Category Archives: Genome

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Android app deals of the day: EZ Voice Notes, Jumanji, Galaxy Genome, and more - 9to5Toys

Indore (Madhya Pradesh)

Even after being the worst hit by Covid-19, Indore will have to wait for more to get the genome sequencing machine as the government has decided to get the machine installed in Hamidia Hospital, Bhopal first.

The decision has surprised the city officials as Bhopal already has the facility of genome sequencing at the All India Institute of Medical Sciences (AIIMS).At present, samples of Covid-19 patients in Indore are being sent to National Centre for Disease Control (NCDC), Delhi and AIIMS, Bhopal for genome sequencing to know about the variant of the prevalent coronavirus.

The Centre has allotted five genome-sequencing machines to the state in December 2021 on the ground that the samples collected in Madhya Pradesh for Covid testing were sent to Delhi for genome sequencing, and it took 10 to 15 days to get reports.

These five machines were to be installed in Bhopal, Indore, Jabalpur, Rewa and Gwalior cities. These machines considerably help shorten the detection time of variants.

MGM Medical College was supposed to deposit the funds for the machine but it couldnt be done due to lack of funds. Now, the machine will be installed in Hamidia Hospital and MGM Medical College, Indore will have to wait for more for the machine, sources said.

However, the MGM Medical College administration believes to get the machine in the next phase.

We have also applied with the government for the genome sequencing machine to be installed in MGM Medical College. We believe that we will get the machine soon, Dean of MGM Medical College Dr Sanjay Dixit said.

Indore was the worst hit by Covid-19 but gets variant reports in 15-20 days

Indore was the worst hit by Covid-19 and adds the highest number of cases in the states tally.

As many as 207951 cases were found positive in the city and as many as 1461 patients lost their lives. As many as nine cases of Omicron were also tested positive in Indore but the samples were tested by a private laboratory.

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Indore: Even after being the worst hit by Covid-19, no end to Indores wait for a genome sequencing machine - Free Press Journal

Bionano Genomics

For the first time at this conference, Bionano will exhibit all of its cytogenetic research solutions: OGM solutions, NxClinical software and laboratory services

In a dedicated OGM scientific session, six presentations will illustrate the application of Bionanos OGM in prenatal and postnatal testing, constitutional disease, and cancer

Dr. Soheil Shams, chief informatics officer of Bionano, will present a scientific session on Analytical Tools to Support Detection of Homologous Recombination Deficiency (HRD) Using Cytogenomic Scar Markers

Dr. Alex Hastie, vice president of clinical affairs at Bionano, will host a sponsored vendor presentation on integrating OGM and next generation sequencing (NGS) for a comprehensive analysis of the genome

Following the conference, Bionano will host a user spotlight event at an OGM center of excellence at the Georgia Esoteric Molecular Laboratory at Augusta University

SAN DIEGO, May 13, 2022 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO), pioneer of optical genome mapping (OGM) solutions on the Saphyr system and provider of NxClinical software, the leading solution for visualization, interpretation and reporting of genomic data, today announced that it is participating in-person at the American Cytogenomics Conference (ACC). In addition to having six presentations that highlight the application of OGM in clinical genetics research, Bionano will host a user spotlight event at Augusta University, a center of excellence for OGM.

ACC is a biennial conference that brings together industry and academic professionals to discuss new technologies and advances in the field of cytogenetics. ACC sessions will take place May 15-18, 2022, in Hilton Head, South Carolina. Bionano will exhibit its complete portfolio of products and services relevant to the cytogenetics research community for the first time, including OGM solutions, NxClinical software and laboratory services. Multiple attendees from both Bionanos scientific and commercial teams will participate in the conference.

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Dr. Solheil Shams, chief informatics officer at Bionano, will present on the utilization of three new measures of genomic instability available in NxClinical v6.2 software to detect homologous recombination repair deficiency (HRD) in solid tumors. In a spotlight talk immediately following the OGM scientific session, Dr. Alex Hastie, Bionanos vice president of clinical affairs, will present examples of research where OGM may complement next generation sequencing (NGS) to potentially provide a more comprehensive analysis of the genome, for applications in genetic disease and cancer.

