is not possible through transgene addition. Rise in the number of diseases and applications is likely to expand the scope of genome editing in the near future. It includes understanding the role of specific genes and processes of organ specific stem cells, such as, neural stem cells and spermatogonial stem cells. Genome editing has a significant scope to treat genetically affected cells, variety of cancers, and agents of infectious diseases such as viruses, bacteria, parasites, etc. However, genetic alteration of human germline for medicinal purpose has been debated for years. Ethical issues, comprising concern for animal welfare, can arise at all stages of generation and life span of genetically engineered animal.

Read More Information: https://www.transparencymarketresearch.com/genome-editing-market.html

The global genome editing market can be segmented based on technology, application, end-user, and geography. In terms of technology, the genome editing market can be categorized into CRISPR, TALEN, ZFN, and other technologies. Bioinformatics has eased the process of data analysis through various technological applications. On the basis of application, the global genome editing market can be classified cell-line engineering, animal genome engineering, plant genome engineering, and others. Based on end-user, the genome editing market can be segmented into pharmaceutical and biotechnological companies and academic and clinical research organizations. In terms of region, the global genome editing market can be segmented into North America, Europe, Asia Pacific, Latin America, and Middle East & Africa. North America is projected to continue its dominance in the global genome editing market owing to high government funding for research on genetic modification in the region. Asia Pacific is a rapidly growing genome editing market due to rise in investments by key players in the region. Rise in drug discovery and development activities, coupled with increasing government initiatives toward funding small and start-up companies in the biotechnology and life sciences industry, is a major factor expected to drive the genome editing market in North America during the forecast period. Players should invest in the emerging economies and the countries of Asia-Pacific like China, South Korea, Australia, India and Singapore in which the genome editing market is expected to grow at rapid pace in future, due to growing funding in research.

Key players operating in the global genome editing market are CRISPR Therapeutics, Thermo Fisher Scientific, GenScript Corporation, Merck KgaA, Sangamo Therapeutics, Inc., Horizon Discovery Group, Integrated DNA Technologies, New England Biolabs, OriGene Technologies, Lonza Group, and Editas Medicine.

Browse More Trending Reports by Transparency Market Research:

North America Direct to Consumer Laboratory Testing Market :

The widespread diagnostic and serological testing is emerging as one of the key measures to mitigate the COVID-19 pandemic. The increased load on healthcare systems, social distancing, and convenience needs of individuals is anticipated to boost the growth of the North America direct-to-consumer laboratory testing market.

Topical Antibiotics Market :

Topical antibiotics have emerged as a popular drug class for the treatment and management of a range of medical conditions. Among different indications such as the skin, eye, and Bromhidrosis, the use of topical antibiotics to fight bacterial skin infection has witnessed consistent growth over the past few decades a trend that is expected to continue over the upcoming years. Research and development activities around the world are likely to fuel the growth of the global topical antibiotics market, as new topical antibiotics continue to enter the market. While the growing popularity of antiseptics could potentially hinder market growth, the growing awareness pertaining to the benefits of topical antibiotics is anticipated to boost the demand.

About Us

Transparency Market Research is a next-generation market intelligence provider, offering fact-based solutions to business leaders, consultants, and strategy professionals.

Our reports are single-point solutions for businesses to grow, evolve, and mature. Our real-time data collection methods along with ability to track more than one million high growth niche products are aligned with your aims. The detailed and proprietary statistical models used by our analysts offer insights for making right decision in the shortest span of time. For organizations that require specific but comprehensive information we offer customized solutions through ad hoc reports. These requests are delivered with the perfect combination of right sense of fact-oriented problem solving methodologies and leveraging existing data repositories.

TMR believes that unison of solutions for clients-specific problems with right methodology of research is the key to help enterprises reach right decision.

Contact

Mr. Rohit BhiseyTransparency Market Research

State Tower,

90 State Street,

Suite 700,

Albany NY - 12207

United States

USA - Canada Toll Free: 866-552-3453

Email: sales@transparencymarketresearch.com

Website: https://www.transparencymarketresearch.com/

Go here to read the rest:
Genome Editing Market: Rise in drug discovery and development activities to drive the market - BioSpace

DUBLIN, Jan. 24, 2022 /PRNewswire/ -- The "Genomic Cancer Panel and Profiling Markets by Cancer, by Application, by Tissue and by Gene Type with Screening potential Market Size, Forecasting/Analysis, and Executive and Consultant Guides" 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 2021 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.

While Pharmaceutical Companies see the potential to make nearly any therapy viable. The report has data on how test volumes have grown for the biggest players. Find out how this new way of understanding cancer will change cancer diagnostics forever.

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 pulling way out in front and expanding globally. 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.

Key Topics Covered:

1 Market Guides1.1 Cancer Panel Market - Strategic Situation Analysis & COVID Update1.2 Large Comprehensive Cancer Panel Market - Situation Analysis1.3 Guide for Executives, Marketing, Sales and Business Development Staff1.4 Guide for Management Consultants and Investment Advisors1.5 Market Size and Shares - Large Comprehensive

2 Introduction and Market Definition2.1 What are Cancer Gene Panels and Profiling?2.2 The Sequencing Revolution2.3 Market Definition2.3.1 Revenue Market Size2.4 Methodology2.4.1 Authors2.4.2 Sources2.5 A Spending Perspective on Clinical Laboratory Testing2.5.1 An Historical Look at Clinical Testing

3 Market Overview3.1 Players in a Dynamic Market3.1.1 Academic Research Lab3.1.2 Diagnostic Test Developer3.1.3 Instrumentation Supplier3.1.4 Distributor and Reagent Supplier3.1.5 Independent Testing Lab3.1.6 Public National/regional lab3.1.7 Hospital lab3.1.8 Physician Office Labs3.1.9 Audit Body3.1.10 Certification Body3.2 Oncogenomics3.2.1 Carcinogenesis3.2.2 Chromosomes, Genes and Epigenetics3.2.2.1 Chromosomes3.2.2.2 Genes3.2.2.3 Epigenetics3.2.3 Cancer Genes3.2.4 Germline vs Somatic3.2.5 Gene Panels, Single Gene Assays and Multiplexing3.2.6 Genomic Profiling3.2.7 The Comprehensive Assay3.2.8 Changing Clinical Role3.2.9 The Cancer Screening Market Opportunity3.3 Cancer Management vs. Diagnosis3.3.1 The Role of Risk Assessment3.3.2 Diagnosis3.3.3 Managing3.3.4 Monitoring3.4 Phases of Adoption - Looking into The Future3.5 Structure of Industry Plays a Part3.5.1 Hospital Testing Share3.5.2 Economies of Scale3.5.2.1 Hospital vs. Central Lab3.5.3 Physician Office Lab's3.5.4 Physician's and POCT3.6 Currently Available Large Comprehensive Assays3.7 Pricing Profiling vs. Whole Exome (or Genome) Sequencing3.7.1 Medicare Profile Pricing3.7.2 Whole Exome Sequencing

4 Market Trends4.1 Factors Driving Growth4.1.1 Level of Care4.1.2 Companion Dx4.1.3 Immuno-oncology4.1.4 Liability4.1.5 Aging Population4.2 Factors Limiting Growth4.2.1 State of knowledge4.2.2 Genetic Blizzard4.2.3 Protocol Resistance4.2.4 Regulation and coverage4.3 Instrumentation and Automation4.3.1 Instruments Key to Market Share4.3.2 Bioinformatics Plays a Role4.4 Diagnostic Technology Development4.4.1 Next Generation Sequencing Fuels a Revolution4.4.2 Single Cell Genomics Changes the Picture4.4.3 Pharmacogenomics Blurs Diagnosis and Treatment4.4.4 CGES Testing, A Brave New World4.4.5 Biochips/Giant magneto resistance based assay

