Category Archives: Genome

America's 46th president wants to use government policy and technology to address social justice, climate change, and economic prosperity.

President Joe Biden has added a science advisor to his Cabinet and wants tech leaders to help solve the country's biggest problems including climate change, the COVID-19 pandemic, and social justice.

Image: Bet_Noire

President Joe Biden is making science part of the decision-making process again by adding the director of the Office of Science and Technology Policy to his Cabinet. Biden asked Eric Lander to lead the OSTP. Lander was one of the leaders of the Human Genome Project and is now the president ofthe Broad Institute of MIT and Harvard. He also was the co-chair of the President's Council of Advisors on Science and Technology for President Barack Obama.

Gary Shapiro, president and CEO of CTA, said he looks forward to working with the new OSTP and providing a forward-thinking approach to how tech can continue to serve as a tool for helping the country.

SEE: Big data's role in COVID-19 (free PDF) (TechRepublic)

"President-elect Biden's decision to elevate the Office of Science and Technology Policy to Cabinet level reflects tech's vital role in solving pressing challengesfrom creating a cleaner environment to conquering the pandemic," he said.

In his nomination letter to Lander, Biden asked the researcher to consider five specific questions and recommend general strategies, specific actions, and new structures that the federal government should adopt to support these priorities. The five questions are:

Tom Wheeler, a former chairman of the FCC and currently a visiting fellow with the Center for Technology Innovation at The Brookings Institution, said that adding the head of the OSTP to the Cabinet sends the message that science and technology are guiding principles again after four years of an administration that took the opposite approach.

The American Association for the Advancement of Science and The National Academies of Sciences, Engineering, and Medicine both applauded Lander's appointment. Lander is known for his scientific accomplishments but also for his combative management style. Colleagues have accused him of rewriting the history of CRISPR and downplaying contributions of the two women who won a Nobel prize in 2020 for their work on the gene-editing technology.

Wheeler also was on the Obama transition team. He said the new government was facing one existential crisis back in early 2008: The economic collapse. He described the five enormous problems the incoming Biden administration faces:

Wheeler said that the new administration should focus on how technology can help provide solutions to these existential crises.

"An easy one to envision is broadband policy: Connecting those who are not connected because they don't have access or or they can't afford it; that one thing hits four of those issues," he said.

Wheeler said it's time for government leaders to start using policy to put guardrails around all forms of technology.

"It's the innovators who always make the rules early on until those rules begin to infringe on the right of others and the public interest," he said. "That time is now."

This new approach should apply across the board to everything from artificial intelligence to Section 230 to net neutrality, Wheeler said. He was a chief architect of net neutrality during his five years as FCC chairman.

He also said that government policies and the policy-making process should adopt an agile approach, just as many digital companies do.

The existing government regulatory agencies that we know today were created in response to the Industrial Revolution, he said, which resulted in a rules-based hierarchy and a rigid process.

"That structure is handicapped when it comes to dealing with the need for agile, adaptive oversight to handle a rapidly changing tech and marketplace reality," he said. "How do we bring agile regulation into government? That will be the challenge."

Wheeler said digital companies have been able to make the rules for themselves because only those leaders had the vision to see where the industry was going.

"Big Tech was unfathomable to most Americans as well those who represent them in Congress," he said. "We're getting to the point now that the people are aware that their rights are being abused and therefore their representatives are similarly coming up to speed."

At CES 2021, National Economic Council Director-Designate Brian Deese spoke with CES President Gary Shapiro about Biden's tech and economic priorities. Deese will be part of the Cabinet and will help shape economic policy decisions. Deese said Biden wants to reinvest in manufacturing and research and development.

He said the COVID-19 vaccine is "a testament to technology and science," but added that the operational challenge of "getting the vaccines into people's arms will be one of the most costly and complex issues in our country's history." He said tech companies can help with the public health response.

During the Trump administration, the OSTP focused on quantum computing and artificial intelligence. An administration official attended CES 2020 to talk about new guidelines for artificial intelligence (AI). In August 2020, the White House, the National Science Foundation (NSF), and the Department of Energy (DOE) announced more than $1 billion in funding for 12 new AI and QIS research and development (R&D) institutes nationwide.

Learn the latest news and best practices about data science, big data analytics, and artificial intelligence. Delivered Mondays

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Human genome expert to join the Cabinet as Biden brings science and technology back to the table - TechRepublic

Bridgestone Corporation announced results of its four-year collaboration with genomic big data solutions company NRGene to advance the commercialization of guayule, an alternative to natural rubber, as part of the effort to diversify its sources of raw materials. The combined effort focused on analyzing DNA to allow more efficient use of inherent genetic diversity to breed highly productive varieties of guayule.