At the conclusion of ACC, Bionano will host an interactive tour of an OGM center of excellence at the Georgia Esoteric Molecular Laboratory at Augusta University, where Dr. Ravindra Kohle will demonstrate an OGM workflow and provide a tutorial on data interpretation for chromosomal aberrations.

Scientific presentations and poster sessions from Bionano and collaborators include:

Title

Presenters/Authors

Presented

Analytical Tools to Support Detection of Homologous Recombination Deficiency (HRD) Using Cytogenomic Scar Markers

Shams S

May 16, 2022 8:30-8:45 AM

Comparative Benchmarking of Optical Genome Mapping to Chromosomal Microarray Reveals High Technological Concordance in CNV Identification and additional Structural Variant Refinement

Pang AWC, Barseghyan H, Chaubey A, Hastie A

May 16, 202210:30-10:45 AM

Optical Genome Mapping as a Potential Tier1 Test for Postnatal Chromosomal Disorders Results of Multi-Institutional Validation Study of 331 Retrospective Clinical Samples

Iqbal M, Broeckel U, Levy B, Skinner S, Sahajpal N,Rodriguez V, Stence A, Awayda K, Scharer G, Skinner C, Stevenson R, Bossler A, Nagy P, Kolhe R

May 16, 202210:45-11:00 AM

Optical Genome Mapping for Prenatal Diagnostic Testing

Sahajpal N, Mondal A, Fee T, Hastie A, Chaubey A, DuPont B, Kohle R

May 16, 202211:00-11:15 AM

Optical Genome Mapping Analysis of FMR1 Expansions in Fragile X Syndrome

Barseghyan H, Muggli M, Ramandi B, Miller N, Zhang D, Lam E, Wang J, Wang T, Lee J, Pang AWC, Sadowski H, Hastie A, Oldakowski M

May 16, 202211:15-11:30 AM

Optical Genome Mapping Workflow for Identification and Annotation of Variants in Hematological Malignancy

Clifford B, Hauenstain J, Pang AWC, Chaubey A, Hastie A

May 16, 202211:30-11:45 AM

Capture-Based Transcriptome Sequencing (RNA-Seq) and Optical Genome Mapping (OGM) Enhance Detection of Newly Described Molecular Subtypes of Pediatric B-lymphoblastic Leukemia (B-ALL)

Raca G, Kovach A, Doan A, Ostrow D, Yellapantula V, Ji J, Schmidt R, Biegel J, Bhojwani D

May 16, 202211:45 AM-12:00 PM

Find More Answers: Integrating NGS and OGM for a Comprehensive Analysis of the Genome

Hastie A

May 16, 2022 12:00-12:30 PM

GDA-Cyto: Infinum Arrays Propel Cytogenomics Laboratories to New Heights

Saul D, Hagan J

May 16, 2022 12:30-1:45 PM

All presentations and poster sessions will be held in the Santee Ballroom, rooms E-H. The presentations will be made available on the Bionano Genomics website once presented at the conference. More details on ACC can be found here.

The lineup of content that will be presented on Bionanos solutions at ACC this year is world class. What makes our participation unique this year, is that we will have the combination of OGM products and our NxClinical software for attendees to view. We are focused on addressing their needs and now we can show them how, in person. After the show, we will be hosted at Augusta University where several scientists and cytogeneticists will join us for a hands-on experience of the journey that Dr. Ravi Kohles lab has taken to become an OGM center of excellence, said Erik Holmlin, PhD, president and chief executive officer of Bionano.

