Category Archives: Genome

Meanwhile, one person lost life to COVID19 today, J&K Government said while 104 fresh cases were confirmed in the UT.

Official bulletin on COVID19 by J&K Government today said one person from Kashmir division succumbed to COVID19 while no death from Jammu division was reported. No case of Mucormycosis has been reported in the UT, the official bulletin on COVID19 said.

The number of fresh cases reported today was 108, showing a falling trail of cases. Of the new cases, 78 were from Kashmir division and 26 from Jammu division. There were 40 new cases in Srinagar and 15 in Kupwara. District Jammu had 18 new cases. In the past 24 hours, 46173 tests were reported in the UT.

The number of recoveries reported today was 139. Of these, 110 were from Kashmir division and 29 from Jammu division. The number of active cases thus reached 332 in Jammu and 995 in Kashmir division, the total active cases in J&K 1327. Today, 64343 people received COVID19 vaccine.

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3 cases of Omicron variant confirmed in Jammu - Greater Kashmir

The Piedmont Study, a Real-World Data Analysis in Patients Treated with Platinum Doublet Chemotherapy and/or Pembrolizumab, Identifies Predictive Biomarkers for Approved First-Line Treatments in NSCLC

DURHAM, N.C.--(BUSINESS WIRE)-- GeneCentric Therapeutics, a company making precision medicine more precise through RNA-based diagnostics, announced today the completion of its Piedmont Study, conducted in collaboration with Atrium Health Levine Cancer Institute.

Early results suggest that GeneCentrics Antifolate Predictive Response Signature (AF-PRS), one of the signatures included in the recently announced strategic collaboration with Labcorp, identified a distinct population of patients who clearly benefit from treatment with pemetrexed/platinum doublet chemotherapy. Leveraging this deeper understanding with RNA-based tests such as the AF-PRS may help identify a broader patient population that may benefit from therapy, compared to DNA mutation analysis.

We founded GeneCentric over a decade ago to study the genomics of lung cancer using the deep insights that can be obtained through gene expression analysis, said Neil Hayes, M.D., GeneCentric co-founder and Director of the University of Tennessee Health Science Center for Cancer Research. While our work has expanded well beyond the lung, the actionable clinical and genomic datasets we have developed have led to multiple signatures and related prototype tests. As a treating physician, I am excited about the promise of the predictive insights that can be gained from the Piedmont Study as we navigate the existing and emerging treatment options for lung cancer patients.

In this retrospective study of real-world data, clinical response data and existing tumor samples were collected from about 250 patients with non-squamous non-small cell lung cancer (NSCLC) who were treated with either pemetrexed/platinum doublet chemotherapy, pembrolizumab (Keytruda), or the combination of the two. The Piedmont Study paired highly curated real-world clinical and demographic data with bulk tumor RNA transcriptome analysis from patients with NSCLC, which was analyzed using GeneCentrics RNA-based Tumor and Immune Micro-Environment (rT(I)ME) Explorer platform.

There has been great progress with the development of new treatment options for patients with locally advanced or metastatic non-small cell lung cancer, said Kathryn Mileham, M.D., Piedmont Study Principal Investigator and Chief of the Section of Thoracic Medical Oncology at Atrium Health Levine Cancer Institute. With the prevalent use of immune oncology agents alone or in combination with chemotherapy, there needs to be a deeper understanding of how to select the right treatment for the right patient, and the Piedmont Study will aid in this endeavor.

The clinical and genomic data analysis from this study is ongoing. The AF-PRS test and associated lung adenocarcinoma (LUAD) molecular subtype classifier assay explored in the current study will support GeneCentrics growing pipeline of novel RNA-based predictive response signatures and related tests. In addition, this real-world evidence dataset joins the expanding number of highly curated clinicogenomic datasets across multiple tumor types and therapeutics areas that GeneCentric has developed and deployed, in collaboration with pharmaceutical and biotechnology partners, to explore novel oncology therapeutic options and diagnostic tests.

About the Piedmont Study

Utilizing Atrium Health Levine Cancer Institutes broad network of 25+ clinical centers that see around 20,000 new cancer cases per year, retrospective baseline clinical, demographic and clinical response data were collected on over 500 patients receiving systemic first-line treatment for locally advanced or metastatic non-squamous NSCLC. The primary focus of the study was a subset of approximately 250 patients with existing tumor samples who received either pemetrexed-containing platinum doublet chemotherapy, pembrolizumab (Keytruda) or the combination of the two. Tumor samples underwent transcriptome RNA sequencing (RNAseq) and were analyzed using GeneCentrics RNA-based Tumor and Immune Micro-Environment (rT(I)ME) Explorer platform, which is an integrated pipeline used to translate tumor biology insights into actionable genomic signatures predictive of drug response.