Native to the desert regions of the southwestern United States and northern Mexico, guayule is a shrub capable of producing natural rubber and can grow on marginal farmland with minimal fertilizer inputs. Guayule has the physical and genetic characteristics of a desert plant, successfully tolerating arid environments and making its demand for water lower than other commercial crops grown in the region. This is important since dwindling water resources in the Southwest US are demanding that agriculture find ways to reduce water usage and guayule could be a solution.

Utilizing NRGenes DeNovoMAGIC system, scientists at Bridgestone and NRGene have successfully assembled a specific guayule genome. This achievement provided a complete description of the genome sequence and all its genes, allowing for the use of additional genomic diversity in the identification of the genetic basis for important traits such as rubber percentage.

Furthermore, Bridgestone developed mapping populations that allowed NRGene to construct a genetic and physical map by successfully identifying the correct order of DNA fragments. These maps enable Bridgestone to use the information contained in the genetic code to assist in its breeding efforts. The joint work was successful in constructing pseudochromosomes (i.e. molecules that contain most of the information of the chromosomes) using an approach that combines multiple genomes, marking a historic milestone in guayule research.

The collaboration between Bridgestone and NRGene will provide important advances for the future of the automotive and rubber industries. The combination of our previous work with the sequencing and assembly of the hevea genome and our current work with guayule uniquely positions Bridgestone to utilize these resources for comparative genetic analysis of the rubber biosynthetic pathways and become a leader in the genetics and improvement of rubber-producing plants.

William Niaura, director, Innovation, Bridgestone Americas

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Bridgestone collaboration with NRGene achieves new milestones in assembly of multiple guayule genomes; alternative to natural rubber - Green Car...

This article was originally published here

Mol Reprod Dev. 2021 Jan 20. doi: 10.1002/mrd.23449. Online ahead of print.

ABSTRACT

BRDT, a member of the BET family of double bromodomain-containing proteins, is essential for spermatogenesis in the mouse and has been postulated to be a key regulator of transcription in meiotic and post-meiotic cells. To understand the function of BRDT in these processes, we first characterized the genome-wide distribution of the BRDT binding sites, in particular within gene units, by ChIP-Seq analysis of enriched fractions of pachytene spermatocytes and round spermatids. In both cell types, BRDT binding sites were mainly located in promoters, first exons, and introns of genes. BRDT binding sites in promoters overlapped with several histone modifications and histone variants associated with active transcription, and were enriched for consensus sequences for specific transcription factors, including MYB, RFX, ETS, and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE, and RFX in round spermatids. Subsequent integration of the ChIP-seq data with available transcriptome data revealed that stage-specific gene expression programs are associated with BRDT binding to their gene promoters, with most of the BDRT-bound genes being upregulated. Gene Ontology analysis further identified unique sets of genes enriched in diverse biological processes essential for meiosis and spermiogenesis between the two cell types, suggesting distinct developmentally stage-specific functions for BRDT. Taken together, our data suggest that BRDT cooperates with different transcription factors at distinctive chromatin regions within gene units to regulate diverse downstream target genes that function in male meiosis and spermiogenesis.

PMID:33469999 | DOI:10.1002/mrd.23449

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Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate...

SAN DIEGO, Jan. 18, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO) announced that the last day of its five-day Next-Generation Cytogenomics Symposium featured presentations by members of the COVID-19 Host Genome Structural Variant (SV) Consortiumusing the Saphyr system for optical genome mapping (OGM) to analyze the genomes of patients with severe COVID-19 disease. The presentations by scientists and clinicians from leading hospitals and research institutions in Europe and the US showed that Saphyr was able to detect structural variants that may predispose to severe or mild COVID-19 disease, which had not been identified previously by large studies using next-generation sequencing (NGS) or array-based methods to analyze genomic variation.

Dr. Alex Hoischen, Radboud University, discussed his published results on genomic variants found in families with severe COVID-19. In two families with severely ill brothers, mutations were found in the Toll Like Receptor 7 gene (TLR7), which affects the production of interferons, signaling molecules used to control the immune response. Several other studies have since made similar findings in other genes of the TLR family. Dr. Hoischen discussed how individual patients each may carry individually rare variants, that are collectively common and point to important pathways involved in the disease. His interest in the consortium is based on his understanding that larger SVs have a greater chance to be rare and disruptive, and genome-wide studies have lacked so far in their assessment.