About Bionano Genomics

Bionano Genomics is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Companys mission is to transform the way the world sees the genome through OGM solutions, diagnostic services and software. The Company offers OGM solutions for applications across basic, translational and clinical research. Through its Lineagen business, the Company also provides diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through its BioDiscovery business, the Company also offers an industry-leading, platform-agnostic software solution, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. For more information, visit bionanogenomics.com, lineagen.com or biodiscovery.com

Forward-Looking Statements of Bionano Genomics

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, potentially, and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things, the potential contribution of our OGM and software solutions in the analysis of genetic diseases and cancer or the use of software solutions for homologous recombination repair deficiency (HRD) detection. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive technologies or improvements in existing technologies; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of medical and research institutions to obtain funding to support additional studies, adoption or continued use of our technologies; the ability of our OGM, NxClinical software and laboratory services solutions to offer the anticipated benefits for and contributions to pre and postnatal genomic analysis, cancer research, structural variant analysis as well as other areas of research; future study results contradicting the results reported in the presentations given and posters made available at ACC; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2021 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on managements assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTS

Company Contact: Erik Holmlin, CEO Bionano Genomics, Inc. +1 (858) 888-7610 eholmlin@bionanogenomics.com

Investor Relations: Amy Conrad Juniper Point +1 (858) 366-3243 amy@juniper-point.com Source: Bionano Genomic

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Bionano Genomics Announces Participation at the 2022 American Cytogenomics Conference (ACC) and a User Spotlight Event at Augusta University, a Center...

As the Covid-19 virus (coronavirus SARS-CoV-2) continues to spread and claim victims worldwide, its origins remain unknown. Each scientific community puts forward its own theory, with some suggesting the virus may have leaked out of a laboratory.

Another theory, based on recent studies of the Wuhan wet market in China, along with others carried out in Cambodia, Laos, Japan, China, and Thailand, posits that an ancestral virus in rhinolophus bats went on from infecting wild and/or domestic animals to humans. Indeed, in these different studies, several viruses with genetic sequences very similar to SARS-CoV-2 were isolated in these bats.

Though it has been shown some bat species have hosted these coronaviruses naturally, the wild or domestic animal (or animals) that acted as a bridge between them and humans the missing link remains unidentified. Pangolins were first suspected, but now appear to have been collateral victims rather than one of these much-talked-about missing links. A coronavirus genome sequence detected in pangolins was indeed related to that of SARS-CoV-2, but the rest of the genome was too distant from it genetically to back the hypothesis.

Moreover, the pangolins hosts in which the viruses that were genetically close to SARS-CoV-2 were found had mostly been confiscated at live-animal markets, at the end of the supply chain. As a result, they had been in lengthy contact with other animal species. It is very likely they were infected along this supply chain rather than in their natural environment. Mink farms were also suspected of being an intermediate host in China.

Lastly, pangolins and rhinolophus bats do not share the same habitat, making it highly unlikely there was any contact between the two species in which the virus jumped from one to the other. On the other hand, civets and raccoon dogs could be an intermediate source of SARS-CoV-1). Rodents or primates could also carry pathogens with zoonotic potential, such as hantaviruses which can cause haemorrhagic fever with renal syndrome or filoviruses, which include the Ebola virus. The latter is passed on to humans through wild animals, in particular bats, antelopes, and primates such as chimpanzees and gorillas, then spreads among humans, mainly by direct contact with blood, secretions and other bodily fluids from infected people. The average case fatality rate is around 50%.

In 2013, initial cases of disease from the Ebola virus were detected in West Africa. The rise of these cases led to over 10,000 deaths, mainly in Guinea, Liberia, and Sierra Leone.

Activities such as hunting, animal-handling or eating meat from wild animals therefore create the conditions for viruses to spread from animals to humans a potentially devastating phenomenon called spillover.

The ZooCov project has sought to define and quantify this risk in Cambodia. For almost two years and right from the start of the pandemic it has adopted a One Health approach to explore whether and how pathogens such as coronaviruses can be passed on to humans from wild animals that are hunted and eaten.

Indeed, in South-East Asia, wild animals are regularly traded, and bushmeat is customarily eaten. This eating habit is often opportunistic. In some communities, it complements a low-protein diet. It can also be frequent and targeted. In Cambodia, 77% of 107 families interviewed in the ZooCov project said they had eaten bushmeat in the past month.