5 Cancer Panels & Profiles Recent Developments5.1 Recent Developments - Importance and How to Use This Section5.1.1 Importance of These Developments5.1.2 How to Use This Section5.2 Dante Labs Acquires Cambridge Cancer Genomics5.3 Celemics, Strand Partner on Integrated Platform for NGS Analysis5.4 Myriad Genetics Recalibrates Breast Cancer Panel for All Ancestries5.5 Burning Rock Revenues Rise5.6 Caris Life Sciences to Expand Liquid Biopsy Testing5.7 OncoDiag Announces Multiplex Test for Bladder Cancer Recurrence5.8 Intermountain and Myriad Combine Test Offering5.9 Illumina, Geneseeq to Offer Cancer Testing Kits in China5.10 Exact Sciences to Offer End-to-End Cancer Testing5.11 Guardant Health Turns to Tumor Tissue Sequencing5.12 Tempus Inks Oncology Testing Collaboration With Bayer5.13 Biocartis Collaborating With GeneproDx, Endpoint Health on Tests for Idylla Platform5.14 Wales to Routinely Screen Cancer Patients With Yourgene Elucigene Test5.15 Metastatic Cancer Markers Identified in Clinical WGS Study5.16 Stitch Bio Bets on CRISPR Tech5.17 Bayer, LifeLabs Launch Free NTRK Genetic Testing Program5.18 Foundation Medicine Liquid Biopsy Gets FDA Approval for Multiple Companion Dx5.19 Progress, Challenges in Liquid Biopsy Reimbursement5.20 Israeli Startup Curesponse Raises $6M5.21 Invitae, ArcherDX Merge to Advance Precision Oncology Offerings5.22 MD Anderson Precision Oncology Decision Support to Use Philips' Informatics Solution5.23 NeoGenomics, Lilly Oncology Partner for Thyroid Cancer Testing Program5.24 Germline Results Guides Precision Therapy in Advanced Cancer5.25 FDA Clears Cancer Genomic Profiling Kit From Personal Genome Diagnostics5.26 ArcherDX, Premier Collaborate to Evaluate Genomic Sequencing Assay for Cancers5.27 Labs Reporting Cancer Risk Mutations from Tumor Testing5.28 Users Begin Integrating Genomics Data for Clinical Decision Support5.29 Fujitsu Improves Efficiency in Cancer Genomic Medicine5.30 Thermo Fisher's automated sequencer to offer same-day, pan-cancer test results5.31 Universal Genetic Testing for All Breast Cancer Patients5.32 Exact Sciences buys Genomic Health5.33 Multi-Gene Liquid Biopsy Breast Cancer Panel5.34 Thrive to Develop Earlier Detection of Multiple Cancer Types5.35 New Gene Panel Identifies High Risk Prostate Cancer5.36 Guardant Health Liquid Biopsy Test to be Covered by EviCore5.37 Biocept Partnership Offering for Liquid Biopsy Adds Several Key Services5.38 Natera Commercializes Tumor Whole Exome Sequencing from Plasma5.39 Inivata Completes 39.8M Series B Funding Round5.40 Bio-Rad Clinical ddPCR Test, Diagnostic System Get FDA Clearance5.41 CellMax, Medigen Biotech Partner in Colorectal Cancer Clinical Trials5.42 Biodesix Acquires Integrated Diagnostics5.43 Predicine, Kintor Pharmaceuticals Partner on Clinical Trials, CDx

6 Profiles of Key Players6.1 10x Genomics, Inc6.2 Abbott Diagnostics6.3 AccuraGen Inc6.4 Adaptive Biotechnologies6.5 Aethlon Medical6.6 Agena Bioscience, Inc6.7 Agilent/Dako6.8 Anchor Dx6.9 ANGLE plc6.10 ApoCell, Inc.6.11 ArcherDx, Inc6.12 ARUP Laboratories6.13 Asuragen6.14 AVIVA Biosciences6.15 Baylor Miraca Genetics Laboratories6.16 Beckman Coulter Diagnostics6.17 Becton, Dickinson and Company6.18 BGI Genomics Co. Ltd6.19 Bioarray Genetics6.20 Biocartis6.21 Biocept, Inc6.22 Biodesix Inc6.23 BioFluidica6.24 BioGenex6.25 BioIVT6.26 Biolidics Ltd6.27 bioMerieux Diagnostics6.28 Bioneer Corporation6.29 Bio-Rad Laboratories, Inc6.30 Bio-Reference Laboratories6.31 Bio-Techne6.32 Bioview6.33 Bolidics6.34 Boreal Genomics6.35 Bristol-Myers Squibb6.36 Burning Rock6.37 Cancer Genetics6.38 Caris Molecular Diagnostics6.39 Castle Biosciences, Inc.6.40 Celemics6.41 CellMax Life6.42 Cepheid (Danaher)6.43 Charles River Laboratories6.44 Chronix Biomedical6.45 Circulogene6.46 Clinical Genomics6.47 Cynvenio6.48 Cytolumina Technologies Corp6.49 CytoTrack6.50 Datar Cancer Genetics Limited6.51 Diagnologix LLC6.52 Diasorin S.p.A6.53 Enzo Life Sciences, Inc6.54 Epic Sciences6.55 Epigenomics AG6.56 Eurofins Scientific6.57 Exact Sciences6.58 Exosome Diagnostics6.59 Exosome Sciences6.60 Fabric Genomics6.61 Fluidigm Corp6.62 Fluxion Biosciences6.63 Foundation Medicine6.64 Freenome6.65 FUJIFILM Wako Diagnostics6.66 GeneFirst Ltd.6.67 Genetron Holdings6.68 GenomOncology6.69 GILUPI Nanomedizin6.70 Grail, Inc.6.71 Guardant Health6.72 HalioDx6.73 HansaBiomed6.74 HeiScreen6.75 Helomics6.76 Horizon Discovery6.77 HTG Molecular Diagnostics6.78 iCellate6.79 Illumina6.80 Incell Dx6.81 Inivata6.82 Integrated Diagnostics6.83 Invitae Corporation6.84 Invivogen6.85 Invivoscribe6.86 Janssen Diagnostics6.87 MDNA Life SCIENCES, Inc6.88 MDx Health6.89 Menarini Silicon Biosystems6.90 Millipore Sigma6.91 Miltenyi Biotec6.92 MIODx6.93 miR Scientific6.94 Molecular MD6.95 MyCartis6.96 Myriad Genetics/Myriad RBM6.97 NantHealth, Inc.6.98 Natera6.99 NeoGenomics6.100 New Oncology6.101 NGeneBio6.102 Novogene Bioinformatics Technology Co., Ltd.6.103 Oncocyte6.104 OncoDNA6.105 Ortho Clinical Diagnostics6.106 Oxford Nanopore Technologies6.107 Panagene6.108 Perkin Elmer6.109 Personal Genome Diagnostics6.110 Personalis6.111 Precipio6.112 PrecisionMed6.113 Promega6.114 Qiagen Gmbh6.115 Rarecells SAS6.116 RareCyte6.117 Roche Molecular Diagnostics6.118 Screencell6.119 Sense Biodetection6.120 Serametrix6.121 Siemens Healthineers6.122 Silicon Biosystems6.123 simfo GmbH6.124 Singlera Genomics Inc6.125 Singulomics6.126 SkylineDx6.127 Stratos Genomics6.128 Sysmex Inostics6.129 Tempus Labs, Inc6.130 Thermo Fisher Scientific Inc6.131 Thrive Earlier Detection6.132 Todos Medical6.133 Trovagene6.134 Variantyx6.135 Volition6.136 Vortex Biosciences

7 The Global Market for Cancer Gene Panels and Profiles

8 Global Cancer Gene Panels & Profiles Markets - By Type of Cancer

9 Global Cancer Gene Panels & Profiles Markets - By Type of Application

10 Global Cancer Gene Panels & Profiles Markets - By Tissue Type

11 Global Cancer Gene Testing Markets - Germline and Somatic11.1 Global Market Somatic11.1.1 Table Somatic - by Country11.1.2 Chart - Somatic Testing Growth11.2 Global Market Germline11.2.1 Table Germline - by Country11.2.2 Chart - Germline Testing Growth

12 Potential Market Opportunity Sizes12.1 Potential Cancer Screening by Country: Lung, Breast & Colorectal12.2 Potential Cancer Screening by Country: Prostate, Other Cancer & All Cancer12.3 Potential Market Size - Cancer Diagnosis12.4 Potential Market Size - Therapy Selection

13 Appendices

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

Media Contact:

Research and Markets Laura Wood, Senior Manager [emailprotected]

For E.S.T Office Hours Call +1-917-300-0470 For U.S./CAN Toll Free Call +1-800-526-8630 For GMT Office Hours Call +353-1-416-8900

U.S. Fax: 646-607-1904 Fax (outside U.S.): +353-1-481-1716

SOURCE Research and Markets

See the rest here:
Worldwide Genomic Cancer Panel and Profiling Industry to 2024 - Next Generation Sequencing Fuels a Revolution - PRNewswire

Is the pandemic finally looking to burn itself out? While the weeks trailing average of infections recorded daily has risen above 270,000, what stands out for its absence in Indias third wave is a fatality spike. Nearly three weeks in, our official 7-day curve of lives claimed daily by covid has stayed mostly flat under the 400 level. That this waves chief culprit Omicron sickens us far less than Delta, even as it spreads faster, would appear well borne out by the latest numbers. Reason enough to breathe easier and ease up on covid curbs? Not quite, some would argue. No one is safe until everyone is safe, we await confirmation that Omicron has achieved dominance, and as long as Delta lurks in the air, so do mortal risks. After being caught off-guard by last years horrid outbreak, which was identified as a Delta wave only after it had peaked, administrations across the country seem inclined not to take chances on safety this time. Yet, our lack of clarity on the mix of Sars-CoV-2 variants that Indians are exposed to speaks of yet another surveillance let-down. Unless Indian authorities have held genomic findings back, the scope for good data-driven decisions remains as narrow as before. In a country that boasts of sufficient diagnostic and statistical resources, this is odd indeed.