Dr. Erich Jarvis, Howard Hughes Medical Institute investigator, professor at The Rockefeller University and head of the Vertebrate Genome Project (VGP),discussed an interesting difference between hospitalized patients and controls where the severely ill show more variation in a part of the Interferon Alpha and Beta Receptor Subunit 1 gene, a key part of the interferon pathway that regulates immune response. Dr. Jarvis is using Saphyr and the pipeline he developed for the VGP to build reference-quality genomes of patients and controls and will compare them with each other and with animal species that are sensitive to infection with SARS-CoV-2 or not, as previously reported.

Dr. Ravindra Kolhe, Vice-Chairman of Pathology at the Medical College of Georgia at Augusta University and founder of the COVID-19 Host Genome SV Consortium explained that he founded the consortium because COVID-19 shows a split mortality where a very large number of people get infected, but only a small percentage of those get sick or die. Mortalities are associated with diabetes, hypertension and a history of heart failure, yet independent of that a seemingly random group of patients get extremely ill. Since other studies looking at host genetics use NGS or single nucleotide polymorphism (SNP) arrays that are ill suited to analyze SVs, the consortium focuses on the use of OGM to detect the larger genomic variants most likely to make the largest impact.

Dr. Kolhe presented the previously announced finding from the consortium on 37 ICU-admitted, severely ill COVID-19 patients whose genomes were analyzed using Saphyr.In several severely ill patients Saphyr detected structural variants affecting important immune genes. In another patient Saphyr found a duplication of the STK26 gene, which reduces the production of interferon likelyleading to reduced viral clearance and increasing the disease severity. When other severely ill patients were compared with asymptomatic COVID-19 patients, the sameSTK26gene was found to be significantly more active in all the sick patients, making it a possible biomarker for disease severity. OGM identified many more variants in the severely ill patients affecting genes controlling immunity, airway mucous, and viral replication. Dr. Kolhe stated that his team wants to use structural variants identified with Saphyr to design preventative measures for those people whose genomes show them to be the most vulnerable and develop a biomarker panel that can be run at the time of patient admission, to make sure that appropriate measures are taken based on the genetic makeup and patients get the treatment they need as early as possible. In order to do so, the consortium has announced plans to analyze 1000 genomes with Saphyr allowing them to determine with high confidence which SV are involved in disease susceptibility and severity.

Siavash Raisi, Dr. Vineet Bafnas laboratory at UCSD presented on FaNDOM, an algorithm they developed that is used by the consortium to quickly and efficiently verify the structural variants identified by the Saphyr system. It was able to provide an independent confirmation of all of the variants identified by Saphyr using Bionano Access and Solve software and reported in the consortium publication.

Dr. Silviu-Alin Bacanu, Virginia Commonwealth University described how existing resources and other host genome studies can be used to prioritize genes and structural variants identified with Saphyr.He described several studies including the genome-wide association studies on COVID-19 host genetics and the UK Biobank which has collected genomic data on more than 250,000 individuals. Although these large studies are unable to identify important large variants directly, their data can help prioritize variants detected by OGM based on whether they affect genes or pathways which these larger studies have identified as possible correlated with disease severity and outcome.

Dr. Alan Beggs and Dr. Catherine Brownstein, Boston Childrens Hospital (BCH) discussed their previously announced study on the genomes of patients with Multisystem Inflammatory Syndrome in Children (MIS-C), a severe inflammatory attack of multiple organs weeks after COVID-19 infection in children with an average age of 8 years old. BCH has reported 67 cases of hospitalized MIS-C, and the Childrens Rare Disease Cohort Initiative has banked their specimens. Drs. Beggs and Brownstein are enrolling 50 patients each with MIS-C, severe COVID-19, and asymptomatic or mildly affected patients and will compare their genomes using OGM with Saphyr and with NGS.

Dr. Michael Zody, New York Genome Center (NYGC) presented on the use of NGS on patients also analyzed with Saphyr. The NYGC has an active research project to sequence both the viral and the patient genomes using NGS. Their study is focused on patients with severe COVID-19 without prior high-risk diseases and on MIS-C cases, and in a collaboration with Dr. Jean-Laurent Casanova has found rare defects in immunity that affect the disease severity by altering the interferon response in patients. By combining the NGS data collected by NYGC with the OGM data from the consortium, smaller events and single nucleotide variants detected by NGS and large variants detected by Saphyr can be analyzed together.