About GeneCentric

GeneCentric Therapeutics, Inc. is an RNA-based genomic solutions provider based in Durham, North Carolina. The company designed its technologies to parse the complexity of tumor and immune biology using its RNA-based Tumor and Immune Micro-Environment (rT(I)ME) Explorer platform to discover and develop signatures of responder populations to oncology therapeutics. GeneCentric commercializes its technology through strategic collaborations with pharmaceutical, biotechnology and diagnostics companies in applications throughout preclinical testing, clinical drug development and commercialization lifecycle phases. For more information, visit http://www.genecentric.com or follow us on LinkedIn.

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GeneCentric Therapeutics Identifies RNA-Based Genomic Markers of Clinical Response in Lung Cancer - BioSpace

It remains unclear how long the Omicron wave will last or how much harm it will do.

We need to prepare for the possibility that this could have substantial impact, said Jacob Lemieux, an infectious disease specialist at Massachusetts General Hospital and co-leader of the viral variants program at the Massachusetts Consortium on Pathogen Readiness.

Early evidence suggests that Omicron replicates quickly in the upper airway, but is less likely to spread deep into the lung, said Dr. Jeremy Luban, chairman in AIDS research at the UMass Chan Medical School. That could explain why some Omicron infections have appeared milder.

In South Africa, Omicron cases have proved less severe than previous variants, but experts emphasize that theres no guarantee that it will play out the same way in the United States, already in the grips of a massive surge of the Delta variant.

The data out of the UK was a sobering contrast, MacInnis said. Hospitalizations are up 10 percent with no evidence that Omicron causes less severe illness than Delta.

In any case, she said, With the transmission levels were seeing, even a small percentage of severe cases will still be a large number. And as the virus spreads, it will continue to mutate, risking the rise of a new variant.

Broad scientists, in partnership with the Massachusetts Department of Public Health tested 1,108 specimens collected throughout Massachusetts Dec. 13 through 16, using a new technology called mCARMEN. They found that 45 percent of samples showed strong evidence of the Omicron variant. Based on the trends observed during this time period, the team estimates Omicron crossed the 50 percent mark on Friday and has continued to soar in prevalence.

Developed at the Broad, mCarmen can rapidly differentiate among variants, providing what officials called a provisional look at the rising prevalence of Omicron in the state. The technology allows researchers to hunt for Omicrons fingerprint by quickly analyzing snippets of the viral genome.

In experiments, it was shown to be as accurate as full genome sequencing 97 percent of the time. But because it only analyzes snippets, this method produces results in a day rather than the week or more that full genomic sequencing takes. Researchers are examining samples from across the state, rather than using those from just one hospital or region, capturing a more representative cross-section of infections.

Although the technology was developed two years ago, Omicrons arrival marks the first time when a variant increased exponentially at such a pace that results from genomic sequencing came in too late to guide the public health response.

The Broad is using this technique on about 1,000 samples a day, performed by graduate student Nicole Welch.

We have a pretty good sense of where this is going to go, MacInnis said.

Around New England, states reported a smattering of Omicron cases three in New Hampshire, 40 in Connecticut, one each in Rhode Island and Maine, about three in Vermont but current case counts give little indication of current infections. Massachusetts has not released the states Omicron case counts.

If someone tells you today that the most recent data is that Omicron is 15 percent of all cases, its safe to say the real number is twice that, said Dr. Bruce Walker, director of the Ragon Institute of MGH, MIT, and Harvard.

I dont think there is any lab in the world that can keep up with the number of cases we are going to be seeing, even in terms of testing, because its already straining the system, Walker said.

If you look at whats going on today, its actually what already happened 10, 14 days ago, said Salim Abdool Karim, clinical infectious disease epidemiologist and director of the Centre for the AIDS Program of Research in South Africa. Time is not on your side.

Karim, Lemieux, and Luban spoke at an online briefing Monday sponsored by the Massachusetts Consortium for Pathogen Readiness.

Vermont, the most vaccinated state in the country, reported its first Omicron case Saturday, and a state spokesman said there have been several more confirmed through genomic sequencing since then, but declined to say the precise number. At the same time, Vermont is reporting a slight decline in COVID cases overall and hospitalizations in the past two weeks, but that followed a large spike that lasted for weeks.

This would be great if we werent looking at the potential of an Omicron surge, said Ben Truman, spokesman for Vermonts health department.

But in New Hampshire, New Englands least-vaccinated state, the Dartmouth-Hitchcock Medical Center saw the largest number of patients on ventilators since the start of the pandemic last week, driven largely by unvaccinated patients with COVID-19, according to Dr. Michael Calderwood, the hospitals chief quality officer.

Now the hospital is girding for the Omicron wave.

Right now, the variant makes up about 3 percent of all COVID cases in the hospital, according to Calderwood. But he expects that share to increase quickly. To prepare, Dartmouth-Hitchcock is asking smaller hospitals to take on the care of less-sick COVID patients so the larger hospital can expand its capacity to treat the seriously ill.

Our biggest focus right now is making sure that we are able to increase critical care capacity to serve the needs of northern New England, he said.