Our efforts at cracking viral gene codes have been tardy all along, but virus identification by genome sequencing was assumed to have got a major boost in late 2020, when India set up its genome consortium Insacog, with 38 government labs jointly charged with studying the pandemics genetic profile. In theory, representative samples drawn periodically from cases across the nation can offer a dynamic and therefore useful map of which strain is on the loose where. In reality, Insacogs reports on our variant break-up have lagged too far behind to be of policy-input help. Its website features monthly data. Omicron was found to be only a sliver last month; Delta, which made up the bulk of cases identified over May, June and July 2021, had been losing share but saw this trend reverse in November and December. As for the third wave that began this January, we remain mostly in the dark. All that has emerged so far is a stray remark on TV by the chief of our vaccine advisory panel more than a fortnight ago about three-fourths of all cases in Delhi, Mumbai and Kolkata being Omicron. Insacog, however, seems to be in silent mode, even as experts demand an update.

Insacogs website says it has sequenced about 91,300 genomes in allless than a tenth of the million-plus done by the update-happy UK that has far fewer people. Indias state-wise tallies show sharp variations, explained by big gaps in viral receipts, the inadequacy of which may have been the key problem. Unless data is valued equally by all stakeholders, it is hard to improve. Sadly, covid statistics remain a touchy topic in some parts, made touchier still by compensation claims having exceeded the official toll vastly in states like Gujarat and Telangana. In related news, Delhi has said it plans to identify the strains that had sickened the capitals deceased. This could reveal a bit about peoples health risk, but would hardly suffice. We also need to step up research on long covid, especially the bugs possible effects on organs other than our lungs. A preliminary paper published recently in the West reports some headway made on the brain fog that some patients experience. In India, wed be glad just to get a clear genomic snapshot.

Subscribe to Mint Newsletters

* Enter a valid email

* Thank you for subscribing to our newsletter.

Never miss a story! Stay connected and informed with Mint. Download our App Now!!

Read the original:
Wanted: A genomic map of our third covid wave - Mint

This article was originally published here

Clin Chim Acta. 2022 Jan 19:S0009-8981(22)00019-5. doi: 10.1016/j.cca.2022.01.010. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Cleidocranial dysplasia (CCD) represents a rare autosomal dominant skeletal dysplasia caused by mutations that induce haploinsufficiency in RUNX2, the important transcription factor of osteoblasts related to bone/cartilage development and maintenance. Clavicular hypoplasia, which involves aberrant tooth/craniofacial bone/skeletal formation, is a feature of classic CCD. RUNX2 mutations can be found in approximately 60-70% of patients with CCD, and around 10% of these mutations are microdeletions. The present paper describes the radiological and clinical characteristics of a 5-year-old girl who showed representative CCD features, including extra teeth, aplasia of clavicles, sloping shoulders, marked calvarial hypomineralization, and osteoporosis.

MATERIALS AND METHODS: We obtained genomic DNA of her family members and performed whole-genome sequencing (WGS) for samples collected from the proband. Quantitative fluorescent PCR (QF-PCR) and specific PCR plus electrophoresis were then performed as validation assays for all participants. In vitro analysis was performed. Luciferase assay for Runx2 transcription activity and evaluation of mRNA levels of Runx2 downstream osteogenic markers were conducted.

RESULTS: WGS identified a 11.38-kb microdeletion in RUNX2 comprising 8-9 exons, which was validated by QF-PCR and specific PCR plus electrophoresis. In vitro experiments confirmed the pathogenicity of this variation.

CONCLUSION: The present study identified a 11.38-kb microdeletion in RUNX2 that causes CCD. The deletion in the PST domain of RUNX2 reduces its transcription activity and reduces osteogenic marker levels, eventually decreasing the differentiation of osteoblasts. These findings clarify the role of the CCD-related mechanism in the development of CCD and suggest that it is important to consider copy number variation for the suspected familial patients early.

PMID:35065050 | DOI:10.1016/j.cca.2022.01.010

See more here:
Genome sequencing identified a novel exonic microdeletion in the RUNX2 gene that causes cleidocranial dysplasia - DocWire News

January 20, 2022

TheDepartment for Environment, Food and Rural Affairs (DEFRA) has announced new legislation to cut red tape for gene editing plant research.

Prof Andrew Thompson, Head of the Cranfield Soil and AgriFood Institute, said:

The older technology of genetic manipulation has allowed us to create plants that use water more efficiently, generating more crop per drop- vital where food production is limited by water availability. Achieving the same goal using novel gene editing approaches in a more permissive regulatory framework will certainly help this and other beneficial traits to be fully exploited for the benefit of farmers, consumers and the environment.

Prof John Dupre, Professor in Philosophy of Science, and Director of Egenis, the Centre for the Study of Life Sciences, University of Exeter, said:

This announcement on genome editing of plants looks like a positive movement forward. Provided, crucially, that a robust regulatory process remains in place and that this is integrated into a general and wide-ranging agricultural strategy, it should open up the possibility of valuable improvements in quantity, quality and environmental impact of crop production.

Professor Robbie Waugh, director of the International Barley Hub, said:

If the response to COVID-19 has sent one important message to the British public, its been to listen to the science.Relaxation of the regulations around gene-edited plants announced today by DEFRA is, I believe, a positive reflection of DEFRA listening to scientific evidence that unequivocally demonstrates that minor genetic changes induced by gene editing are indistinguishable from those that randomly arise in nature all of the time.The big difference is they can be introduced reliably and with incredible precision.For those of us involved in developing strategies to address some of the major challenges facing the planet today, the announcement reflects a progressive and scientifically justifiable decision based on science, and will undoubtedly increase our ability to address these challenges head-on.

Prof Wendy Harwood, Head of the Crop Transformation Group at the John Innes Centre, said:

Genome editing allows us, for the first time, to make small precise changes in a plants existing DNA that mimic changes that could occur naturally. The technique overcomes the random nature and long time-scales associated with older traditional technologies. This means that essential characteristics such as better resilience to climate extremes could be made available more rapidly, helping to ensure a secure food supply. Field trials are an essential part of the process to develop improved crops. The changes announced are welcomed as they will make field trials of genome edited crops easier and less expensive, further speeding up the process of delivering benefits to farmers and consumers.

Prof Martin Warren, Head, Food Innovation and Health Programme, Quadram Institute, said:

Gene editing provides the opportunity to enhance the nutritional quality of plants a really important issue as we embrace more plant-rich diets.

Gene editing represents a very precise way to improve specific qualities such as the accumulation of higher levels of micronutrients, including minerals and vitamins, which are often found in low abundance in crops.

The announcement by Defra is welcomed as it will allow the faster development of such plants, which can be used to tackle key national and global challenges associated with malnutrition.

Dr Brittany Hazard, Group Leader, Quadram Institute, said:

The ability to employ gene editing technology in our research program will provide a substantial opportunity to accelerate the development of staple crops that can deliver health benefits to consumers.

We anticipate that gene editing will allow us to overcome many challenges and lengthy timescales of conventional breeding and rapidly generate wheat with enhanced levels of dietary fibre that could easily be adopted by plant breeders.

Prof Ian A Graham FRS, Director of BioYork and Weston Chair of Biochemical Genetics at the University of York, said:

The Defra Gene Editing Announcement is an exciting prospect for UK agriculture at a time when we need to be urgently responding to the challenges of climate change and biodiversity loss. Deployment of gene editing will enable careful, precision engineering based improvement of existing crops and the development of novel agricultural products in a way that was simply not possible until now. The Governments decision has come not a moment too soon.

