Daily Archives: March 20, 2021

An international team led by the IPK Leibniz Institute in Germany and including University of Saskatchewan (USask) researchers has succeeded in completely decoding the genome of rye, despite its large size and complexity.

Rye is a distinctly climate-resistant cereal plant that is of considerable importance for Germany and northeastern Europe. In Canada, most rye is grown in Saskatchewan and Manitoba.

At USask, the research team includes professor Curtis Pozniak, director of USasks Crop Development Centre and Ministry of Agriculture Strategic Research Program Chair in Durum and High-Yield Wheat Breeding and Genetics, plant molecular geneticist Andrew Sharpe, director of Genomics and Bioinformatics at USasks Global Institute for Food Security (GIFS), Sean Walkowiak (Pozniaks former research officer, now research scientist for Canadian Grain Commission), bioinformatics analyst Brook Byrns, and plant sciences emeritus professor Brian Fowler.

Rye is one of the most cold-tolerant cereal crops and can survive the harshest winters typical of the Canadian Prairies, says Pozniak. The genome sequence of rye points to important genes that could be used to enhance the cold tolerance of other important winter crops, including wheat.

The results published today in the journalNature Geneticsare promising for both science and breeding. Rye offers access to a diverse gene pool, not only for rye breeding but also for wheat breeding.

The delivery of the rye genome represents the work of a large and dedicated group of partners across the world, says Sharpe. These results are significant, as they provide a complete genome that is closely related to other grass crop species such as wheat and barley, thus allowing a deeper insight into the evolutionary relationships between them.

All the research data is available to the general public, meaning the extensive genetic diversity of rye can be systematically discovered and used by breeders in a more targeted approach.

The comparatively low economic importance on a global scale, combined with the great complexity of the genome, interfered with rye getting into the focus of the international research community and thus its genome sequence has been revealed only recently, explains professor Nils Stein, lead of the research group Genomics of Genetic Resources at IPKand holder of a joint professorship at the University of Gttingen.

Rye shares a close and long evolutionary history with barley and wheat. However, its role as an important crop is much shorter. While barley and wheat were domesticated about 10,000 years ago in the so-called Fertile Crescent of the Near East, rye initially spread to Northern Europe as a weed growing in barley and wheat fields. Gradually, rye adopted the characteristics of its two big brothers before becoming a purely cultivated species 5,000-6,000 years ago.

There are important biological differences between rye and its two relatives: rye is fertilized through cross-pollination, thus individual genetic traits cannot be fixed as easily as in a self-fertile plant species, and the rye genome is highly complex, which is mainly due to the large number of highly repeated DNA segments.

Knowing the reference sequence makes it easier to transfer positive properties of rye, such as resistances, to wheat without negatively affecting baking properties, for example.

For example, resistance genes from rye can be transferred to wheat through classical cross-breeding, which has already been used repeatedly in the past, says Stein. Sothe significance of our research extends far beyond rye.

The technical prerequisites for sequencing such a complex genome are available today, Stein emphasizes.

The research used homozygous seeds from the plant breeding company KWS SAAT SE & Co. KGaA.

Thenew genome sequence of our inbred line Lo7 is a great technological achievement and an important step forward towards a more comprehensive genetic characterisation of this crop, says Andres Gordillo, lead of rye breeding at KWS.

It will considerably enhance breeding progress and, therefore, the attractiveness of rye. More specific, it will substantially improve our ability to link resistance traits observed in the field with their underlying genes and their location on the rye genome.

Parallel to the work of the international research team led by Stein, Chinese researchers created a reference sequence of a Chinese landrace.

We worked very well with our Chinese colleagues, which ultimately brought great added value for rye breeding and research. We were able to use two different methods to study two very different rye varieties, of which the complete reference sequences are now available, says Stein.With these two studies, rye has caught up with barley and wheat and is in the middle of the genome research era.

Source: University of Saskatchewan

Read the rest here:
USask Scientists Help Find the Key to Decoding Rye Genome - Seed World

New York, March 18, 2021 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "Genome Sequencing Market - Global Outlook and Forecast 2021-2026" - https://www.reportlinker.com/p06036817/?utm_source=GNW

The global market is expected to grow due to the growing number of rare, terminal, and complex diseases, especially cancer. The constant increase in cancer cases is proportionately increasing the number of sequencing-based diagnostics and treatment options in the market. The introduction of single-cell sequencing technology performs advanced sequencing, thereby helping in cell mapping of tumor cells. This technology is widely used in several tumor researches and has been significantly beneficial for developing new diagnostic and anti-tumor treatment methods. The single-cell analysis has become a standard application both in basic and translational research. This technology is widely used in the field of reproductive and embryonic medicine. It can sequence and quantify the whole genome of germ cells and embryonic cells at the single-cell level, thereby helping researchers to understand the occurrence of germ cells.

The following factors are likely to contribute to the growth of the genome sequencing market during the forecast period: Increase in Demand for Single Cell Sequencing Introduction of Portable Genome Sequencing Devices The emergence of Nanopore, Third Generation Genome Sequencing Platform

The study considers the genome sequencing markets present scenario and its market dynamics for the period 2020?2026. It covers a detailed overview of several market growth enablers, restraints, and trends. The report offers both the demand and supply aspects of the market. It profiles and examines leading companies and other prominent ones operating in the market.