He added that the vast majority of his hospitalized patients are unvaccinated, and that information about the safety and effectiveness of vaccines and boosters is still not reaching the right people. He recalled seeing a patient recently who had decided to put off their booster shot until after the holidays so they wouldnt have to tell their anti-vaccine family about it. This is a person at very high risk, said Calderwood. We need to figure out how to change that dialogue and try to get that correct info out there. That is the hardest thing, and sometimes it feels like were shouting into a vacuum and the people who most need to hear that info arent hearing it.

Felice J. Freyer can be reached at felice.freyer@globe.com. Follow her on Twitter @felicejfreyer. Kay Lazar can be reached at kay.lazar@globe.com Follow her on Twitter @GlobeKayLazar.

Originally posted here:
Omicron becomes dominant variant in Mass., already straining the system - The Boston Globe

When scientists want to understand how individual human genomes vary, they turn to a single, central genetic sequence: the reference genome. That genome serves as a kind of standardized measurement, a yardstick, against which all other human variation can be measured.

But heres the surprise: About 70 percent of that reference genome comes from a single man in Buffalo, New York, whose DNA was sequenced during the 1990 to 2003 Human Genome Project, the first attempt to record the full genome of a person. That raises obvious questions: Are variations from the reference genome actually abnormal? The man behind the reference genome, known as RP11, is likely of mixed African and European ancestry, but how much information can one genome give about variation among 7 billion of us?

Geneticists have toyed with a variety of fixes for the problem. Sometimes, genetic medicine practitioners use population-specific reference genomes that might be more representative of someone with sub-Saharan African or East Asian ancestry. Others have proposed developing a consensus reference, which would be a Frankenstein-style assembly of the most common genetic variants, all stitched together. There could even be a reference genome based on that of humanitys most recent common ancestor.

But all of those share a central limitation: reference genomes rely on the assumption that there is a baseline human genetic blueprint, and genetic diversity must be understood as variations from that baseline.

This week, research in Science lays out a new tool for investigating the human pangenome. The pangenome allows geneticists to map differences in an unlimited number of genomes all at once, which researchers say could capture complex variations and better tailor genetic medicine to people who arent European.

What would be better would instead be, lets compare to a whole diverse collection of a sampling of what we think humanity looks like, says Benedict Paten, a computational biologist at the University of California Santa Cruz, and the senior author on the research.

Instead of looking at one single genome, says Paten, we map out a network of possibilities. Imagine two people with a slightly different sequence: AGTCA and ATTGA. In the pangenomic point of view, variations are represented as a series of branches on a tree: A leads to T or G, which leads back to T, which leads to C or G, which leads to A. Where two genomes are identical, they follow the same path. Where the genomes are different, the paths split off. Many people with similar genomes would be a bit like a bundle of strings, following the same pathway through a network of possible sequences.

[Related: Were just beginning to understand how our genes and COVID-19 mix]

That makes it much easier to see variations in context, rather than as deviations from a norm. Traditionally, when we have a reference, we talk about edits, says Paten. So we say, position one million and blah, there was a flip from an A to G. In a pangenome, instead of being described as edits, theyre just a sequence. Theyre just a point in that network.

Most immediately, that will help researchers understand deep patterns in our genes. The simplest changesswaps of a single letter, or short insertions and deletionsare easy to identify using a reference genome. But there are more complicated patterns, which scientists call structural variants. An entire stretch of DNA might be reversed or repeated, or cut out and plopped down elsewhere. And even the best reference genome is a bad tool for understanding the full complement of structural variation.

Because genomic patterns vary somewhat by ancestry, the reference genome is especially bad at explaining variation in undersampled communities, from Tuscans to Yorubait may simply not have an analogue for a common feature of genomes in those communities. (Its important to remember that ancestry doesnt generally map onto cultural definitions of race, and that variations between populations are superficial or minor next to overwhelming commonalities.)

When youre looking at structural variants, says Stephanie Fullerton, a bioethicist at the University of Washington who studies genetic medicine, scientists ask whether the variant is very unusual that is probably breaking something super important? Or is this just something floating around in the human genome that is effectively neutral?

Because the vast majority of genomic research has looked at people of European ancestry, researchers often dont understand what population-specific variants mean for the health of non-Europeans.

Ambroise Wonkam, a human geneticist at the University of Cape Town, wrote in Nature earlier this year that in people of African descent, biased research means that the likelihood of cardiomyopathies [a heart disease] or schizophrenia can be unreliable or even misleading using tools that work well in Europeans. And, he pointed out, fewer than 2 percent of human genome sequences come from individuals in sub-Saharan Africa.

In the new paper, the researchers put the tool into action onto a variety of genomic databases from across the planet. They were able to pick out one structural variant, a deletion of a gene called RAMACL, that showed up in half of people of African descent, four percent of Americans with mixed ancestry, and just one percent in other groups. That suggests that the variant is a perfectly normal part of human diversity, when it otherwise might have been flagged as unusual, and potentially harmful.

This has been a problem up and down, says Paten, where people have studied one subpopulation and found a variant that looks interesting, and might be associated with something, but they havent had the context of how common that variant is in other populations.

Fullerton agrees. But does that help us help individual patients from underrepresented groups? she asks. Thats a far bigger question.