Dr Penny Hundleby, Senior Scientist at the John Innes Centre, said:

Defras announcement sends a clear message of support for UK science and the future of our agritech and farming industries. These technologies will help support agrobiodiversity, plant health and our commitment to food security, sustainability and developing crops for a changing climate.

Gene editing, together with access to genome sequencing (where the UK is strong) moves us into an exciting era of affordable, intelligent and precision-based plant breeding. We will also see more products aimed at the convenience / consumer preference markets e.g. more nutrient-dense salads, pitless cherries, naturally decaffeinated coffee etc.

Professor Sophien Kamoun FRS, Group Leader at The Sainsbury Laboratory in Norwich, said:

Genome editing technology can be used to remove genes from crop genomes that make them susceptible to diseases. Researchers at The Sainsbury Laboratory demonstrated this by removing 48 nucleotides from the tomato genome to make it resistant to powdery mildew. Powdery mildew disease is one of the main reasons why UK tomato growers spray fungicides on their crops. The edited tomato, named Tomelo, offers the opportunity to dramatically reduce these chemical inputs with benefits for farmers health and the environment, not to mention reduced production costs. We need to be able to use these innovations if we want to provide enough food for our growing human population without causing further damage to our environment.

Back in 2013, our scientists at The Sainsbury Laboratory were among the very first to develop the CRISPR gene editing tech in plants, a technology that carries so much potential and so many opportunities for world agriculture. Yet, we had to sit back and watch other countries, like the US and Japan, bring their CRISPR bio-edited plants to market. I hope that we can finally capitalize on the world-leading research base we have in this country in plant sciences and help make agriculture more sustainable.

Prof Derek Stewart, director of the James Hutton Institutes Advanced Plant Growth Centre, said:

The relaxation of the regulation of gene-edited crops offers many opportunities to deliver the next generation of crops that will be able to deliver simultaneously to the economic, environmental, biodiversity and net-zero agendas in the UK. To do this, we will need state-of-the-art science and translation facilities such as the Advanced Plant Growth Centre at the James Hutton Institute to create, develop and translate these new crops into the field environment and ensure they are both suitable for purpose and environmentally appropriate.

Prof Ian Crute, former Chief Scientist of AHDB and former Director of Rothamsted Research, said:

After decades of research, plant scientists now better understand the genetic components of crops defences against pests and pathogens. Gene editing provides the logical next-step in applying this knowledge to deliver, more efficiently, pest and disease resistant varieties that can be grown successfully without recourse to the regular use of agrochemicals.

Prof Johnathan Napier, Flagship Leader at Rothamsted Research, said:

This is a really positive development and I am genuinely excited by the opportunities this shift in the classification of genome editing in plants will bring. When I carried out the UKs first field trial of a GE crop in 2018, Defra was of the opinion that our edited Camelina plants were not GM, so it is great to see a return to that position. I strongly believe that genome editing can contribute to making crops to be more nutritious, more sustainable and more resilient, and this change to how field trials are regulated is a welcome first step in liberalising how the UK regulates new genetic technologies like GE and GM. I look forward to being part of this exciting new chapter, one where the UK can better realise its potential as a world leader in plant biotechnology to deliver food security.

Prof Huw Jones, Chair in Translational Genomics for Plant Breeding, Aberystwyth University, said:

Investigating how plants with novel genetic traits behave under field conditions should be a natural part of the experimental process. The use of some modern breeding methods have until now made this transition difficult and hampered applied plant research. I welcome this announcement, which will normalise the lab to field step for innovative breeding via gene editing that has the potential to make food production safer and more sustainable. To ensure a level playing field for research, I urge the Welsh and Scottish authorities to make similar changes.

Prof Lesley Torrance, Executive Director of Science at the James Hutton Institute, said:

We welcome this decision; while it is important to thoroughly scrutinise new breeding technologies to ensure the highest standards for food safety, it is also important that regulations are updated to take account of new information and new developments.This decision reflects this approach and is a step in the right direction by facilitating field trials in relevant environments.Further work is needed to develop the rules around gene-edited crops for commercial release and we look forward to contributing to the next steps to enable new gene-edited crops to be safely released and fulfil their potential for climate resilience and provide healthy, nutritious food while safeguarding the environment.

Prof Nick Talbot FRS, Executive Director of The Sainsbury Laboratory in Norwich, said:

Genome editing provides the opportunity to deliver knowledge-based plant breeding and harness plant biodiversity. We can achieve the outcomes of plant breedingwhich has been so successful in controlling diseases and improving yieldsbut in a much more precise manner. In this way, we can aim to produce nutritious crops requiring much lower fertiliser inputs and with greater resilience. We need innovation to help us escape from the chemical treadmill of current agriculture. In the face of the climate emergency, doing nothing is no longer an option.

Prof Jonathan Jones FRS, Group Leader at The Sainsbury Laboratory in Norwich, said:

I welcome the decision of DEFRA to act on the scientific consensus about the utility and safety of gene editing for crop improvement. Enabling plant breeders to take advantage of these benign and useful methods is essential to increase food production by 50% by 2050, in a warming world, while minimizing agrichemical use.

Im also pleased to see in the DEFRA statement that there are plans to adopt a more scientific and proportionate approach to the regulation of genetic technologies. In our own work, we use the GM method to move immune receptors from one plant to another, increasing the plants capacity to activate its defences quickly enough to thwart disease. The government must not miss the opportunity to facilitate use of this benign and helpful method for reducing the environmental impact of agriculture, and I look forward to seeing this reassessment implemented.

Declared interests

Prof Nick Talbot:Nick is in receipt of funding from The Gatsby Charitable Foundation, The Leverhulme Trust and UKRI (BBSRC and GCRF Funding) and is a Gatsby Plant Science Advisor. He is also a member of the John Innes Governing Council and Board member of PBL Technology.

Prof Jonathan Jones:Professor Jonathan Jones is a senior investigator at The Sainsbury Laboratory in Norwich, and uses molecular and genetic approaches to study disease resistance in plants. Jones co-founded Norfolk Plant Sciences in 2007 with Prof Cathie Martin of JIC, with the goal of bringing flavonoid-enriched tomatoes to market (www.norfolkplantsciences.com). Jones is on the board ofwww.isaaa.org, the science advisory board of the 2Blades foundation (www.2blades.org) and the board of NIAB Cambridge University Farm. Jones has isolated and is deploying new resistance genes against potato late blight from wild relatives of potato, and conducting field trials to evaluate how well they work to protect the crop in the field and to generate improved varieties of potato (seehttp://www.tsl.ac.uk/news/blight-resistant-maris-piper/). See alsohttp://www.tsl.ac.uk/groups/jones-group/.

Dr Penny Hundleby: uses gene editing in crops to better understand the role of plant genes. She is currently on secondment to the Anglian Innovation Partnership as a Science Advisor covering the Norwich Research Park.

Prof Sophien Kamoun: I consult and receive funding from the biotech and plant breeding industry, notably BASF, Limagrain and Rijk Zwaan. Im a member of the Two Blades Foundation Science Advisory Board. My other professional activities and recent research funding are listed athttp://kamounlab.dreamhosters.com/pdfs/SKamoun_CV.pdf.

Prof Johnathan Napier: is currently running both GM and GE field trials at Rothamsted, and last year sowed 600,000 GM camelina plants growing in the field, as part of a project to make a sustainable source of omega-3 fish oils.

Prof Huw Jones:

Direct employment: Aberystwyth University 2016 current; Rothamsted Research 1998 2016.

Other fee-paid work from relevant organisations, consultancies etc.: BBSRC grant review panels 2000 current; FSA ACNFP 2019 current; Expert, GMO panel, European Food Safety Authority 2009 2018. As external examiner of the university PhD viva process, I have sometimes receive a small honorarium in addition to travel and accommodation costs from the university hosting the examination (since 2007 I have been external examiner for ten PhD viva voce examinations in UK and abroad). I have received small payments of royalties from publishers for academic books written or edited.

Membership, affiliation, trusteeships or decision-making position with relevant organisations: Fellow of Royal Society of Biology 2002 current. Honorary Professor, School of Biosciences, Nottingham University 2009 2018. Honorary researcher, Rothamsted Research UK, 2016-2019. Member of the EPSO Plants for the Future. Gene editing working group 2019 current. Chair, UK Plant Sciences Federation Working Group on Regulatory Frameworks 2014-2015. Monogram steering committee, 2011 2015. Member of BBSRC pool of experts, Jan 2017 current.