Global Genome Sequencing Market Segmentation The global genome sequencing market research report includes a detailed segmentation by product, application, end-user, geography. The steady rise in the sale of high-end consumables in commercial laboratories, research institutes, academic institutes, and large pharma and biotech companies performing a high volume of sequencing-based processes is a significant factor responsible for the growth of consumables. In 2020, the consumables segment accounted for the largest share in the market with 81%. The recurring application of consumables to perform a wide range of sequencing-based studies and diagnostics is another critical factor for high sales for consumables. Moreover, increased preference for array-based genotyping consumables for a wide range of analysis, disease-related mutations, and genetic characteristics associated with cancer research is further expected to increase the demand for consumables during the forecast period. High innovations and the introduction of high throughput advanced technologies are likely to drive the application of sequencing devices. These devices are capable of sequencing million to billion reads in a single run in less time.

New cancer cases are expected to reach 24 million by 2030, which is likely to augur well for oncology genome sequencing growth. As cancer prevalence is growing, the need for effective patient stratification is driving research efforts to identify biomarkers and develop companion diagnostics. Genome sequencing has opened new ways of studying cancer-related conditions. Cancer sequencing using next-generation sequencing (NGS) methods provides more information in less time compared to traditional single-gene and array-based approaches. Hence, NGS technology has the potential to change the future of oncology and deliver personalized medicine. They have revolutionized the diagnosis and treatment of acute myeloid leukemia (AML) with accurate testing, classification, and the ability to take advantage of precision medicine.

The presence of several research institutes and stand-alone genomic laboratories in the US, the UK, Germany, France, and China is a major factor responsible for the growth of genome sequencing devices. To develop personalized and effective new therapies that restore mobility, enhance the quality of life, and improve surgical outcomes for patients with multiple disorders, these centers perform extensive research on sequence structural levels of genomics. Hence, the increased focus on unraveling genetic components of common and complex diseases, including cancer diagnostics, neurological disorders, infectious diseases, and rare childhood disorders, influences the market.

Product Consumables Sequencers & Software Application Oncology Reproductive Health Complex Disease Research Microbial Research Others End-user Academic & Research Institutes Pharma & Biotech Companies Consumer Genomic Service Providers Government & Commercial Laboratories Others

INSIGHTS BY GEOGRAPHY North America and Europe are the largest genome sequencing market across the globe. They are the leading countries to increase the usage of genome sequencing-based healthcare and diagnostics. The US is the largest revenue contributor to the North American market. The advanced healthcare infrastructure and the increased awareness have slowly increased genome sequencing and cell and gene therapies technology penetration. Multiple initiatives for human genome projects in the US have improved patients flow seeking treatment for several terminal and genetic diseases. With advances in technology and the increased demand for personalized treatment, the US genomic sequencing market is poised for growth. The increased awareness among European patients drives the application of personal genome sequencing testing, especially for reproductive health. There is an increased number of consumer genomic service providers in the market.

Geography North America o US o Canada Europe o UK o Germany o France o Italy o Spain APAC o China o India o Japan o South Korea o Australia Latin America o Mexico o Brazil o Argentina Middle East & Africa o Saudi Arabia o Turkey o South Africa o UAE

INSIGHTS BY VENDORS Illumina, Thermo Fisher Scientific, F. Hoffmann-La Roche, BGI, Pacific Biosciences, Oxford Nanopore Technology are the major vendors in the market. The market is competitive and is evolving with the introduction of new technologies in the market. Several companies are developing or commercializing products, expanding their manufacturing facilities, partnering with others in the market. For instance, in 2020, Illumina introduced software for whole-genome analysis to examine rare diseases. Similarly, Thermo Fischer scientific has made a strategic partnership with First genetics JCS to promote NGS in Russia. The Oxford Nanopore technology, nanopore-based sequencing, and Pacbios SMRT technology-based sequencing revolutionize genome sequencing by reducing cost and increasing throughput, attracting end-users to shift from conventional sanger methods to advanced methods in the market.

Prominent Vendors Illumina Thermo Fisher Scientific Oxford Nanopore Technology Pacific Biosciences F. Hoffmann-La Roche BGI

Other Prominent Vendors PerkinElmer Siemens Healthineers Qiagen Macrogen Myriad Intrexon Bioinformatics Biomatters Cytiva 10x Genomics MGI Tech New England Biolabs DNASTAR Beckman Coulter VEROGEN Bio-Rad

KEY QUESTIONS ANSWERED 1. What technological advances are the genome sequencing market observing? 2. What is the growth rate of the genome sequencing market during the forecast period? 3. How the outbreak of the COVID-19 pandemic affect the genome sequencing market? 4. Which regions are likely to hold the largest revenue share during the forecast period? 5. Which end-user segment accounted for the largest market share in 2021?Read the full report: https://www.reportlinker.com/p06036817/?utm_source=GNW

About ReportlinkerReportLinker is an award-winning market research solution. Reportlinker finds and organizes the latest industry data so you get all the market research you need - instantly, in one place.