Use for medicinal purposes is also widespread. In Vietnam, an analysis of records of the Vietnamese authorities confiscating pangolins and related by-products between 2016 and 2020 reported 1,342 live pangolins (6,330 kg), 759 dead pangolins or pangolin carcasses (3,305 kg), and 43,902 kg of pangolin scales.

Yet this consumption also has a cultural and social dimension that is still not properly understood. Among the well-off and often in big cities people sometimes eat bushmeat out of a desire for social status, and a belief that eating it endows them with the physical or physiological attributes of the animal. They also sometimes eat bushmeat out of rejection of industrially produced meat, considered unhealthy. Animals are widely reared to meet this demand and the demand for fur production.

In the Stung Treng and Mondolkiri provinces of Cambodia, where protected forest areas remain, researchers surveyed more than 900 people living on the edge of these forests to determine the structure of the illegal bushmeat trade. Statistical analyses are underway to identify the people most at risk of contact with wildlife thus with such pathogens. We already know those exposed are mostly young middle-class men, and that some communities are more exposed than others. Sociological studies have also helped better grasp todays context: the legal framework, the profiles of players in the trade, their motives and deterrents in trade and consumption of wild animals, and how the context has changed with each different health crisis (bird flu, Ebola, SARS-CoV-1, etc.).

These successive crises seem to have scarcely affected the habits of these communities. Beyond regularly eating bushmeat, one fourth of the families surveyed said they still hunted or ensnared wild animals, and 11% claimed to sell bushmeat or wild animals. Furthermore, in the same areas of study, over 2,000 samples taken from wild animals trafficked or eaten for subsistence bats, rodents, turtles, monkeys, birds, wild pigs, etc. were analysed. Some of these samples tested positive for coronaviruses and scientists at the Institut Pasteur du Cambodge (IPC) are currently sequencing their genome in a bid to learn more about their origin, evolution, and zoonotic potential. Finally, researchers collected blood samples from over 900 people from the same region to find out whether they had been in contact with a coronavirus or coronaviruses. These analyses are still underway, but what we do know is that these people had not been exposed to SARS-CoV-2 when the survey was conducted.

If the Covid crisis has taught us anything, it is the importance of detecting such emergences early in order to nip the pathogens in the bud. While many questions remain about the way cases emerge, there are just as many questions about the monitoring systems that should be set up to track them. The results of the ZooCov project will be used to develop a system for detecting spillover of zoonotic viruses early, particularly by strengthening the system for monitoring wildlife health that is already in operation in Cambodia, which was set up by the Wildlife Conservation Society (WCS). Other large-scale projects in research and development will help us understand, detect, and prevent these phenomena of emerging cases.

The authors would like to thank Cambodias Ministry of Health, its Ministry of Agriculture, Forestry and Fisheries, and its Ministry of Environment, as well as all the projects partners: Institut Pasteur du Cambodge (IPC), the Wildlife Conservation Society (WCS), Flora and Fauna International (FFI), Institut de Recherche pour le Dveloppement (IRD), Hong Kong University (HKU), the GREASE network, International Development Enterprise (iDE), the World Wildlife Fund (WWF), Elephant Livelihood Initiative Environment (ELIE), BirdLife International, Jahoo, and World Hope International.

Translated from the French by Thomas Young for Fast ForWord.

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On the trail of the origins of Covid-19 - The Conversation

An international team of researchers, including one from The University of Western Australia, has successfully unravelled the genomes of 418 unique samples of rapeseed from across the globe to identify traits that breeders can use to improve crop yield.

The study Genomic selection and genetic architecture of agronomic traits during modern rapeseedBreeding published in Nature Genetics, follows a four-year collaboration between the scientists from Australia, China and the United States.

Professor Jacqueline Batley, from UWAs School of Biological Sciences and The UWA Institute of Agriculture, who is an author on the paper, said that rapeseed, known as canola in Australia, is the second most important oil-producing crop worldwide.