Other personal interests: I am invited to attend typically between 5 and 10 conferences or other meetings per year where the travel and accommodation (if applicable) are paid for by the host organisations. I have never received a fee to participate in such meetings.

Indirect financial or non-financial support from relevant organisations: I am a member of the IBERS Aberystwyth University research team in receipt of a BBSRC Core Strategic Programme Grant Resilient Crops BBS/E/W/0012843. I am one of four academic supervisors for an Aberystwyth University/Syngenta PhD studentship, using molecular genetics to design sentinel plants for detecting biotic stress, 2017-2020. I am a UK representative of an EU COST Action PlantEd Genome editing in plants a technology with transformative potential 2019 2022. I am a UK representative, working group and management committee member of an EU COST Action iPlanta CA15223. Modifying plants to produce interfering RNA 2017 2020. I led a research project: Smart Labels for GMO foods, Aberystwyth University Transforming Social Science Fund, 1K Jan, 2017. Rothamsted Research was in receipt of funding from BBSRC Tools and Resources Development Fund BB/L017768/1, 2014 2016, HD Jones & K Edwards, Development of specific TALENs for precision engineering in wheat.

Prof Wendy Harwood: I am a member of the Food Standards Agency Advisory Committee on Novel Foods and Processes (ACNFP) but this quotation is in a personal capacity.

None others received.

Follow this link:
expert reaction to new legislation for genome editing in plants, as announced by Defra - Science Media Centre

Genomics, from its inception, has encompassed evolutionary and interspecies comparisons (1), in a tacit acknowledgment that genome sequence is almost meaningless without context. Comparative genomics harnesses evolution to investigate genome function. The second genome sequenced for a free-living organism (Mycoplasma genitalium) was immediately compared to the first (Haemophilus influenzae) (2). The human genome was compared to mouse (3), chicken (4), dog (5), and then 28 mammals simultaneously (6), and recently to 240 mammals (7). The first plant genome, the model organism Arabidopsis thaliana (8), was compared to eight other crucifers (9). Genomic positions that resist change over long periods of time may be essential for survival, and those that accumulate changes unusually quickly in particular lineages may be involved in development and propagation of advantageous phenotypes.

Evolutionary innovations in nonhuman species have already resulted in new therapeutics. Decades before the advent of genomics, the ovarian cancer drug paclitaxel (Taxol) was discovered in the Pacific yew tree, where it protected against pathogens (10). Transcription activator-like effectors, discovered in a plant pathogenic bacterium, led to the development of novel genome editing tools and a new therapeutic for acute lymphoblastic leukemia (11).

Despite this legacy, genomics has increasingly focused on humans (Fig. 1). The United Kingdom Biobank Project (12) and All Of Us Research Program (13) are scaling to millions of humans. Meanwhile, only 4% of animals and 2% of plants have a single representative genome assembly (14). Rather than advocating a shift away from humans, we propose broadening the scope to include more nonhuman data. By removing barriers that silo comparative genomics and human genomics into distinct disciplines, and integrating with nongenomic disciplines, we can transform every species into a model organism and accelerate discovery.

A broader focus is essential to protecting the ecosystems we depend on. Biodiversity is the unrecoverable foundation of comparative genomics. It is being lost at an alarming rate (15). Combining genomic tools with meticulous phenotyping and creative cross-disciplinary collaboration can help address this crisis (16, 17).

Evolution is an unparalleled tool for research. Functionally, it is somewhat analogous to a long-term clinical trial, initiated several billion years ago and enrolling all life on Earth. It includes species with evolutionary trajectories altered by human action, through both accelerated natural selection and experimental selection, creating populations we use as research models (Fig. 2 and SI Appendix, Table S1). As mutations arise, they are evaluated for their effect on survival and reproduction, as eloquently described by Charles Darwin more than 150 y ago:

Different types of study populations have different strengths. Diversity: genetic diversity in populations, ranging from inbred (e.g., laboratory mice) to outbred/highly diverse. Humans (midpoint) are outbred but less diverse than many species. Complexity: genetic complexity of traits; low in the laboratory mouse, with controlled genetic background and environment, and high in humans, where most traits are complex. Phenotyping: ease of collecting phenotype data, ranging from only noninvasive phenotyping in natural environments, to invasive laboratory phenotyping. In humans (midpoint), resources like electronic medical records make it possible, but not easy, to collect detailed phenotypes at scale. Sampling: ease of collecting samples, ranging from only minimally invasive sampling in wild-caught individuals, to populations where euthanasia and tissue collection are feasible. Sample size: number of individuals that can be sampled, ranging from <100 (endangered species or laboratory animals requiring costly care) to millions (humans). Function: potential for functional genomics (epigenomics, cellular and organoid models, genetic engineering, and so forth). In humans, cellular models are well developed, but organism-level experimentation is not possible.

It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life (18).

By comparing genomes within and between species, and connecting genomic variation to changes in cells, organisms, and ecosystems, we access the results of a natural experiment carried out on an unfathomable scale.

Genomic studies that include only humans capture just the last 50,000 y or so of evolution. Even so, naturally occurring human mutations guided the design of safe and effective drugs. Rare coding mutations that cause abnormally low cholesterol inspired the new class of PCSK9 inhibitor drugs (19), which reduce the risk of vascular events without major offsetting adverse events.

Other species routinely exhibit evolutionary adaptations that allow them to tolerate conditions that are disease-causing in humans. Hibernating mammals become obese and insulin-resistant in preparation for hibernation and, while hibernating, lose synaptic connectivity and suffer repeated episodes of ischemia and reperfusion (20). Yet they emerge healthy each spring in a physiological feat that holds clues for treating obesity, neurodegeneration, and heart disease (21).

Traits like hibernation are the outcome of a complex and iterative evolutionary process. Organisms adapt to changes in their environment, and by doing so, change that environment, driving adaptation in other species, and so on, ad infinitum. The substrate for this evolutionary arms race is mutation, both small (single nucleotide) and large-scale (structural variants and polyploidy), and the backdrop is a series of unpredictable natural events that constantly reset the stage. The mass extinction that marked the demise of nonavian dinosaurs opened up ecospace for the diversification of mammals (22) and birds (23) into thousands of species extant today.

The sheer complexity of evolution may encourage a reductionist approach, but this is insufficient. Even when the mechanism of a single variant is known in great detail, its effect in the context of other genome variation can be unpredictable (24). Discovering the emergent properties of complex systems using large datasets is a more powerful approach, as demonstrated in biophysics (25), comparative genomics (7, 26), and human genomics (12).

We are poised to enter a new age of science heralded by new genome-editing technologies (27, 28). Scientists can directly edit DNA to achieve desired outcomes, whether curing heritable diseases, depleting invasive populations, reducing pathogen reservoirs, or engineering crops resilient to environmental stress. Even as we contemplate the role of genetic creators, we cannot yet predict the organismal impact of changing even simple genomes.

To understand how genomic variation shapes organismal variation and function, it is both possible and necessary for research to encompass the full scope of the evolution of life. We can now measure and modify the natural world with unprecedented precision, but researchers pursuing innovative and cross-disciplinary research encounter systemic and logistical barriers. By addressing these challenges, all species can contribute as genetic systems for understanding and protecting our world.

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved (18).

All organisms on Earth share a common origin, each being one of billions of variations on a common theme. Hundreds of genes shared between yeast and humans are so functionally similar that the human version can substitute in yeast (29). Sponge enhancers control cell-typespecific gene expression in zebrafish and mice, lineages that last shared a common ancestor 700 million y ago (30).

If genomes are the source code of life, then the interpretation is an interaction between that code, the cellular machinery that reads it, and the environment in which it is manifested. While a genome sequence may be essential, it is not sufficient to elucidate the complex processes underlying development, growth, differentiation, host defense, environmental responses, and countless other facets of biology. This requires transcriptomic and epigenomic data that vary by cell type and over time, samples from many individuals per species, and many samples per individual (31). It also requires new technology for collecting functional data, phenotypes, and environmental measurements at scale, including epigenomic assays (32), remote sensing [e.g., airborne lidar (33)], thermal and fluorescence imaging (34), passive environmental sampling (35), geographic information system mapping (36), and participatory science (37). Finally, it requires situating genomic change in the evolutionary timeline and in relation to geologic, ecologic, and anthropologic events.