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Originally posted here:
The global genome sequencing market by revenue is expected to grow at a CAGR of over 9% during the period 20212026 - GlobeNewswire

SAN RAMON, Calif., March 17, 2021 /PRNewswire/ -- WANdisco, the LiveData company, announced today that it donated its LiveData Platform to help Korea Research Institute of Bioscience & Biotechnology conduct faster analysis in its efforts towards Covid-19 research. Using the automated data migration and replication platform, the institute has been able to replicate files between Hadoop-based big data clusters and Linux-based analysis clusters 13 times faster than before, and reduce analysis time by over 30 percent.

In early 2020, WANdisco announced free access to their suite of cloud migration and big data tools for teams involved in research and developing potential treatments and cures for the Covid-19 pandemic. WANdisco provided its LiveData Platform along with technical resources to Korean Bioinformation Center (KOBIC)to assist the organization in enhancing its architecture, developing products, and introducing WANdisco's automated replication technology into KOBIC's workflow.

"Donating our LiveData platform to the Covid-19 research was absolutely the right thing to do," said David Richards, Chairman and CEO, WANdisco. "Every minute, new data is being generated about people suffering from Covid-19. Velocity has become more important than anything else in the development of vaccines and treatments to overcome infectious diseases. We were grateful for the opportunity to assist Korea accelerate its Covid-19 research and analysis."

KOBICprovides Bio-Express, a cloud service free to bio-engineering researchers at Korean hospitals, businesses, universities, and research institutes for large-capacity genome analysis and storage. Since March 2020, the platform's Covid-19 research information portalhas provided Covid-19-related genomes and proteomic data from around the world. As the amount of data and users skyrocketed last year, so did the time to replicate terabytes of data between the Hadoop Distributed File System (HDFS) and the Linux/Unix based Lustre file system to support the analysis tools within different operating environments. More than 40 percent of Bio-Express's total processing time was solely dedicated to replicate an average of 20TB of data per day.

Upon hearing about Korea's data replication challenges, WANdisco donated its LiveData Platform to reduce large-scale data replication time while ensuring data availability and consistency to researchers. KOBIC administrators could easily and immediately move HDFS data to Bio-Express with automated migration and replication capabilities. No changes were required to applications, cluster or node configuration or operation while ensuring data changes were replicated completely and consistently.

With this new capacity, KOBIC expects to significantly increase the next generation of Bio-Express's efficiency to perform large-scale genome analysis in 2021. WANdisco has since provided KOBIC with an ongoing license to LiveData Platform alongside technical support to help enhance its architecture, developing products, and applying automated replication into the workflow.

"KOBIC uses the WANdisco live data platform to automate file transfer 13 times faster in both directions between Hadoop-based Big Data Analysis Program Execution Cluster (HDFS) and Linux-based Genomic Analysis Program Execution Cluster (Lustre)," said Kun-Hwan Ko, Researcher at KOBIC Computational Development Team. "We were able to reduce the overall average time to analyze user genomic data of Bio-Express service by more than 30 percent."

About WANdisco

WANdisco is the LiveData company. WANdisco solutions enable enterprises to create an environment where data is always available, accurate and protected, creating a strong backbone for their IT infrastructure and a bedrock for running consistent, accurate machine learning applications. With zero downtime and zero data loss, WANdisco LiveData Platform keeps geographically dispersed data at any scale consistent between on-premises and cloud environments allowing businesses to operate seamlessly in a hybrid or multi-cloud environment. For more information on WANdisco, visit http://www.wandisco.com.

About KOBIC

The Korea Bioinformation Center (KOBIC) is a national bio-resource information center for general management of domestic bio-resource information and research in the field of bioinformation. KOBIC helps domestic research institutes, hospitals, companies, and universities to research genomic data and Covid-19 for free. One of KOBIC's main missions is to develop and operate a system that can analyze large-scale genomic data using the state-of-the-art information technology.

Media Contact:

Josh TurnerSilicon Valley Communications[emailprotected]+1 (917) 231-0550

SOURCE WANdisco

Originally posted here:
WANdisco grants industry leading LiveData Platform to fast-track high-volume genome analysis and Covid-19 research in South Korea - PRNewswire

NEW DELHI: As the total number of covid-19 cases caused by mutant variants of coronavirus mounted to 400, centre on Friday, the Centre asked states to follow up on sending samples for genome testing to track circulating virus variants of concern.

All states and Union territories have been tagged to 10 national laboratories under the Indian SARS-CoV-2 Genomics (INSACOG) consortium with National Centre for Disease Control (NCDC) as the nodal institute, the Union health ministry said. The Indian government has recently confirmed circulation of UK, South Africa and Brazil mutant variants of coronavirus in the country.