Which means that breeders are looking at ways that they can generate plants with the desired characteristics or traits that will allow them to minimise crop losses and maximise crop yields, Professor Batley said.

While the adaption, yield and quality of canola have all considerably improved in recent decades due to intensive breeding the genetics underlying desirable traits such as the architecture of the plant, seed weight and oil content have remained unclear because these are controlled by multiple genes.

Working together, the research team unravelled the genomes of 418 diverse rapeseed accessions from different geographical locations representing global genetic diversity. In doing so, they were able to identify the genes behind 56 traits that were modified during rapeseed improvement.

This provided us with insights into the genetic control of these important traits, Professor Batley said.

Taken together, our study revealed a landscape of genomic variation for diverse varieties and artificial selection or adaptation during rapeseed breeding. The results are a real insight into the make-up of rapeseed and should help accelerate future breeding for crop improvement.

Professor Batley said the complex genetic sequencing generated in the ground-breaking study will not only be an indispensable resource for genome-assisted rapeseed breeding but also a valuable database for other scientists conducting research on rapeseed.

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Unravelling the genetic keys to improve canola crop yield - University News: The University of Western Australia

In Nature News, Smriti Mallapaty describes the ethical debate surrounding care for the twin girls whose birth was reported by genome editing researcher He Jiankui.

He, who was jailed for his research, claims to have used CRISPR-Cas9-based gene editing to edit the CCR5 gene in twin embryos that were implanted in a woman who gave birth in 2018. A third genome-edited baby was born to other parents. CCR5 codes for a protein that HIV uses to make its way into human cells.

Two Chinese bioethicists would like to see a research center "dedicated to ensuring the well-being of the first children born with edited genomes," Mallapaty explains, though other experts "are concerned that the pair's approach would lead to unnecessary surveillance of the children."

While no other genome-edited babies have been reported, likely owing to He's punishment and backlash to the work in the scientific community, interest in the approach has persisted, she explains. In the meantime, experts are grappling with bioethical and practical issues surrounding the genome-edited children from their medical care and health testing to the potential social and psychological effects of their experience.

"Researchers say that the latest proposal, in a document by Qiu Renzong at the Chinese Academy of Social Science in Beijing and Lei Ruipeng at the Huanzhong University of Science and Technology in Wuhan, is the first to discuss how to manage the children's unique situation," Mallapaty writes. Among their recommendations, the pair calls for "regular sequencing of the children's genomes to check for 'abnormalities,' including conducting genetic tests of their embryos in the future."

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Think of the Children? | Genomeweb - GenomeWeb

OverviewCGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, and as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file or a tab-delimited file. CGView converts the input into a graphical map (PNG, JPG, or SVG format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery.

In addition to the CGView application, an API is available for generating maps from within other Java applications, using the cgview package.

CGView can be used for any of the following:

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CGView - Overview

Pacific Biosciences of California, Inc.

SickKids will use HiFi Sequencing to explore potential genetic causes of a range of medical and developmental conditions

MENLO PARK, Calif., Feb. 28, 2022 (GLOBE NEWSWIRE) -- PacBio, a leading provider of high-quality, highly accurate sequencing platforms, today announced it will be supporting The Hospital for Sick Children (SickKids) in Toronto, Canada in using HiFi whole genome sequencing (HiFi WGS) to potentially identify genetic variants that may be associated with medical and developmental conditions. Samples that will be examined using HiFi WGS were previously sequenced using short-read DNA sequencing technology, but still lack the identification of a disease-causing variant.

Even though more than 70 percent of rare disease, autism and intellectual disability have genetic causes, more than 50 percent lack an identified causative genetic alteration despite the use of microarrays, whole-exome or short-read whole-genome sequencing (srWGS).

SickKids will use HiFi WGS to analyze samples from research participants who are highly suspected to have a genetic condition but have not yet received a diagnosis despite previous genetic testing, including srWGS. The team will explore whether HiFi WGS can detect potential genetic causes for a range of conditions, such as autism spectrum disorder and congenital diseases.