Just as technology for large-scale sequencing transformed genomics, new technologies for large-scale data collection are transforming how we study the natural world. Biology is transitioning from a single-investigator, hypothesis-based endeavor to team-driven, discovery-based science. Collaborations that encompass biology, medicine, computer sciences, and historical sciences, as well as data-driven methods for studying complex systems, can support a more systems-based, and less reductionist, investigation of organisms and ecosystems.

Here, we call for a more Darwinian approach to genomics that considers all forms of life, their interactions, and the natural environment that shaped them. Charles Darwin developed his theory of evolution by natural selection by studying a wide range of species, including insects, plants, arthropods, and vertebrates. The groundbreaking first edition of On the Origin of Species (18) illustrates how a broader perspective enables discoveries not possible when focused on a single species. For scientists today, this requires collaborations that span diverse communities, within and outside of science, and the technology, scale, and skills to address multidimensional questions. Below, we review key discoveries that illustrate the potential of this approach, and propose strategies to support the cross-disciplinary integration essential to success (Box 1).

Perspectives in Comparative Genomics and Evolution Workshop.

In August 2019, three funding agenciesthe National Human Genome Research Institute (NIH), the National Institute of Food and Agriculture (US Department of Agriculture), and the National Science Foundationconvened a 2-d workshop on Perspectives in Comparative Genomics and Evolution, where 120 participants evaluated the state of the field, focusing on commonalities across humans, model organisms (traditional and nontraditional), agricultural and wildlife species, and microbes. For this paper, the authors synthesized common themes, roadblocks, and strategies that emerged from the workshop.

We use the term Darwinian after careful deliberation. For many scientists, Darwins name, more than any other single word, evokes the connection between the processes of evolution and the organisms and ecosystems most beautiful and most wonderful (18) of the natural world. Since its publication, Darwins work has been misused to lend a false veneer of scientific credibility to racist, ableist, and sexist beliefs that continue to cause immeasurable damage. We recognize our obligation to confront this history, and to work to undo the harm it has caused.

Collaboration is essential for expanding the scope of comparative genomics; this requires overcoming traditional barriers separating disciplines and scientists from communities. To reconstruct the historic dispersal of Oryza sativa ssp. japonica, the progenitor of much of our domesticated rice, sequence data for 1,400 strains was insufficient. Combining geographic, environmental, archaeobotanical, and paleoclimate information revealed that rice diversified into temperate and tropical japonica rice during a global cooling event 4,200 y ago, suggesting that further research might find adaptations to changing climates (38).

Collaborations that span ethnic, geographic, and socioeconomic backgrounds improve productivity and data richness (39), but require communication, leadership, open thinking, and appreciation for all participants (40). Particularly when collaborations span fields with different norms, or include remote study locations, success depends on trust and ensuring all participants are acknowledged (41). Funding agencies, journal editors, and academic institutions can encourage collaborations with reward structures that credit all team members(42) . Scientists sequencing the genome of the tuatara, a reptile endemic to New Zealand and the only living member of its order, partnered with Ngtiwai, the Mori iwi (tribe) holding guardianship over the individual tuatara studied (43). Their successful collaboration, recognized with authorship, was guided by common goals of increasing knowledge and supporting conservation, with Ngtiwai participating in data-use and benefit-sharing discussions. People working within Indigenous or traditional knowledge systems can offer information on species behavior, habitats, and conservation issues unfamiliar to scientists working within Western knowledge systems (44). Using DNA barcoding technology, scientists in the Velliangiri Hills of India identified three species of herbaceous plants new to science, but already classified as distinct species in the local traditional knowledge system (45).

Engaging community members directly in research can facilitate collection of large and geographically disparate datasets needed to explore real-world evolutionary processes, while positively impacting communities. Using eBird, a community science project whose participants have collected over 915 million bird observations (46), scientists had sufficient data to assess whether speciation is associated with niche divergence in Aphelocoma jays (47). The spread of the cabbage white butterfly, Pieris rapae, a destructive agricultural pest, was traced using samples collected by over 150 volunteers from 32 countries, which implicated specific human activities as possible drivers (48). Children in India, Kenya, Mexico, and the United States surveyed mammalian biodiversity near their schools using camera traps, collecting high-quality data while learning to value their local natural history (49).

Such research should align with the Convention on Biological Diversity, ensuring local knowledge is included and attributed, that data are correctly interpreted, and that cultural practices are respected (44). All stakeholders, including local communities, should benefit (50). Full partnership with field scientists is vital. Their meticulous observations and careful sample collection, along with the curation and annotation of the specimens in both living and natural history collections, are the keystone of interdisciplinary research.

Our conception of a more collaborative approach to comparative genomics is rooted in the open-data culture of genomics, exemplified by the Human Genome Project (51) and the sometimes controversial (52) shift to team projects that generate and analyze multidimensional datasets (53). Today, genomic data dominate, but other data types are expanding [imaging, personal wearable devices, remote sensing, and electronic medical records (54)]. Resources like the Global Biodiversity Information Facility (GBIF) (55) and the Integrated Digitized Biocollections (iDigBio) provide standards and open-source tools for unifying disparate organismal occurrence data (56). The Genomic Observatories Metadatabase (GEOME) (57) links the Sequence Read Archive (SRA) (58) to ecological data repositories not configured for genomic information.

A single reference genome is rarely sufficient for answering biological questions, but when shared, supports many different studies (53). Historically, researchers were forced to weigh the often considerable cost of generating a reference against the value of other data that could be collected instead. Today, falling costs and new technology are making high-quality reference genomes more achievable (59). The Earth BioGenome Project proposes producing reference genomes for 2 million known eukaryotic species in the next 10 years (60).

High-quality reference genomes can lead to discoveries even in well-studied organisms. Using the highly contiguous genome for the bioenergy crop switchgrass (Panicum virgatum), scientists compared hundreds of plants grown in common gardens spanning 1,800 km of latitude. They discovered genetic variation accumulating on the less constrained subgenome, suggesting a polyploid genome may enhance adaptive potential (36). Comparing high-contiguity genomes for six bat species revealed positive selection at hearing-related genes, suggesting echolocation is an ancestral trait lost in the nonecholocating bats (61).

Data structures that accommodate genetic diversity within species are still under development. The traditional linear genome structure struggles even with human data, introducing pervasive reference biases (62). For species with more genetic diversity, like gorillas and butterflies (63, 64), new representations, like graph-based pangenomes, are essential (65).

With falling sequencing costs, functional genomic assays [e.g., RNA-sequencing, chromatin accessibility assays, Hi-C, PRO-seq, and ribosome profiling (6669)] can capture cellular change over time, by cell and tissue types, and with environment. Comparing the epigenomic landscape in 10 mammalian species using chromatin immunoprecipitation-sequencing uncovered unexpected plasticity in regulatory elements, including switching from promoter to enhancer, and vice versa (70).

Functional genomic assays are essential for investigating mechanisms of action. To pinpoint a variant conferring increased obesity risk in humans, scientists combined long-range chromatin interactions, expression quantitative-trait locus analysis, luciferase reporter assays, and directed perturbations in primary cells (71). Joint analysis with comparative genomic data identified an endogenous retrovirus insertion that encoded an enhancer involved in activating the inflammasome, and may be a pathogen-response adaptation (72).

In more easily manipulated laboratory models, single-cell, single-nucleus, and spatial sequencing methods are revealing the fundamental biology of the cell. By embedding sequence barcodes in fertilized zebrafish eggs, and editing them with each cell division, cell lineages were tracked throughout embryo development and the lineage tree reconstructed (73).

For single-cell organismsincluding bacteria, archaea, and protistssingle-cell genomics captures culture-independent diversity. Single-cell transcriptomics on organisms from the hindgut of wood-feeding termites showed four protist species with distinct roles in wood degradation, suggesting microbiome diversity is essential for termite survival (74).

Cloud-computing resources, which offer massive compute and storage capacity, are essential as sequence datasets grow (75). When cohorts reach half a million, and phenotypes number over 7,000, correlating genotype and phenotype requires millions of CPU hours. Using cloud-based clusters, such jobs are completed in a week (76). Today, the compute time required to align genomes, essential for comparative genomics, scales quadratically with genome size (77), although algorithmic advances could improve efficiency. To make protein structure prediction more accurate and efficient, AlphaFolds neural network-based algorithm predicts energy landscapes rather than calculating binary contact maps (21, 74).