On the one hand, it could give patients clarity on whether a feature of their genome is something to worry about, and give doctors tools for understanding the links between genes and illness. If youve ever had any health concerns and had a doctor tell you, we dont know what that means, its very frustrating, right? she says. As genetic counseling, to guide management of breast cancer risk or inform complicated diagnoses, becomes more common, patients who arent represented by the reference genome could be left out. So it can help with that information problem. But at the end of the day, knowing that this [gene] is causing disease doesnt get you to, this is what we do about it. Particularly if youre talking about patients who are lower socioeconomic status, or dont have social capital to navigate the healthcare system, getting it answered is important, but its the very first step of a very long odyssey.

And without more sequences from people who are underrepresentedparticularly in the global south and Indigenous communitiesthere wont be the underlying data to understand the link between disease and genetics. How to collect and share those sequences is a whole different set of questions: the history of genetics is full of ethical failures by academic researchers. Wonkam, the South African researcher, is calling for a project to sequence 2 million genomes in Africaand to give the owners of those genomes power over how they will be used. The pangenome provides a framework for understanding human diversity, but people should decide how to fill it in.

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The benchmark for human diversity is based on one man's genome. A new tool could change that. - Popular Science

With Covid-19 cases rising in Chandigarh since the last week, and with the first case of Omicron detected in the city, the Chandigarh Administration had been considering starting whole-genome sequencing of Covid samples in the city. The samples are now being sent to the National Centre of Disease Control, Delhi for testing, with the report taking about two weeks.

Dr Sanjeev Khosla, Director, IMTech, Chandigarh, which is part of the National Laboratory Network says, The Institute is all equipped and ready to carry out whole genome sequencing of the samples as and when received from the Chandigarh Administration and neighbouring states. We have already informed the Chandigarh administration about our willingness and capabilities. It usually takes a minimum of seven days to process the samples for whole-genome sequencing.

The CSIR-IMTech is a research institute of the Council of Scientific and Industrial Research (CSIR). The Institute of Microbial Technology (IMTech), Chandigarh, is part of the Indian SARS-CoV-2 Consortium on Genomics (INSACOG), which is mandated to carry out genome sequencing for studying the virus variations of the circulating SARS-CoV-2 strains in India.

In August, the Department of Virology, PGI, had done a pilot project on genome sequencing of some samples. According to Prof. Surjit Singh, Director PGI, whole-genome sequencing for Covid is not in the mandate of PGI, as the institute is involved in a host of other services related to patient care, with the OPD numbers very high. We are also taking care of mentoring and training for doctors across the region. Genome sequencing for other diseases in the Department of Paediatrics is being done for more than 13 years now, adds Prof. Singh.

Prof. Mini P Singh, Professor and Nodal Officer, Covid-19 Testing at PGIMER, says, We are involved in so many diagnostic portfolios in the Department of Virology, so we cant justify the work of whole-genome sequencing. Here at PGI, we are deeply immersed in diagnostics and patient care and are also handling seven portfolios of the ICMR, and the idea is to do the best in your area of work. Also, this is an extremely sensitive area, and a lot of criteria have to be fulfilled before you can even apply for such a facility. Also, there is a dedicated system and experts needed to run such a facility, and we dont have a Next-Gen Sequencer in Virology. Since March 2020, we have been doing Covid testing 247 and testing close to 2,000 samples a day, even when the cases were not too many. None of the premier institutes in the country are doing this kind of work, and we want to focus and give our best to the diagnostic services and portfolios at hand.

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Chandigarh: IMTech all equipped to carry out whole-genome sequencing - The Indian Express

Special to The T&D

Clemson researcher Chris Saski admits sending the universitys iconic Tiger Paw to space aboard a SpaceX Dragon spacecraft is, quite literally, an out-of-this-world experience.

But its the potential for the experiments in the flight hardware to which the Paw is attached that truly excites him.

Saskis cotton regeneration research, adorned with Clemson stickers, intends to take off Dec. 21 from NASAs Kennedy Space Center in Florida bound for the International Space Station (ISS). Upon arrival, Saskis research project titled Unlocking the Cotton Genome to Precision Genetics will be conducted in microgravity with the goal of facilitating the ability to directly edit the genome of elite cotton varieties, quickly adding traits like disease resistance or drought tolerance without the need for the lengthy conventional breeding process that can take over a decade.

Understanding gene function and subsequent genome engineering technology has the potential to change the lives of everyone and everything on the planet.

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With no solution yet in place to satisfy a growing demand for fuel, food and fiber as the global population continues to expand, Saski believes this research is a large step in the right direction toward solving that problem.

Conducting these experiments in microgravity gives us a unique environment to disentangle the genetics of somatic embryogenesis regenerating a whole plant from a single cell and we believe we can translate this research into application, he said. This project will lead to new understanding of the genes involved. As we understand it now, this genetic program is encoded in all crop genomes, but it is suppressed. This research could ultimately allow us to switch on this genetic program in other crops and be able to do genome editing and engineering more readily and directly on commercial varieties and eventually provide an accelerated path to food, fuel and fiber for a growing population of people on Earth.