HiFi sequencing allows us to investigate the entire genome in a way that is not accessible with other technologies, said Dr. Christian Marshall, Clinical Laboratory Director, Genome Diagnostics and Associate Director at The Centre for Applied Genomics (TCAG) at SickKids. We hope HiFi sequencing will enable us to take an exploratory look at classes of variation and large sections of the genome that were not detected previously, potentially showing unidentified causative genomic variants in these samples.

PacBios technology has been used to help genetic disease researchers explain mysteries where other technologies could not, said Edd Lee, Director of Human Genomics at PacBio. We are excited to support the SickKids team to hopefully uncover the answers they have been seeking.

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To learn more about the benefits of HiFi WGS in genetic disease, visit http://www.pacb.com/rare-disease.

About PacBioPacific Biosciences of California, Inc. (NASDAQ: PACB) is empowering life scientists with highly accurate sequencing platforms. The companys innovative instruments are based on Single Molecule, Real-Time (SMRT) Sequencing technology, which delivers a comprehensive view of genomes, transcriptomes, and epigenomes, enabling access to the full spectrum of genetic variation in any organism. Cited in thousands of peer-reviewed publications, PacBio sequencing systems are in use by scientists around the world to drive discovery in human biomedical research, plant and animal sciences, and microbiology. For more information, please visit http://www.pacb.com and follow @PacBio.

PacBio products are provided for Research Use Only. Not for use in diagnostic procedures.

Forward-Looking Statements This press release may contain forward-looking statements within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and the U.S. Private Securities Litigation Reform Act of 1995, including statements relating to future availability, uses, accuracy, advantages, quality or performance of, or benefits or expected benefits of using, PacBio products or technologies; the suitability or utility of such products or technologies for particular applications or projects, including in connection with the SickKids collaboration; potential increases in variant detection and providing answers for rare disease samples, in the SickKids collaboration in particular and rare disease research in general; and other future events. Readers are cautioned not to place undue reliance on these forward-looking statements and any such forward-looking statements are qualified in their entirety by reference to the following cautionary statements. All forward-looking statements speak only as of the date of this press release and are based on current expectations and involve a number of assumptions, risks and uncertainties that could cause the actual results to differ materially from such forward-looking statements. Readers are strongly encouraged to read the full cautionary statements contained in the Companys filings with the Securities and Exchange Commission, including the risks set forth in the companys Forms 8-K, 10-K, and 10-Q. The Company disclaims any obligation to update or revise any forward-looking statements.

Contacts

Investors: Todd Friedmanir@pacb.com

Media:Lizelda Lopezpr@pacb.com

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PacBio Supports SickKids to Investigate Use of HiFi Sequencing in Undiagnosed Genetic Conditions - Yahoo Finance

Genomic sequencing has been a key tool throughout Aotearoas COVID-19 pandemic, with data generated here now part of the 8.5 million genomes shared globally.

It has helped us understand how cases arrived here and the extent of community outbreaks. It has also given us detailed insight into how the virus is transmitted from person to person, on a plane or quarantine facility.

As Omicron spreads rapidly across the country, it is important to consider how we best deploy genomics to achieve our public health goals. Which cases should we sequence and why? What is the role of wastewater when we know cases are already in our cities and regions?

Even as our testing and genomics capacity gets overwhelmed by the sheer number of cases, sequencing will continue to play an important role.

Firstly, we need to keep an eye open for new viral variants and keep track of those already circulating in the community. This is a core role of genomic surveillance and part of a global effort, with scientists around the world sequencing variants in their backyard.

Read more: How COVID-19 transformed genomics and changed the handling of disease outbreaks forever

One thing we are looking for is changes (mutations) in the virus that may affect its ability to transmit, evade our vaccines or immune defences, or cause even more serious disease. Particular scrutiny is given to mutations in the viral spike protein, on the outside of the virus, which allows it to latch onto cells and infect them.