Extending genomics to consider all forms of life requires prioritizing sample collection in challenging environments. Long-read sequencing technology is of little use if the input DNA is fragmented due to sample degradation. Chromatin conformation capture can measure the three-dimensional structure of the genome only if samples have intact nuclei. To measure the response of cells to stimuli, living cell cultures are needed, an expensive and labor-intensive resource to establish (SI Appendix, Fig. S1).

Collecting high-quality samples from species living in regions remote from scientists is particularly challenging. Sampling three highland wild dogs in New Guinea required field biology studies, GPS tagging, video, and collaboration with local scientists, but rediscovered a population of free-living dogs long thought extinct (78). While captive populations may be easier to sample, zoos house representatives of only 12% of the 31,771 terrestrial vertebrate species (79, 80), and botanical gardens capture only a fraction of plant species (81).

The number of samples is sometimes more critical than sample quality, particularly when a high-quality reference genome is available. Pairing samples with metadata, such as collection dates, locations, and phenotypes, makes it possible to evaluate population demography, and identify mutations that can impact fitness. Whole-genome sequencing of century-old gorilla specimens, annotated with collection dates, revealed a drop in genetic diversity associated with increased inbreeding in the critically endangered Grauers gorillas, but not in the mountain gorilla, which did not experience the same population declines (82).

New methods for extracting and analyzing DNA allow samples in less-than-ideal condition to be used. The oldest DNA sequence, recovered from wooly mammoths living in Siberia 1 million y ago, shows that North American mammoths likely descended from a hybridization event, with cold climate adaptations already present (83). By sequencing slow-degrading structural proteins in samples 3.5 million y old, the origin of modern camels was traced to the forested Arctic of the Mid-Pliocene (84). Sequencing can characterize complex mixes of species in paleo-samples. Fossil rodent middens are mixtures of plant and animal remains, collected by foraging rodents ranging 100 m, and preserved for thousands of years. Sequencing them captures the community of plants, animals, bacteria, and fungi at a single location in the past with exquisite resolution (85). Epigenomic profiling of ancient specimens, while technically challenging, could improve predictions of species resilience (86).

Methods developed for old or degraded samples support studies of natural populations where invasive collections are not possible. Methods that enrich host DNA make feces samples, dominated by microbes, more useful (87). DNA extracted from elephant tusks traced samples to their source, helping law enforcement disrupt poaching activities (88).

Portable sequencing technology, deployable in remote locations, could be transformative by eliminating shipping risks and supporting field-based training with local scientists leading environmental efforts (89). In the Ecuadorian Choc rainforest, one of the world's most imperiled biodiversity hotspots, on-site sequencing distinguished species through DNA barcoding (90). In Hawaii, long ribosomal DNA sequencing in the field yielded a phylogeny of 83 spiders that captured the adaptive radiation of the genus Tetragnatha (91).

Genomic, epigenomic, and proteomic assays all require destructive sampling, and this cost should be carefully considered. The scientists who identified the first archaic human from the Denisovan lineage did so by destroying part of a tiny sliver of bone, the only sample available for DNA extraction (92). Their work showed Denisovans were evolutionarily distinct from Neanderthals and modern humans, transforming our understanding of human evolution.

Destructive sampling puts museums in the difficult position of judging which projects are worthy. Genomic data offers a window into the past unattainable through other technology (93). Sequencing of 28 fossils, including 7 from museums, discovered a now-extinct horse genus endemic to North America, adding a branch to the phylogeny of mammals (94). Museums may be reluctant to authorize damage to specimens in their care (95), but collecting genomic data could also mitigate, somewhat, loss of collections in the future. Even minimal genomic data from the 20 million samples lost when Brazils National Museum burned down in 2018 (96) would comprise an unparalleled scientific resource. Further complicating the question, the same sample may yield more information with time. Two years after the first Denisovan paper (92), a subsequent paper described a DNA library preparation method requiring half as much input (97). Guidelines are needed for researchers, museums, and journals to ensure samples are used responsibly, projects are high quality and ethically executed, and that data and specimen information are shared (98).

Collecting, quantifying, and comparing complex phenotypes in diverse species, at scale, is perhaps the greatest challenge in comparative genomics (99). The observable phenotype of an organism reflects the interaction of preprogrammed traits encoded in a genome with its environment, suggesting we could, in theory, predict its structure and function from its genome. To understand how phenotypes evolve, we must compare the same species in differing environments (36), different species with shared traits (100), and outliers with incredible adaptations.

In laboratory models, phenotyping technology is well developed and genomic resources are robust, elevating species such as yeast, fruit fly, nematodes, zebrafish, rat, mouse, Arabidopsis, rice, and others as primary models for fundamental biological questions. Using an experimental design that inverts traditional gene mapping, the International Mouse Phenotyping Consortium disrupted 3,328 genes and produced models for 360 human diseases, including the first for some bleeding disorders and ciliopathies (101). Deeply sequencing 1,504 mutant lines of the model rice cultivar Kitaake (O. sativa ssp. japonica) found 90,000 mutations affecting 58% of genes, including a causal mutation for short-grain rice (102).

Laboratory models are diversifying with the emergence of versatile, species-agnostic gene knockout technology. Making a primate model carrying even one biallelic mutation through breeding is difficult, given long maturation times and low reproduction rates. With CRISPR-based genome editing, multiple variants can be engineered in parallel, producing new models for human polygenic diseases (103). Integrating large DNA constructs into mammalian stem cells allows systematic locus-scale analysis of genome function (104). In the future, editing ancient DNA sequences into living cells could enable paleoepigenomics.

Domesticated species are natural models for linking phenotypes, many from intentional and inadvertent selective breeding, to genomic changes. The phenotypically diverse food cropscabbage, kale, collards, Brussels sprouts, broccoli, and cauliflowerwere developed from a single plant species, Brassica oleracea, primed for a dramatic response to breeding by an ancient whole-genome triplication (105). Strong, recent selective breeding, as in ornamental goldfish (106) and dog breeds (107), leaves distinctive signals around causal variants. Testing for signals of selection in 82 strains of budding yeast connected the unique ability of cheese-making strains to grow quickly on galactose to the replacement of the GAL1, GAL7, and GAL10 genes with orthologs from another species (108).

The very large population sizes and, for commercially relevant traits, rigorous phenotyping in modern commercial livestock make them useful genomic models. One million chickens are vaccinated every hour against an oncogenic herpesvirus using a vaccine repeatedly reformulated for more virulent strains (109), making commercial chicken farms a model for intersecting host genomics, viral evolution, and disease epidemiology. The vaccine prevents severe disease but not transmission, and effectively controls outbreaks (110), reassuring for humans suffering through the COVID-19 pandemic.

In natural populations, genomic studies focused on dissecting the etiology of traits are challenged by the need for large numbers of well-phenotyped samples (111), yet technologies like Google Earth (112) can provide rich new data sources. To detect systems-level patterns in ecological diversity, and the impact of environmental change, researchers paired sequencing of samples collected by community scientists with habitat, bioclimate, soil, topography, and vegetation data (113). To collect tick samples with the geographic, temporal, and image data needed to study pathogen transmission dynamics, scientists used social media to enlist the help of thousands of community scientists (114).

Combining genomic and nongenomic data can identify drivers of disease spread, thereby informing the design of effective interventions. Phylogenomic analysis of 772 complete SARS-CoV-2 genomes, when paired with epidemiology data, showed how superspreader events shaped the course of the COVID-19 pandemic (115).

A perspective that considers all species, rather than focusing on humans or a few familiar models, provides more options for selecting the optimal model for the scientific question at hand (Fig. 2). The protein CD163 was identified as the likely host receptor for the porcine virus PRRSV (116) using cells from African green monkey cells (116), leading to the production of PRRSV-resistant pigs that could save hundreds of millions of dollars per year (117).

After my return to England it appeared to me that collecting all facts which bore in any way on the variation of animals & plants under domestication & nature, some light might perhaps be thrown on the whole subject ( 128).

Darwin developed his theory of natural selection by considering patterns shared across seemingly very different species. His input data were a naturalists observations, but adopting this approach in genomics requires far more complex resources. We must go beyond the obvious (e.g., integrating genetics, bioinformatics, and medicine), and engage with anthropology and other historical sciences, experts using different knowledge systems, and the public. In the process, it is critical to address the systemic racism, sexism, and ableism that has been reinforced by twisted interpretations of Darwins evolutionary theory. Collaborations where each field retains its unique strengths, rather than developing a single perspective, are essential, as are new modalities for communicating across skill sets that are currently domain specific (SI Appendix, Table S1). We suggest six pillars for accomplishing this.