Food for thought or living on another planet

But if potentially addressing issues such as global hunger wasnt enough, the possibilities go far beyond, said Saski, who admitted he never imagined space missions would one day be part of his work.

When I started my position as a researcher here at Clemson, I quickly realized that there really are no boundaries to the questions that one can ask, he said. I just created a vision, worked hard and tried to set the bar high. I envision that translation of this research into application could enable deep space exploration missions, it could allow for plants to be stored as single cells and you could store and supply a diversity of plant species for astronauts that are doing research or even living on another planet.

Broadly, the project seeks to explore the cotton genome and how it reacts in microgravity and normal gravity. It was selected as a winner in the Cotton Sustainability Challenge, which was run by the Center for the Advancement of Science in Space (CASIS) and funded by Target Corporation, providing researchers and innovators the opportunity to propose solutions to improve crop production on Earth by sending their concepts to the ISS U.S. National Laboratory. CASIS is the organization tasked by NASA to manage the ISS National Lab.

One of Saskis collaborators is Jeremy Schmutz, faculty investigator at HudsonAlpha Institute for Biotechnology since 2008, who said the project aims to understand how callus cells divide and regenerate in space and how this affects the quality of transformed cells.

We have shown that cotton has very little diversity as a species, which greatly limits the possibilities of improving the sustainability of cotton through traditional breeding techniques, Schmutz said. Accelerating the speed at which we can transform cotton opens up the ability to rapidly test genes linked to beneficial traits and also make positive targeted modifications in important cotton lines for U.S. growers and the many industries that depend on high-quality cotton production.

Embryogenesis in microgravity

Conventional breeding process currently takes more than a decade

And why does conducting research in microgravity make a difference?

Microgravity is the condition in which people or objects appear weightless. Plants have evolved at a force of 1g the force of gravity on Earth, responsible for things such as keeping our feet planted firmly on the ground but without that force, or in microgravity, there can be a drastic effect on gene expression.

Studying developmental programs like embryogenesis in microgravity allows us to disentangle what genes are involved by comparing experiments on the ISS and on Earth, according to Saski.

Our experiment is aimed at understanding the genetic architecture and coordination of embryogenesis, he said. Understanding this program could facilitate the ability to directly edit the genome of elite breeding germplasm, adding traits such as disease resistance or drought tolerance without the need for the long conventional breeding process.

Don Jones, director of Breeding, Genetics and Biotechnology at Cotton Incorporated, echoed Saskis sentiment that this understanding could be a direct and immediate benefit of sending the project to space but said the potential for longer-term benefits is also vast.

Past space exploration has resulted in benefits for all of humanity that oftentimes far exceeds the expectations of those who were conducting the initial research. Conventional breeding now takes at least a decade to deliver improved varieties to cotton growers that can withstand drought and disease, both of which will increase with climate change, Jones said. Understanding and improving embryogenesis will allow such varieties to be developed significantly faster, and when the payoff is faster, more companies and institutions become interested in investing real dollars into cotton research with a shortened payoff time horizon.

Low Earth orbit: Falling around the planet

The effects of microgravity can be seen when astronauts and objects float in space. But the prefix micro- means very small, not nonexistent, so microgravity refers to the condition where gravity seems to be very small.

The ISS operates in Low Earth Orbit (LEO) or about 200 to 250 miles high. At that height, Earths gravity is still very strong, thus a person who weighs 100 pounds on the ground would weigh 90 pounds there.

Earths gravity pulls objects, including the space station, toward its surface. As a result, the ISS is constantly falling toward Earth. But the station also is moving very fast so fast it matches the curve of the Earths surface.

If you throw a baseball, gravity will cause it to curve down; it will hit the ground soon, Saski said. A spacecraft in orbit moves at the right speed so that the curve of its fall matches the curve of Earth. For the space station, that speed is 17,500 miles per hour. The spacecraft keeps falling toward the ground but never hits it. Instead, it falls around the planet. The moon stays in orbit around Earth for this same reason.

For the purposes of this research, however, that difference between 1g gravitational force and microgravity can have a significant effect.

Saski and Clemson postdoctoral research scientist Sonika Kumar are studying plant cells analogous to human stem cells; in this case, plants cells that are not de-differentiated not a certain part of the plant allowing for complementary experiments to disentangle the genetic architecture of somatic embryogenesis.

That disentanglement would enable scientists to turn on this programming in other crops and do genome editing and genome engineering more readily. The potential, then, is for growers to feed a growing and expanding population of people on Earth.

Genetic and epigenetic changes control the process of somatic embryogenesis, Kumar said. Discovering the mechanism and genetic factors behind somatic embryogenesis will open new avenues to stimulate the cellular reprogramming of somatic embryogenesis that will be helpful in fast delivery of cotton varieties having a combination of multiple traits like excellent fiber quality, climate resilience and tolerance to biotic and abiotic stresses. This project with the objective of cotton sustainability challenge will improve the social and economic development of growers, stakeholders and industries.