The Pfizer vaccine we have used in Aotearoa essentially presents the body with a copy of the spike protein to train the immune system to create antibodies and other defences against it. Major changes in the spike might allow the virus to evade at least the first line of our immune defences as we have seen with the Omicron variant, which contains more than 30 different mutations in the spike protein.

With relatively few cases overall in New Zealand, and only the Delta variant that has persisted in the community for more than a few months, we have so far not seen any concerning new mutations or variants arise here. But small mutations or deletions in the viruss genetic code remain helpful for linking clusters and detecting new introductions into the community.

The majority of New Zealanders are now vaccinated, which means there is increasing pressure on the virus to escape our immunity. This is an arms race we have been playing with viruses for millennia. The game has changed somewhat as genomics allows us to watch viral evolution in real time.

By sequencing the virus from individual cases, we can tell exactly which variant the person has and, over time, we can detect patterns of variants rising in frequency or resulting in a more severe infection.

Currently, genomic surveillance tells us there is a mix of Omicron (including major variants BA.1, and BA.2) and a stubborn tail of Delta.

The BA.1 lineage was given an early boost at a wedding-related super-spreading event and now makes up 74% of Omicron cases. The remaining 26% of Omicron cases are BA.2 which was spread early on at the SoundSplash festival. In the last week, about 7% of cases sequenced were Delta. Without sequencing, we would be blind to this.

To maintain high-quality surveillance in the face of very high case numbers, we need to be selective in which samples we sequence and balance competing priorities.The top priority is the prevention of severe disease and there will be a focus on the genomes of cases in hospital. Overseas, many of the serious, hospitalised cases are Delta, not Omicron.

Some patients may have the misfortune of chronic COVID-19 infections. In such cases, multiple samples may be sequenced to see if the virus is changing within a single patient.

A leading hypothesis of how variants of concern such as Omicron and Delta have emerged is via chronically infected patients who act as an incubator for the virus. We need to continue monitoring patients with long-haul COVID.

We will also need to continue to monitor and sequence new cases that arrive at the border, either in MIQ or in recently returned travellers who test positive. Nearly all the genetic variation of SARS-CoV-2 we have seen in Aotearoa has been imported (as opposed to developed here), and this is a common pattern we see with other diseases such as influenza. By sequencing border cases, we get an early view of what we may need to prepare for.

Read more: Genomic sequencing: Here's how researchers identify omicron and other COVID-19 variants

Finally, to get a high-level view of cases and mutations, we sequence a random sample of cases across the country. Genomic sequences taken across time and space build a picture of which parts of the country are host to which variants and lineages. It is very much a case of know thy enemy.

Currently we are monitoring the areas where Delta is persisting. We can also monitor how the vaccine status of an individual affects the variant that is detected. Such data helps to build a picture of vaccine efficacy and population-level protection against a fast-changing virus.

The last piece of the genomic sequencing puzzle is wastewater testing for SARS-CoV-2. While sequencing from wastewater samples has been used for specific public health investigations in the past, low case numbers and quantities in most wastewater samples has made it difficult. Instead, wastewater testing has focused on using a sensitive method to allow for the early detection of the virus.

With the Omicron surge, we are now seeing an increase in both the number of positive wastewater samples and the amount of virus in those samples. This means we can use wastewater to indicate increasing or decreasing trends in cases at community level, and also to monitor known and new variants through sequencing and other tools.

In the weeks to come, there will be enough viral matter to make trends in wastewater data evident. In some cities, where regular sampling occurs, we will see viral wastewater loads trending up and down with case numbers. This information, along with regular case reporting, will inform the public about the relative risk of various regions. Such data may help people to understand the risks of travelling to a certain region or city.

Genomics remains a key tool in our pandemic management. There will be changes in how we use it, but it remains a core part of our surveillance toolkit. Prior to the genomics era, changes in the viral genetic blueprint were invisible to us. While many will dread another story about a new variant, we would be in a far worse position without this information.

If we step outside of our COVID-19 bubble for a second, the use of fast and affordable genomic technology in this pandemic also provides a glimpse of what genomic medicine may look like in the future but that is a discussion for another day.