Also Read | Vaccine utilization rates lower in states witnessing second wave

Public health experts have said that as the mutant strains continue to increase the disease burden, the government needs to look at the diagnostics more closely. Analysing power as well as the density of sequencing ability will be important for India. We need to update our regulatory processes as well for the same and these modifications can be quickly brought to fruition. The US FDA guidelines have provided a relatively easy guideline for achieving the same. Countries need to be alert and create diagnostic kits for the future depending on the presence of mutations," said professor N.K. Ganguly, president, Jawaharlal Institute of Post Graduate Medical Education and Research, and former director general of the Indian Council of Medical Research (ICMR). Ganguly suggested that booster shots in the existing vaccines can be given to neutralise the effects of mutations alongside a few other vaccines.

The Centre has also advised states/UTs to improve testing in districts reporting reduction in testing and increase the overall share of RT-PCR tests (more than 70%), especially in districts dependent on high levels of antigen testing in line with the Test Track & Treat strategy of the government.

While the covid-19 vaccination is progressing in the country administering over 40 million doses to immunise people against the highly infectious disease, Indias covid-19 burden continues to increase. According to the Union health ministry data, some states in the country are reporting a surge in the daily new covid-19 cases. Maharashtra, Punjab, Karnataka, Gujarat and Chhattisgarh together account 80.63% of the daily new cases.

Over 39,726 new daily cases were reported in the last 24 hours, the highest this year. Maharashtra continues to report the highest daily new cases at 25,833, 65% of the daily cases. It is followed by Punjab with 2,369 cases, while Kerala reported 1,899 new cases. The country also recorded over 156 deaths.

Indias total active caseload stood at 2.71 lakh (2,71,282) on Friday, 2.82% of the total positive cases in the country. This is a net incline of 18,918 cases recorded from the total active caseload in the last 24 hours, the government data showed. Three states of Maharashtra, Kerala and Punjab account for 76.48% of Indias total active cases.

Meanwhile, the Central government has also advised states and UTs to carry out an average close contact tracing of a minimum of 20 persons per positive case (in the first 72 hours) along with isolation and early treatment of the serious cases as per clinical protocol. It is also advised to focus on surveillance and stringent containment of those areas in selected districts which are seeing a cluster of cases and focus on clinical management in districts reporting higher deaths," the Union health ministry said in a statement.

States/UTs have been asked to limit the gathering in public places along with promoting covid-appropriate behaviour through communication and enforcement, and accelerate vaccination for priority population groups in districts reporting higher cases. Accelerating the pace of vaccination has also been stressed upon, the Central government said.

Recently, the Centre had deputed high-level public health teams to Maharashtra and Punjab to assist in covid-19 control and containment measures in view of the recent spike in cases in these states.

The Centre had earlier deputed high-level teams to Maharashtra, Kerala, Chhattisgarh, Madhya Pradesh, Gujarat, Punjab, Karnataka, Tamil Nadu, West Bengal, as well as Jammu and Kashmir to support them in their fight against the recent spike in covid-19 cases.

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Centre asks states to focus on genome testing to track mutated virus - Mint

Dublin, March 15, 2021 (GLOBE NEWSWIRE) -- The "North America Digital Genome Market 2021-2028" report has been added to ResearchAndMarkets.com's offering.

North America market for digital genome is expected to rise with a CAGR of 9.75%

The United States dominates North America's genome editing market. The high rate of adoption of advanced technology, the presence of big industry names, high funds for genomic research are all factors attributable to the major share of the country in this market.

Further, extensive research activities in genomics, gene editing, cell line culture, and modification are being conducted, which is boosting the market growth in the US. Several globally-renowned manufacturers of DNA sequencing technologies, equipment, and platforms are active in the US.

For instance, several prominent names in the DNA sequencing industry, such as Thermo Fisher Scientific, Illumina, and others have their corporate presence in the nation, and the enhanced adoption of DNA sequencing has led to a rise in the creation of genomic databases like Ensembl Human Genome Server, UCSC Human Genome Browser Gateway, and others. These factors are projected to drive the digital genome market in the US.

In addition, factors like growing awareness of DNA sequencing, and its applications in different fields, including personalized medicine, clinical diseases, agri-genomics, and others, are contributing to market progress.

COMPETITIVE OUTLOOK

Some of the companies present in this market include Oxford Nanopore Technologies Ltd, Inscripta, Agilent Technologies Inc., Bio-Rad Laboratories Inc., Becton Dickinson and Company (BD), Pacific Bioscience, and Abbott Laboratories.

Key Topics Covered:

1. North America Digital Genome Market - Summary

2. Industry Outlook2.1. Porter's Five Forces Model2.2. Impact of Covid-19 on Digital Genome Market2.3. Market Attractiveness Index2.4. Vendor Landscape2.5. Key Insights2.6. Key Drivers2.6.1. Proliferating Burden of Chronic Diseases2.6.2. Continuous Funding by the Manufacturers and Government in the Field of Genomics2.7. Key Restraints2.7.1. Security Risks Associated With Digital Genome2.7.2. Lack of Skilled Professionals in the Field of Genome Technology2.8. Key Opportunities2.8.1. Technological Advancements2.8.2. Prevailing Awareness in the Developing Economies Regarding Dna Sequencing Technologies

3. Digital Genome Market Outlook - by Product3.1. Sequencing and Analyzer Instruments3.2. Dna/Rna Analysis3.3. Sequencing and Analysis Software3.4. Sequencing Chips3.5. Sample Prep Instruments