Power of the Paw

As for the Tiger Paw, Saski said the ISS-required custom flight and operations hardware the payload that will be aboard the SpaceX Dragon spacecraft looked largely bare and boring in its original state.

Mission Director Dave Reed and his team at Techshot, a company recently acquired by space infrastructure company Redwire, are converting Saskis experiments into a payload for space travel and designing the operational hardware they are also responsible for putting the Clemson stickers on the flight hardware.

The evolution from scientific proposal to spaceflight is typically referred to as payload development, and the Redwire payload development team has the challenging task of merging the scientific investigation with the capability of spaceflight hardware and the constraints of resources such as upmass, astronaut time and cold stowage return of harvested material.

On behalf of our whole payload development team, we are proud to be supporting this exciting investigation that promises to yield new discoveries for the benefit of life on Earth, Reed said. Much of our work on ISS is about exploring how microgravity can positively impact industries, people and systems back on Earth, and this investigation supports this mission.

Saskis project represents the first time that a plant tissue culture experiment will be performed on orbit in NASAs Advanced Plant Habitat, which is designed to provide sunlight-strength illumination in order to grow plants such as radishes, peppers and tomatoes.

Plant tissue culture requires very, very low daytime light levels, just enough to maintain a circadian rhythm in the culture and a tiny fraction of what Plant Habitat was designed to produce, Reed said. To provide such a low light level, Redwire engineers developed an elegantly simple sun shade akin to one you would find at a terrestrial plant nursery.

As the team began to work on developing a payload to such specifications, Saski also inquired about the possibility of putting a Tiger Paw sticker on any of the hardward a request Reed said was not trivial.

In spaceflight, labels are serious business. Everything from font size to color to label material is prescribed, Reed said. Our team worked with the label approval team to find a spot where the sticker could be acceptably placed. For Dr. Saski, it was all a part of the great revelation about the intricacies of the spaceflight experience.

Because competition for research space aboard the ISS, which is roughly the size of a football field, is on a global scale, the presence of the Paw is no small feat.

Being able to send the beloved Tiger Paw to space has been an amazing experience, Saski said. Being selected for this opportunity and conducting research and being able to put it out there as far as it could possibly go has been a vision of my research program and aspirations since Ive joined the faculty here at Clemson.

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Cotton in orbit: Clemson genome study bound for space station - The Times and Democrat

SAN DIEGO, Dec. 16, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO), provider of optical genome mapping (OGM) solutions on the Saphyr system and the leading software for genomic data visualization, interpretation and reporting, today announced the launch of version 6.1 of BioDiscoverys NxClinical software with expanded capabilities for next-generation sequencing (NGS) data in genetic diseases and cancer. NxClinical is an industry-leading, platform-agnostic software solution, which integrates NGS and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants (CNV), single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view.

This new version is designed to address requests from our NxClinical customers around the world seeking to see more of what matters in their NGS data, commented Soheil Shams, PhD, Chief Informatics Officer of Bionano Genomics. We are committed to helping customers reveal more clinically relevant variants from genomic data across multiple platforms with a streamlined workflow that can allow for optimal turnaround time. This software upgrade represents another step further as we continue toward laying the groundwork for our goal of integrating OGM data with NGS data to provide what we believe can become the most comprehensive view of genome variation.

We believe version 6.1 significantly improves the ability of NxClinical to detect more clinically relevant variants from NGS data with the inclusion of uniparental disomy functionality and the expanded sequence knowledgebase for visualization and reporting of relevant genomic variants. In addition, data interpretation has been streamlined with the automated annotation of clinically relevant variants using the American College of Medical Genetics and Genomics (ACMG) technical standards. This feature automatically calculates the relevance for many of the evidence categories described by the ACMG technical standards for CNV interpretation, which can simplify data interpretation and reduce time to reportable result.

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At Bionano, we are working to transform the way the world sees the genome to elevate human health and wellness, said Erik Holmlin, PhD, President and CEO of Bionano Genomics. Software is the primary way our customers interact with their data and experience our products. Our goal is to increase the number of Bionano subscribers using NxClinical software to create a network effect where customers can obtain more meaningful results from their NGS and microarray data today so that in the future they can more easily implement OGM within the same software tool to see more genomic variants that matter.

About Bionano Genomics

Bionano 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 http://www.bionanogenomics.com, http://www.lineagen.com or http://www.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, will, expect, plan, anticipate, estimate, intend 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 ability and utility of NxClinical software to help visualize, interpret and report NGS data in genetic diseases and cancer; the ability of NxClinical software to integrate OGM data with NGS data to provide a comprehensive view of genome variation; the ability of NxClinical software to create a network effect that combines the synergies of NGS and microarray data to allow implementation of OGM within the same software. 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 products; failure of the new version of NxClinical to perform as intended; the effect on our software of cyber attacks, viruses and the like; 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 adoption or continued use of our technologies; 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, 2020 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.

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

Investor Relations:Amy ConradJuniper Point+1 (858) 366-3243amy@juniper-point.com

Media Relations:Michael SullivanSeismic+1 (503) 799-7520michael@teamseismic.com

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Bionano Genomics Announces the Launch of Version 6.1 of BioDiscoverys NxClinical Software for Genome Analysis with Expanded Capabilities for...