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As New Zealand's Omicron infections rise rapidly, genome surveillance is shifting gears - The Conversation AU

SAN FRANCISCO--(BUSINESS WIRE)--Serotiny, a leader in high-throughput therapeutic Multi-Domain Protein (tMDP) engineering, and Tessera Therapeutics, a biotechnology company pioneering a new approach in genetic medicines known as Gene Writing technology, today announced a collaboration to engineer programmable Gene Writer proteins. This collaboration will build on Tesseras innovations in genome engineering technologies and apply Serotinys tMDP mining and design expertise to further optimize Tesseras programmable Gene Writer proteins, capable of making diverse and directed alterations to the genome.

Were extremely excited to be working with the Tessera team, said Colin Farlow, J.D., Serotinys CEO. It provides Serotiny a unique opportunity to extend the validation of our platform and to continue to advance our efforts in discovering and developing proteins with novel function for the purpose of enhancing the therapeutic utility of next-generation genetic medicines.

Tesseras Gene Writer candidates can allow the substitution, insertion, or deletion of DNA sequences, as well as the writing of entire genes into the genome, offering the potential for a new category of genetic medicines. By partnering with Serotiny, Tessera will have the ability to identify, screen, and optimize a variety of proteins that can serve as the foundation of future Gene Writer therapies across a variety of disease states.

Tesseras mission is to cure disease by writing in the code of life and were committed to continuously innovating to improve and expand our Gene Writing platform, said Geoffrey von Maltzahn, PhD, co-founder and CEO of Tessera. Our R&D engine seeks to learn from billions of years of mobile genetic element evolution to generate novel Gene Writing systems with the ability to solve important challenges in genetic medicine. Serotinys multi-domain engineering expertise has the potential to further optimize our Gene Writer protein libraries and were delighted to partner with the Serotiny team.

Under terms of the agreement Serotiny will receive an upfront payment and is eligible for certain future consideration, contingent upon the collaboration achieving pre-specified performance thresholds.

About Serotiny

Serotiny is a pre-clinical discovery company building better gene and cell therapies through high-throughput engineering of therapeutic Multi-Domain Proteins (tMDP) such as Chimeric Antigen Receptors (CARs), CAR alternatives, accessory proteins, and next generation gene editors. At the heart of Serotinys technology is a discovery platform that harmonizes computationally aided protein design, high-throughput cellular assays, and next generation sequencing. Serotinys platform enables a cross disciplinary approach to engineering large and often unstructured multi-domain proteins, applying expertise from synthetic biology, immunology, machine learning, software engineering and bioinformatics. For more info visit http://www.serotiny.bio, or contact Colin Farlow at info@serotiny.bio.

About Tesseras Gene Writer platform

Tesseras Gene Writer proteins are based on natures genome architects, Mobile Genetic Elements (MGEs)the most abundant class of genes across the tree of life, representing approximately half of the human genome. Tessera has evaluated tens of thousands of natural and synthetic MGEs to create Gene Writer candidates in multiple categories including:

Tesseras research engine further optimizes the discovered Gene Writer candidates for efficiency, specificity, and fidelityessentially compressing eons of evolution into a few months.

About Tessera Therapeutics

Tessera Therapeutics is pioneering Gene Writing technology, which consists of multiple technology platforms designed to offer scientists and clinicians the ability to write therapeutic messages into the human genome, thereby curing diseases at their source. The Gene Writing platform allows the correction of single nucleotides, the deletion or insertion of short sequences of DNA, and the writing of entire genes into the genome, offering the potential for a new category of genetic medicines with broad applications both in vivo and ex vivo. Tessera Therapeutics was founded by Flagship Pioneering, a life sciences enterprise that conceives, resources, and develops first-in-category bioplatform companies to transform human health and sustainability. For more information about Tessera, please visit http://www.tesseratherapeutics.com.

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Serotiny and Tessera Therapeutics enter into collaboration to engineer and optimize programmable Gene Writer proteins - Business Wire