4. Digital Genome Market Outlook - by Application4.1. Diagnostics4.2. Drug Discovery4.3. Academic Research4.4. Personalized Medicine4.5. Agricultural4.6. Other Applications

5. Digital Genome Market Outlook - by End-User5.1. Diagnostics and Forensic Labs5.2. Academic Research Institutes5.3. Hospitals5.4. Other End-Users

6. Digital Genome Market - North America6.1. Country Analysis6.1.1. The United States6.1.2. Canada

7. Company Profile7.1. Qiagen Nv7.2. Oxford Nanopore Technologies Ltd7.3. Becton, Dickinson, and Company (Bd)7.4. Illumina Inc7.5. Thermo Fisher Scientific Inc7.6. Pacific Bioscience7.7. Bio-Rad Laboratories Inc7.8. F. Hoffmann-La Roche7.9. Perkinelmer Inc7.10. Regeneron Pharmaceuticals7.11. Biomerieux Sa7.12. Abbott Laboratories7.13. Agilent Technologies Inc.7.14. Inscripta

8. Research Methodology & Scope

Companies Mentioned

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

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North America Digital Genome Market Report 2021: Continuous Funding by the Manufacturers and Government in the Field of Genomics - Forecast to 2028 -...

BMC Med Genomics. 2021 Mar 18;14(1):84. doi: 10.1186/s12920-021-00907-0.

ABSTRACT

BACKGROUND: Recent studies have identified susceptibility genes of HBV clearance, chronic hepatitis B, liver cirrhosis, hepatocellular carcinoma, and showed the host genetic factors play an important role in these HBV-related outcomes.

METHODS: Collected samples from different outcomes of HBV infection and performed genotyping by Affymetrix 500 k SNP Array. GCTA tool, PLINK, and Bonferroni method were applied for analysis of genotyping and disease progression. ANOVA was used to evaluate the significance of the association between biomarkers and genotypes in healthy controls. PoMo, FST, Vcftools and Rehh package were used for building the racial tree and population analysis. FST statistics accesses 0.15 was used as a threshold to detect the signature of selection.

RESULTS: There are 1031 participants passed quality control from 1104 participants, including 275 HBV clearance, 92 asymptomatic persistence infection (ASPI), 93 chronic hepatitis B (CHB), 188 HBV-related decompensated cirrhosis (DC), 214 HBV-related hepatocellular carcinoma (HCC) and 169 healthy controls (HC). In the case-control study, one novel locus significantly associated with CHB (SNP: rs1264473, Gene: GRHL2, P = 1.57 10-6) and HCC (SNP: rs2833856, Gene: EVA1C, P = 1.62 10-6; SNP: rs4661093, Gene: ETV3, P = 2.26 10-6). In the trend study across progressive stages post HBV infection, one novel locus (SNP: rs1537862, Gene: LACE1, P = 1.85 10-6), and three MHC loci (HLA-DRB1, HLA-DPB1, HLA-DPA2) showed significant increased progressive risk from ASPI to CHB. Underlying the evolutionary study of HBV-related genes in public database, the derived allele of two HBV clearance related loci, rs3077 and rs9277542, are under strong selection in European population.

CONCLUSIONS: In this study, we identified several novel candidate genes associated with individual HBV infectious outcomes, progressive stages, and liver enzymes. Two SNPs that show selective significance (HLA-DPA1, HLA-DPB1) in non-East Asian (European, American, South Asian) versus East Asian, indicating that host genetic factors contribute to the ethnic disparities of susceptibility of HBV infection. Taken together, these findings provided a new insight into the role of host genetic factors in HBV related outcomes and progression.

PMID:33736632 | DOI:10.1186/s12920-021-00907-0

Link:
Genome-wide association study identifies new loci associated with risk of HBV infection and disease progression - DocWire News

(Reuters) Regularboostervaccinesagainst the novel coronavirus will be needed because of mutations that make it more transmissible and better able to evade human immunity, the head of Britains effort to sequence the viruss genomes told Reuters.

The novel coronavirus, which has killed 2.65 million people globally since it emerged in China in late 2019, mutates around once every two weeks, slower than influenza or HIV, but enough to require tweaks tovaccines.

Sharon Peacock, who heads COVID-19 Genomics UK (COG-UK) which has sequenced nearly half of all the novel coronavirus genomes so far mapped globally, said international cooperation was needed in the cat and mouse battle with the virus.

We have to appreciate that we were always going to have to haveboosterdoses; immunity to coronavirus doesnt last forever, Peacock told Reuters at the non-profit Wellcome Sanger Institutes 55-acre campus outside Cambridge.

We already are tweaking thevaccinesto deal with what the virus is doing in terms of evolution so there are variants arising that have a combination of increased transmissibility and an ability to partially evade our immune response, she said.

Peacock said she was confidentregularboostershots such as for influenza would be needed to deal with future variants but that the speed of vaccine innovation meant those shots could be developed at pace and rolled out to the population.