A team of researchers, led by the Agency for Science, Technology and Researchs (A*STAR) Genome Institute of Singapore (GIS), was awarded the prestigious Chan Zuckerberg Initiative (CZI) Ancestry Network Grant in support of their Asian Immune Diversity Atlas (AIDA) project. The project aims to build a map of cells from the blood of healthy Asian individuals spanning 20 distinct populations from eight Asian countries: Singapore, Japan, South Korea, India, Thailand, Russia, Pakistan and Sri Lanka.

Although Asia accounts for nearly 60 percent of the global population, samples from Asian individuals are under-represented in global genomic databases. AIDA, the flagship project of Human Cell Atlas (HCA) Asia, aims to correct this imbalance by studying how immune cells are affected by age, ethnicity, environment and geography.

With the support of the CZI Ancestry Network grant, AIDA will expand representation of diverse Asian population groups within the HCA, promote research participation across Asia, and maintain long-term community engagement to ensure that the project benefits participating communities. AIDA will also provide a baseline measurement of the immune system (the bodys defence mechanism) in healthy individuals, which will be essential for identifying the abnormalities that occur in diverse immune-related diseases, metabolic disorders and cancers.

The project will sequence millions of individual cells from over 1,000 individuals to study the expression of genes as well as the unique immune cell receptors that are involved in mounting a defence against invading pathogens. This will shed light on the properties of immune cells in healthy individuals and serve as a reference and comparison point for understanding immune aberrations in diseases.

Dr Shyam Prabhakar, Associate Director of Spatial and Single Cell Systems at GIS, said, AIDA is the first large-scale effort to characterise immune cell diversity in Asian populations. It will lay a foundation for Precision Medicine in Asia by facilitating therapies tailored to the specifics of the patient. The curated data will be deposited in public repositories for the benefit of the scientific and clinical communities.

Prof Patrick Tan, Executive Director of GIS, said, GIS is honoured to be part of this pioneering regional collaboration, working towards a unified goal of creating a large-scale map of representative traits of immune cells from healthy Asian individuals. It will help us define the changes that cause immune disorders and eventually develop new treatments.

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Scientists from the Genome Institute of Singa - EurekAlert

The crucial role of effective genomic surveillance

With the COVID-19 pandemic progressing, genomic surveillance, conducted in an efficient way, is essential to inform us of circulating viruses and response measures required. The sequencing of representative samples continuously collected in a standardized approach from patients meeting influenza-like illness, acute respiratory infection, and severe acute respiratory infection case definitions, allows us to monitor the evolving trends and relative proportions of existing and emerging genetic variants circulating in the community.

GISRS has monitored influenza viruses since 1952, and since March 2020, SARS-CoV-2 was added to GISRS. In February 2021, the Global Influenza Programme (GIP) published Operational considerations to expedite genomic sequencing component of GISRS surveillance of SARS-CoV-2, to improve the geographic, demographic and temporal representativeness of data, monitor the trends and prevalence of genetic variants, and better understand the associations among the genetic characteristics, transmission fitness and disease profiles of SARS-CoV-2. In October 2021, GIP hosted an e-consultation to update the Operational Considerations and incorporate them with the previously published guidance document Maintaining surveillance of influenza and monitoring SARS-CoV-2: adapting Global Influenza Surveillance and Response System (GISRS) and sentinel systems during COVID-19 pandemic. This new publication is due for publication soon.

GISAID has been an important partner of GISRS, and its EpiFlu database has been a key component of influenza surveillance since 2008. At the start of COVID-19 pandemic GISAID rapidly launched the EpiCoV platform, where the first complete genome of SARS-CoV-2 was shared globally, and various analytical tools were developed to support the rapid sharing and interpreting of SARS-CoV-2 data.

GISRS-GISAID collaboration on influenza has been expanded to other respiratory viruses including SARS-CoV-2 and Respiratory Syncytial Virus (RSV). A joint bioinformatics training programme was developed to support WHO Member States to expedite the effective genomic surveillance of SARS-CoV-2 using influenza surveillance systems.

Training workshops organized

To further strengthen GISRS genomic surveillance capacity, the WHO Global Influenza Programme and GISAID jointly organized a series of workshops with experts from National Influenza Centres (NICs) and National COVID-19 laboratories. The objectives of the training includes:

The course is divided into three modules, from basic to advanced levels.

Module 1 (Introductory) was recently completed. It was attended by more than 110 experts from over 40 countries across the world, from Algeria and Australia to the United States and Venezuela. It comprised online lectures with real-time demonstrations followed by offline exercises. The training was held over a period of several months and grouped into five small groups according to their time zone and language spoken.

The module covered the basics of virus sequencing; considerations for the genomic sequencing component of GISRS surveillance of SARS-CoV-2; and the submission, curation, annotation and basic interpretation of data using GISAID tools.