Recordings of all the presentations from the symposium can be found at http://bit.ly/3pLPT28

About Bionano GenomicsBionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing and providing diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a research use only platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools, and genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for over nine years and has performed over 65,000 tests for those with neurodevelopmental concerns. For more information, visitwww.bionanogenomics.comor http://www.lineagen.com.

Forward-Looking StatementsThis 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 timing and content of the presentations identified in this press release; the effectiveness and utility of Bionanos technology in basic genetic research and clinical settings, and in the contexts and applications contemplated by the presentations identified in this press release; adoption of Saphyr as a standard platform in research and pathology settings; and the execution of Bionanos strategy. 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; 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; the loss of key members of management and our commercial team; and the risks and uncertainties associated withour 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, 2019 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 management's 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 Contact:Ashley R. RobinsonLifeSci Advisors, LLC+1 (617) 430-7577arr@lifesciadvisors.com

Media Contact:Darren Opland, PhDLifeSci Communications+1 (617) 733-7668darren@lifescicomms.com

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Day Five of Bionano's Next-Generation Cytogenomics Symposium: Saphyr Identifies Structural Variants that May Predispose to Severe COVID-19 Illness -...

A new study shows that humans express a powerful hormone during exercise and that treating mice with the hormone improves physical performance, capacity and fitness. Researchers say the findings present new possibilities for addressing age-related physical decline.

The research, published on Wednesday inNature Communications, reveals a detailed look at how the mitochondrial genome encodes instructions for regulating physical capacity, performance and metabolism during aging and may be able to increase healthy lifespan.

Mitochondria are known as the cells energy source, but they are also hubs that coordinate and fine-tune metabolism by actively communicating to the rest of the body, saidChanghan David Lee, assistant professor at theUSC Leonard Davis School of Gerontologyand corresponding author of the study. As we age, that communication network seems to break down, but our study suggests you can restore that network or rejuvenate an older mouse so it is as fit as a younger one.

The study looked at the role of MOTS-c, one of several recently identified hormones known to mimic the effects of exercise. However, MOTS-c is unique because it is encoded in the small genome of mitochondria rather than the larger genome in a cells nucleus. This opens up a whole new genome to target for new interventions, says Lee, who, along with Pinchas Cohen, professor of gerontology, medicine and biological sciences and dean of the USC Leonard Davis School, first described the evolutionarily conserved protein and its effects on metabolism in 2015.

Lees subsequent studies showed how mitochondrial-encoded MOTS-c instructs proteins to interact with the nuclear genome and plays important roles inregulating cell metabolism and stress responses.

Even groups of mice that had been fed a high-fat diet showed marked physical improvement after MOTS-c treatment and less weight gain than untreated mice. These findings echo previous research on MOTS-c treatment in mice, which also found that it reversed diet-induced obesity and diet- and age-dependent insulin resistance.

Additionally, treating the oldest mice nearing the end of their lives with MOTS-c resulted in marked physical improvements. This late-life treatment improved grip strength, gait (measured by stride length) and physical performance, which was assessed with a walking test (running was not possible at this age).

The older mice were the human equivalent of 65 and above and once treated, they doubled their running capacity on the treadmill, Lee said. They were even able to outrun their middle-aged, untreated cohorts.

In muscle cells, levels of MOTS-c significantly increased nearly 12-fold after exercise and remained partially elevated after a four-hour rest, while MOTS-c levels in blood plasma also increased by approximately 50% during and after exercise and then returned to baseline after the rest period. The findings suggest that the exercise itself induced the expression of the mitochondrial-encoded regulatory peptides.

The expression of MOTS-c during exercise in humans and the results from the studies in mice lend support to the idea that aging is regulated by genes in both the mitochondrial and nuclear genomes. While further research on MOTS-c is needed, the data indicates that MOTS-c treatment could increase health span, or the portion of the life span spent in good health, and address frailty and other age-related conditions, Lee said.

The results from MOTS-c treatment in mice are extremely promising for future translation into humans, he added, especially the fact that such results were obtained even with treatment starting at older ages.

Indicators of physical decline in humans, such as reduced stride length or walking capacity, are strongly linked to mortality and morbidity, he said. Interventions targeting age-related decline and frailty that are applied later in life would be more translationally feasible compared to lifelong treatments.

Reference: Reynolds JC, Lai RW, Woodhead JST, et al. MOTS-c is an exercise-induced mitochondrial-encoded regulator of age-dependent physical decline and muscle homeostasis. Nat Comms. 2021;12(1):470. doi:10.1038/s41467-020-20790-0.