COG-UK was set up by Peacock, a professor at Cambridge, exactly a year ago with the help of the Britishs governments chief scientific adviser, Patrick Vallance, as the virus spread across the globe to Britain.

The consortium of public health and academic institutions is now the worlds deepest pool of knowledge about the viruss genetics: At sites across Britain, it has sequenced 349,205 genomes of the virus out of a global effort of around 778,000 genomes.

On the intellectual frontline at the Wellcome Sanger Institute, hundreds of scientists many with PhDs, many working on a voluntary basis and some listening to heavy metal or electronic beats work seven days a week to map the viruss growing family tree for patterns of concern.

Wellcome Sanger Institute has sequenced over half of the UK total sequenced genomes of the virus after processing 19 million samples from PCR tests in a year. COG-UK is sequencing around 30,000 genomes per week more than the UK used to do in a year.

Three main coronavirus variants which were first identified in Britain (known as B.1.1.7), Brazil (known as P1)and South Africa (known as B.1.351) are under particular scrutiny.

Peacock said she was most worried about B.1.351.

It is more transmissible, but it also has a change in a gene mutation, which we refer to as E484K, which is associated with reduced immunity so our immunity is reduced against that virus, Peacock said.

With 120 million cases of COVID-19 around the world, it is getting hard to keep track of all the alphabet soup of variants, so Peacocks teams are thinking in terms of constellations of mutations.

So a constellation of mutations would be like a leaderboard if you like which mutations in the genome that were particularly concerned about, the E484K is must be one of the top of the leaderboard, she said.

So were developing our thinking around that leaderboard to think, regardless of the background and lineage, about what mutations or constellation of mutations are going to be important biologically and different combinations that may have slightly different biological effects.

Peacock, though, warned of humility in the face of a virus that has brought so much death and economic destruction.

One of the things that the virus has taught me is that I can be wrong quiteregularly I have to be quite humble in the face of a virus that we know very little about still, she said.

There may be a variant out there that we havent even discovered yet.

There will, though, be future pandemics.

I think its inevitable that we will have another virus emerge that is of concern. What I hope is that having learned what we have in this global pandemic, that we will be better prepared to detect it and contain it.

Reporting by Guy Faulconbridge; Editing by Kate Holton and Philippa Fletcher 2021 Thomson Reuters.

Originally posted here:
Regular booster vaccines are the future in battle with COVID-19, top genome expert says - WREG NewsChannel 3

CAMBRIDGE, England--(BUSINESS WIRE)--Please replace the release dated March 16, 2021 with the following corrected version due to multiple revisions.

The updated release reads:

ONCOLOGICA IS THE FIRST UK GENOMIC TESTING LAB TO BE GOVERNMENT APPROVED FOR DAY 2 AND DAY 8 TESTING

Oncologica, the world-leading cancer medicine and Covid-19 genomic sequencing laboratory is pleased to announce that its Cambridge based testing laboratory is now the first UK laboratory to receive approval by UKAS and the Department of Health and Social Care (DHSC) to perform Covid PCR testing requirements for day 2 and day 8 as part of the new requirements for Covid International travel certification.

The high throughput laboratory which can process up-to 40,000 Covid-19 tests per day, has undergone a rigorous audit process by the DHSC and UKAS inspectors of its Oncology and Covid-19 PCR genomic testing processes for their personalized cancer medicine and Covid-19 PCR testing /viral genomic sequencing services. These testing capabilities will expedite the UKs return to work and mitigate the risk of superspreading Covid-19 variants in the population. Their state-of-the-art precision cancer medicine genomic profiling services are providing cancer patients with new therapeutic opportunities should standard treatment protocols such as chemotherapy prove inadequate.

Assessments were made of the laboratorys patient sample collection process, interpretation of results methodologies, turnaround times, as well as an inspection of how the company educates and trains its medical laboratory scientists and clinicians and how the organization communicates and consults with health care professionals.

As of February 15th, 2021, all international travellers to the UK from red list countries are required to quarantine for 10 days and undergo a polymerase chain reaction (PCR) Covid-19 test, this is the gold standard for coronavirus detection. On days 2 and 8, if the traveller tests positive, then the sample must be sent to a government-approved lab for genomic sequencing. This is to alert health professionals to potential superspreading coronavirus variants e.g., the UK Kent, Brazilian and South African variants

It is an honour to be the first UK laboratory Covid PCR test and release provider to achieve accreditation for our Covid-19 International travel testing service. At Oncologica, we are committed to achieving and maintaining the highest standard of quality and service in all aspects of our laboratory testing, said Dr Marco Loddo, Co-Founder and Scientific Director at Oncologica.

This commitment is underpinned by the hard work of our entire quality, bioscience and administration teams which has resulted in our achieving this approval.

We are immensely proud of Oncologica achieving government approval as the first UK genomic testing laboratory in the UK to be put on the Governments provider list to undertake day 2 and day 8 Covid-19 PCR testing for travel which is no mean feat. said Professor Gareth Williams, Co-Founder and Medical Director at Oncologica.