Module 2 (Intermediate) and Module 3 (Advanced) will be launched in the coming months.

As we have learnt from the COVID-19 pandemic, an effective genomic surveillance system using GISRS to monitor SARS-CoV-2, as well as for influenza, is a critical component of pandemic and post-pandemic response. WHO will continue to strengthen the global network of laboratories of GISRS.

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The essential task of strengthening genomic surveillance: WHO in collaboration with GISAID organizes training workshops for laboratory experts - World...

By Allison Proffitt

December 14, 2021 | Seven Bridges Genomics has launched a new subsidiary, the Unified Patient Network (UPN), to facilitate clinical research and collaboration between participating health systems and biopharma companies. The UPN will combine de-identified sequencing data and EHR content for five million patients and allow biopharma companies to license cohorts from that dataset for research. Licensing fees from biopharma will fund the network.

The Unified Patient Network is designed to leverage Seven Bridges unique capabilities in building ecosystems and bringing stakeholders together, William Moss, CEO of Seven Bridges, told Clinical Research News.

The UPN will harmonize 30x whole genome coverage for patients that opt-in with electronic health records from large health systems across the country. The UPNs objective is to include full datasets on five million participants within five years. Technical partners include Genome Medical, Amazon Web Services, the Broad Institute of MIT and Harvard, Illumina and others.

Moss serves as CEO of the UPN; David Ledbetter was named the Chief Clinical and Research Officer. Ledbetter was previously executive vice president and chief scientific officer at Geisinger Health System where he was the principal investigator for the MyCode biobank and precision health program that exceeded 175,000 patients with exome sequence data linked to rich, longitudinal EHR and other clinical data.

What makes the Unified Patient Network unique compared to any of the other programs that are out there that might be seen as somewhat similar is our focus on whole genome context, Moss explained. We are providingfrom a genomic perspective30x coverage whole genome data across the entire genome, utilizing similar techniques that we used in producing the content for the UK Biobank.

Connecting Health Systems, Patients, Pharma

The UPN will operate as a collaborative group of nonprofit academic health centers. Washington University School of Medicine in St. Louis and its affiliated health system, BJC HealthCare, is the first academic health system announced as a UPN member. Two others will be announced in the coming weeks, Moss said. These first three health system partners represent an addressable patient population of 20 million.

The UPN will operate across many disease states and therapeutic areas, including rare, complex neurodegenerative, psychiatric and autoimmune diseases and disorders, as well as cancer, cardiology and common diseases such as diabetes. Patients who volunteer for clinical research studies conducted as part of the UPN will need to provide informed consent to participate. A central institutional review board (IRB) will approve all studies.

From within the UPN, Biopharma companies can seek specific cohorts of patient data. Biopharma can actually tell us who they want, Moss said. They can say: were looking for 2,000 individuals with this type of cancer, who have received this treatment, and have either been responsive or non-responsivewhatever attributes those are.

Biopharma has the option of either using the deidentified EHR and genomic data from within the UPN, or re-contacting individual patients for more in-depth study through their health systems and physicians. The UPN does not have the capability of deidentifying patient records, Moss said. Those keys reside with the health systems, and physicians make initial contact with a patient.

A big part of what were doing is were embracing the health systems and the relationships between the health systems, the healthcare providers, and the patients, Moss said. We work with the health systems and the healthcare providers to find the participants who meet the needs of the biopharma, and theyre invited to participate in a research study.

Data licensing fees from biopharma support the UPN and go back to individual health systems to fund their own research as well. Companies have a six-to-nine-month embargo period on the data, Moss said, before it returns to the UPN and can be licensed and used by others. After the embargo period, that data becomes able to be licensed by other biopharmas. More importantly, that data becomes available to each of the health system members in order to enable them to enhance their precision medicine research and to actually be participating as learning health systems in precision medicine, he said.

The Data Plan

Only de-identified genomic and clinical EHR content will be made available via the database. The UPN is leveraging the secure Seven Bridges research and development ecosystem as the interoperability infrastructure for the community. The ARIA scientific intelligence system will enable exploration and analysis for complex cohort stratification across populations of millions of patients. Member health systems will be provided with a base-tier license of the Seven Bridges platform, Moss added.

Content will be made available only to credentialed researchers as part of IRB-approved research studies, as mutually agreed to by the UPN and the health system members, by leveraging Seven Bridges' proven security, authentication and authorization protocols and technologies.

Patients who previously provided consent for the UPN can opt at any time to have their de-identified genetic and clinical data removed from the network's database.

Counseling Commitment

Another foundational partner, Genome Medical, will provide genetics and genomics counseling for both participants and physicians. Sequencing findings will be returned to participantsthe specific list of returned results is still being decided, Moss saidand Genome Medical will also handle peer-to-peer counseling for physicians whose patients have new results.

This is about bringing along the population and the physician, and thats why we include peer-to-peer counseling, Moss said, so that the physician can learn from a genetics expert as to what are the meanings of the results and how does that get integrated into a care plan.

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Seven Bridges Launches the Unified Patient Network With Genomic, EHR Data - Bio-IT World