First, we propose that biology is the starting point for developing a common dialogue. In genomics, the work of biologists is too often perceived as the sample-collecting prelude to the main project, but connecting genomic variation to changes in organisms and ecosystems is fundamentally a biological research challenge. Thus, the contribution of biologists, particularly nonmolecular and noncomputational biologists, should be carefully considered and appropriately resourced when setting funding and sample dispersal priorities.

Second, increasing the number of and training for computational biologists is critical. The field is understaffed and underfunded, and those in it struggle with conflicting priorities. We need to recruit computational experts into the biological sciences, and provide the training in biology and biomedicine tailored to their area of interest, ranging from laboratory work to field biology (129).

Third, comprehensive training in computational biology should be a requirement for all fields. While not reducing the need for highly skilled computational biologists, it will enable field and laboratory-based scientists to do crucial initial analyses. Better computational and data literacy, taught as an integral part of science education (130), will facilitate collaborations between those collecting data and those doing much of the analysis. Existing training opportunities [e.g., Data Carpentry workshops (131); weeklong NSF-sponsored Genomics of Diseases of Wildlife courses (132)] should be expanded globally, and more extended programs developed (e.g., embedding in another research group for a semester).

Fourth, training opportunities in science communication should be expanded (133). Genomics is a global science, and as such requires engagement between scientists and nonscientists alike. Education programs that embrace narrative, social learning, digital media, and gamification reach hundreds of thousands of people (134). Ongoing, effective communication between all stakeholders will help ensure that research ultimately benefits public health, sustainable agriculture, and biodiversity conservation.

Fifth, we call for data-sharing with minimal restriction and delay, and adherence to the FAIR (findability, accessibility, interoperability, and reuse of digital assets) data principles (135). The FAIR principles are followed by major genomic consortia including ENCODE (136), FAANG (Functional Annotation of Animal Genomes) (137), the Alliance of Genome Resources (138), and the Genomic Standards Consortium (139). When necessary, we should modify existing data standards to support cross-species comparisons.

Finally, more support for museums, including zoos, aquaria, and botanical gardens, is an absolute necessity (140). Museums are irreplaceable reservoirs of specimens, history, and ideas, and communicate the value of science. They are essential partners in any effort to understand all of the worlds species. Rather than sample providers, we envision museums as something akin to a public library, where information is shared, specimens are protected, and safeguards supporting responsible access are in place.

We stand at the precipice of a new genomic age, with the power to both read and write DNA. Even as therapeutics based on genome editing save lives (141), we grapple with the ethical dilemmas inherent in editing germline cells (142). The most useful guidebook to this brave new world is the evolutionary past, and its constant testing of new variants through natural selection. With the technology to sequence DNA, assay cellular activity, and measure phenotypes at massive scales, we can read the results of that grand experiment.

To understand how genomes shape organisms and ecosystems, we must look outside our own species to all life on Earth. The conceptual foundation is basic evolutionary theory, some of it first described by Charles Darwin, but it requires scale and scope that would have been difficult for the 19th century naturalist to grasp, yet is now achievable. It is incumbent on us to figure out how we use these tools effectively for scientific discovery, for advancing medicine, and for protecting our world.

To illustrate the potential, we return to the Galapagos for a thought experiment with Darwins finches (143). Imagine we could collect genome sequences not just for every bird on those islands, but for all the animals, plants, and microbes interacting with each bird, and imagine we could do so for every generation since the birds first colonized the islands. Our data collection continues to the present day, and we capture the disruption of the Industrial Age, and know the history of geopolitical events. We measure organismal phenotypes, from morphology to health to feeding behavior to reproduction, and record all interactions between species, and changes with each generation, with incredible precision. Finally, we collect detailed data on rainfall, sea and air temperatures, and other meteorological events.

In reality, in-depth monitoring can inflict unacceptable damage on fragile ecosystems, illustrating the need for careful study design, and technology that minimizes harm. Any project so broad in scope raises complicated ethical, legal, and social issues that must be carefully addressed (144). The potential for discovery in such rich datasets, extending far beyond genomics, encapsulates the vision of a more extensive, inclusive, Darwinian approach to genomics.

Read more here:
Darwinian genomics and diversity in the tree of life - pnas.org

British scientists have created a fast, less costly process for genome sequencing each coronavirus case they examine.

Britain is now a world leader in COVID-19 sequencing. This helps public health officials follow the spread of new variants, develop vaccines and decide when restrictions on movement are necessary.

Researchers at the Sanger Institute in Cambridge and other laboratories in Britain have a new mission. They are sharing what they have learned with scientists around the world.

The Omicron variant now spreading in many countries shows the need for worldwide cooperation, said Ewan Harrison. He is a top researcher at Sanger.

Omicron was first found by scientists in southern Africa who quickly informed the world and gave officials time to prepare.

Since dangerous mutations of the virus can happen anywhere, scientists must continually watch its development to protect everyone, Harrison said.

We cant just kind of put a fence around an individual country or parts of the world, because thats just not going to cut it, he said.

Cambridge University Professor Sharon Peacock understood the importance of sequencing the virus early in the pandemic. She knew sequencing would be important to fighting the virus. She received British government money for a national organization of scientists, laboratories and testing centers known as the COVID-19 Genomics UK Consortium.

The consortium is now working to increase knowledge of sequencing around the world. It has built training programs for researchers in developing countries. The programs include planned online classes on information sharing and working with public health officials. The goal is to help researchers build national programs to sequence COVID-19 viruses.

There is inequity in access to sequencing worldwide, the group said, adding that it wants to end the unequal situation.

By sequencing as many cases of the virus as possible, researchers hope to identify variants of concern as quickly as possible. They can then follow their spread and give early warnings to health officials.

Britain has supplied more COVID-19 sequences to researchers around the world than any country other than the United States. It has also sequenced a bigger percentage of its cases than any large nation.

Researchers in Britain have released about 1.68 million sequences, or about 11 percent of reported cases, said GISAID. GISAID is an international organization that works for quick sharing of virus information.

Over the past two years, labs around Britain have refined the process of gathering and studying COVID-19 viruses.

This has helped cut the cost of examining each genome by 50 percent. It has also reduced the time is takes to sequence from three weeks to five days, said the research group Wellcome Sanger.

Increasing sequencing ability is like building a pipeline, said Dr. Eric Topol. He is head of innovative medicine at Scripps Research in San Diego, California. In addition to buying costly sequencing machines, countries need supplies of reactive chemicals for the machines. They also need trained people to do the work and who understand the sequences. They also need systems to share the information quickly.

Meeting those needs has been difficult for many nations, including the U.S. It is even harder for developing nations, Topol said.

Many of these low- and middle-income countries dont have the sequencing capabilities, particularly with any reasonable turnaround time, he said. So, the idea that theres a helping hand there from the Wellcome Center is terrific. We need that.

Virus samples arrive from around the country. Lab assistants carefully prepare the genetic material. It is placed into the sequencing devices that read each samples unique DNA. Scientists then examine the information and compare it with other identified genomes to follow mutations. They want to see how the virus is developing.

Because COVID-19 mutates all the time, it is important to look for new, more dangerous variants that might be resistant to vaccines, Harrison said. This information will help researchers change existing vaccines or create new ones to fight the virus.

Harrison praised South Africa for quickly informing the world about the Omicron variant. But other countries, he said, punished South Africa by restricting travel and harming its economy. All nations must be permitted to publish new variant information without fear of being punished, he said.

Im Susan Shand.

The Associated Press reported this story. Susan Shand adapted it for Learning English.

__________________________________________

genome n. the entire set of genetic instructions found in a cell

sequencing n. a process of finding out the order of the amino acids forming the genetic material of an organism

variant n. something that is different in some way from others of the same kind

mutation n. a permanent change in the genes of an organism

consortium n. a group of people or companies that agree to work together

access n. the ability to get something, enter a place or meet someone

refine v. to improve (something) by making small changes

sample n. a small amount of something that is used to give information about what it was taken from

unique adj. used to say that something or someone is unlike anything or anyone else

We want to hear from you. Write to us in the Comments Section, and visit our Facebook page.

More:
British Labs Supply the World with Genetic Information about COVID-19 - VOA Learning English