We are committed to providing a first-class genetic testing service to all of our clinical partners, patients, business community and the general public, and we demonstrate the highest quality standards whether it is for improving cancer treatment opportunities for patients or for Covid-19 testing across the community. Covid-19 testing is presently being undertaken for businesses, offices, factories, educational institutions, and transport networks facilitating a safe return to work and enabling people to travel."

On receipt of our Coronafocus self-sampling PCR kits, we extract the RNA genetic material out of the sample and copy it into DNA. Now if the virus is there, it is in a DNA form. We put it into a PCR reaction (Polymerase Chain Reaction) and take short snippets of DNA and match these to the virus DNA. If we find the virus DNA, we start a chemical reaction that copies the virus again and again, so that we have lots of copies. We then look at the sample copies. If there is no reaction, then no virus is detected. The Oncologica Covid-19 PCR test is very sensitive and specific. If the Oncologica test finds it, you can believe it.

We understand the importance of our medical genomic laboratory to patient care. Therefore, for those who use our Oncofocus cancer and Coronafocus Covid PCR tests, this accreditation will give added assurance that their testing requirements will be performed to the highest standards for rapid and accurate results, added Dr. Marco Loddo. Read more at https://covid19.oncologica.com/coronafocus-day2-day8/

About Oncologica

Oncologica is a world leading precision cancer medicine and Covid-19 testing and genomic sequencing laboratory based in Cambridge, UK. Our personalised cancer DNA profiling is used to precisely identify the most appropriate clinical targeted therapies and/or immunotherapies which can be used to treat patients as an alternative to chemotherapy.

Our molecular Next Generation Sequencing capabilities are used to sequence tumour DNA and to also sequence Covid-19/ SARS-CoV-2 for virus mutations. SARS-CoV-2 testing, and sequencing is being used to identify high risk Covid-19 variants which can potentially bypass the vaccine. Oncologicas comprehensive NGS DNA profiling covering 505 genes with linkage to over 750 targeted therapies provide patients and clinicians with detailed genomic blueprints that optimize therapy choices, improve outcomes, and helps avoid treatment with drugs unlikely to be of benefit.

Oncologica also undertakes Contract Research supporting biomarker development programmes, clinical trials, and the validation of new diagnostic testing platforms. Our in-house R&D activities focus on the development of novel cancer genomic based diagnostic and therapeutic approaches directed at specific tumour gene mutations or aberrant cancer pathways.

Our government approved Oncofocus and Coronofocus laboratory tests are used by state healthcare providers and the private sector including businesses, factories, healthcare providers, transport, and educational institutions. Personalised genomic data is helping to empower patients and clinicians to increase treatment efficacy and improve human health.

Oncologica UK Ltd, Suite 2, The Newnham Building, Chesterford Research Park, CAMBRIDGE UK CB10 1XL

http://www.oncologica.com

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CORRECTING and REPLACING Oncologica is the First UK Genomic Testing Lab to Be Government Approved for Day 2 and Day 8 Testing - Business Wire

Written by MAYURA JANWALKAR, Edited by Explained Desk | Panaji | Updated: March 16, 2021 1:39:45 pm

A 30-member team of scientists and researchers from the National Institute of Oceanography (NIO) in Panaji and another 30 crew members onboard its research vessel Sindhu Sadhana will spend the next three months traversing the course of over 10,000 nautical miles in the Indian Ocean on a research project to reveal the internal working of the body of the ocean at a cellular level.

The first-of-its-kind research project in the country is aimed at understanding the biochemistry and the response of the ocean to climate change, nutrient stress and increasing pollution. Conceptualised over the last two to three years, the research project has been undertaken at a cost of Rs 25 crore and will take three years to complete, NIO Director Sunil Kumar Singh said.

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The research project that will be flagged off at Visakhapatnam on Thursday will see the team of 30 scientists and researchers including six women course the Indian Ocean from Indias east coast, all the way to Australia, then onward towards Port Louis in Mauritius and up to the border of Pakistan, off Indias west coast, gathering samples for genome mapping of microorganisms in the Indian Ocean. The researchers will collect samples from various stretches of the ocean at an average depth of about 5 km.

Just like gene mapping is carried out on blood samples collected from humans, the scientists will map these in the bacteria, microbes found in the ocean. The mapping of the Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) will show the nutrients present in them, and also those lacking in different parts of the ocean.

NIO Director Sunil Kumar Singh explained that this will help scientists understand the internal working of the ecosystem of the Indian Ocean. The research will enable scientists to identify the factors controlling the changes in RNA, DNA in the oceans, and various stressors impacting them. The ocean has several micronutrients like nitrates, sulphates and silicates, minerals like iron ore and zinc, and trace metals like cadmium or copper. The genome mapping will show the presence of which these microbes have adapted to, in addition to their reaction to atmospheric carbon dioxide. This will help in identifying which part of the ocean has a greater concentration of which mineral or element.

Scientists will then use these as tracers to tackle the causative factors for excess or lack of a certain mineral or element and suggest possible solutions for their mitigation. In addition, the large pool of RNA, DNA library of the oceans will be utilised for using the Indian Ocean to human benefit in the future.

According to the NIO, rapid advances in sequencing technologies and bioinformatics have enabled exploration of the ocean genome. Exploring the ocean genome will enable an increase in the growing number of commercial biotechnology applications, extending from multiple anticancer treatments to cosmetics and industrial enzymes, to antiviral molecules Exploration of the ocean at a genetic level will result in new insights into taxonomy and adaptive capacity that can help optimize conservation efforts, the NIO stated in its project abstract.

What is the objective of studying the interactions of trace metals and marine plant and animal life?

Trace metals like cadmium or copper are supplied to oceans via continental run-offs, atmospheric deposition, hydrothermal activities and continental shelf interaction. They are essential for ocean productivity. Scientists say that it is important to understand the interactions of trace metals with marine biota for having a holistic understanding about nutrient cycling and productivity of the oceans. Apart from their reactions on marine life, isotopic forms of trace metals can be utilised to track the movement of water masses responsible for ocean circulation and as tools to study the biological, geochemical and ecosystem processes and food web analyses. The NIOs project is expected to generate new information about trace metals from underexplored regions of the Indian Ocean, the third largest water body in the world, covering about 20 per cent of the Earths water surface.

How will the scientists collect the samples?

The team of scientists will stay aboard their research vessel for about 90 days with refueling scheduled at Mauritius. The route is from Visakhapatnam to the mouth of the Ganga then down the ocean to Australia, then westward to Mauritius and up to the Pakistan border. At various stages and stretches, samples will be collected by lowering a Kevlar cable of up to 8 km with a set of 24 teflon coated bottles to collect samples. They have a capacity of 12 litres. The Kevler cable and the Teflon coating are to ensure that metals are not inadvertently introduced into the water by the vessel itself. The samples will be collected and the bacteria will be stored at -60 degrees Celsius with the help of liquid nitrogen. While some samples will be tested at six laboratories on board the vessel, several samples will be brought back to NIO for study and analysis over the next three years.

Excerpt from:
Explained: What NIO scientists mapping genomes in the Indian Ocean hope to learn - The Indian Express

Imagine a world where disease can be quickly identified through genetic analysis.

Once considered the stuff of science fiction, genomic sequencing is now emerging to the forefront as a valuable means to identify and quite possibly, predict disease.

Genomic sequencing is an invaluable diagnostic tool for patients with rare genetic diseases. However, in the past, limited access, cost, and the understanding of its usefulness have been major challenges. As genomic testing has now become more available and affordable, it has made the uncovering of rare diseases, as well as the genetic potential for disease, an easier process.

In 2017, the Alabama Genomic Health Initiative (AGHI) was launched to address barriers to understanding genomics. It is one of the nations first state-funded efforts to harness the power of genomic analysis in finding answers for children and adults with undiagnosed medical challenges and adults who may have a high risk for developing certain diseases.

A collaborative effort among the University of Alabama at Birmingham, HudsonAlpha Institute for Biotechnology, and the state of Alabama, AGHI is led by Drs. Bruce Korf and Matthew Might of UAB and Dr. Greg Barsh of HudsonAlpha.

AGHI provides genomic testing, interpretation, and counseling free of charge to Alabama residents. The goal of the program is to engage at least 10,000 Alabamians in genetic testing, while educating participants about their genomic health.

AGHI is helping to improve patient care, not only by providing diagnoses, but also by giving the general public a foundational understanding of the importance and value of being informed about their genomic health, said Barsh. Through the AGHI platform we are able to provide an invaluable opportunity to physicians and geneticists to confirm or identify a diagnosis that has gone undiagnosed despite a vast array of previous medical testing.

The initial AGHI study results were recently published in Genetics in Medicine. The information reflects the first 176 rare disease participants and 5,369 participants in the first screening group.

Participants were recruited statewide. Each participant provided a blood sample, along with their personal and family health histories.

Two distinct groups of participants were identified: children and adults with undiagnosed rare diseases, and adults in the general population that did not have a personal or family history suggesting a genetic condition.

Participants in the rare disease group received genome sequencing, which evaluates a group of variants that are known to increase the likelihood of disease. The general population group received a genotyping test, a test that assesses each letter of a participants genetic code.

Of the 176 affected individuals in the rare disease group, thirty-five (19.9 percent) received a pathogenic or likely pathogenic result, indicating that a genetic variant was identified and thought to contribute to disease. Forty-two participants (23.9 percent) received an uncertain result, suggesting that a found genetic variant might have the potential to contribute to disease.

All participants received a report summarizing the results of their tests. Individuals whose results include actionable findings received genetic counseling and a referral to appropriate medical care.

Understanding the results and the implications associated with the findings are crucial for participants, as well as for their families. In some instances, the new genetic information might help physicians to make a diagnosis for a disease that has been yet undiscovered for months or years.

Being able to provide answers to individuals and their families who have been impacted by rare disease who may not have been able to otherwise access genome sequencing is one of the crowning achievements of AGHI to date, said co-author Kelly East, a genetic counselor at HudsonAlpha. We hope that the AGHI model can help inform similar programs elsewhere to give more communities awareness of and access to genomic testing.

For more information, visit hudsonalpha.org.

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The Alabama Genomic Health Initiative: Knowledge is Power - Huntsville Business Journal