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

Link:
Treating Mice With Hormone Improves Physical Performance - Technology Networks

Genomics is one of the premier disruptive technologies. While several exchange traded funds provide access to this fast-growing industry, the ARK Genomic Revolution Multi-Sector Fund (CBOE: ARKG) is arguably the best when it comes to keeping pace with the rapidly changing world of genomics advances.

Take the case of HiFi sequencing chemistry, a still nascent healthcare technology, but one some ARKG components already have exposure to.

During the J.P. Morgan Healthcare Conference last week, Invitae (NVTA), a leading medical genetics company, and Pacific Biosciences PacBio (PACB), a provider of long-read sequencing instruments, announced a collaboration to develop an ultra-high-throughput sequencing platform based on PacBios HiFi sequencing chemistry. This collaboration could increase the number of threats to companies focused on short-read sequencing, according to ARK research.

Genomics companies try to better understand how biological information is collected, processed, and applied by reducing guesswork and enhancing precision, restructuring health care, agriculture, pharmaceuticals, and enhancing our quality of life. Data confirm that genomics is a booming market with epic potential for investors.

Securities within ARKG are substantially focused on and are expected to substantially benefit from extending and enhancing the quality of human and other life by incorporating technological and scientific developments, improvements and advancements in genomics into their business. One such way this is accomplished is by offering new products or services that rely on genomic sequencing, analysis, synthesis or instrumentation, according to the issuer.

HiFi sequencing could be the latest in a long line of compelling catalysts for ARKG.

Bolsterednot onlyby results from thisyearsPrecisionFDA Truth Challengebutalsoby improvementsinHiFiaccuracy viaGoogles (GOOGL)DeepVariantas well asresearch community feedback,we thinkPacBiosHiFi sequencingmethodprovidesthe most complete andaccurateview of thehumangenome, according to ARK.

HiFi is also important in helping ARKG components differentiate themselves from rivals.

In our opinion, HiFisequencing shouldhelpInvitaepullfurther away from its competition in the molecular diagnostics space, enabling the detection and evaluation of hard-to-sequencevariants that could change patient managementmeaningfully, notes ARK. Unlikewithshort-read sequencing, HiFi-sequenced genomesshouldallow forthedigital reassessment of patientsDNAthroughout their lifetimes, especially as researchers learn more about hard-to-sequence genes and the effects of structural variation within the human genome.

For more on disruptive technologies, visit our Disruptive Technology Channel.

The opinions and forecasts expressed herein are solely those of Tom Lydon, and may not actually come to pass. Information on this site should not be used or construed as an offer to sell, a solicitation of an offer to buy, or a recommendation for any product.

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ARKG: Access the Latest and Greatest Genomics Innovation - ETF Trends

SAN JOSE, Calif.--(BUSINESS WIRE)--OmniTier today announced that its genomic secondary analysis appliance, CompStor Novos, has added somatic variant calling from matched, whole genome sequencing (WGS) tumor-normal sample pairs.

About Somatic Variant Calling

The biggest challenge of somatic variant calling is to disambiguate low-frequency variants from artifacts. To solve that challenge OmniTier implemented sensitive statistical modeling to develop a new somatic variant caller that will provide superior accuracy from low to high allele frequencies. CompStor Novos can detect somatic mutations across the whole human genome with coverages up to 300x, reporting SNVs, indels and structural variants from NGS sequenced reads.

About CompStor Novos

CompStor Novos is a high throughput, low cost, easy to use, secondary analysis appliance, supporting Illumina, PacBio and BGI sequencers. Delivering end-to-end, WGS and WES secondary analysis pipelines, CompStor Novos includes both alignment and de novo assembly for genome identification. A GATK Mutect2 variant caller from the Broad Institute, and OmniTiers proprietary, higher accuracy variant caller are also included, providing a choice of caller outputs.

CompStor Novos is designed to be used as an on-premise appliance, or located in the Cloud or at the Edge to deliver secondary analysis services. By locating the CompStor Novos appliance on the same network as their sequencer, institutions can benefit from dramatic annual storage costs savings compared to cloud analysis services, whilst speeding up secondary analysis and throughput. For analyzing very large numbers of genomes quickly, CompStor Novos automatically allocates processing across two or more CompStor Novos appliances.

Availability

Somatic variant calling is included at no additional charge to new CompStor Novos customers, and for those customers on support and maintenance.

For a limited time OmniTier is offering a free trial to demonstrate CompStor Novos variant output results. Please contact us for more information.

About OmniTier

OmniTier develops AI and multiomics appliances and software for bioinformaticians and clinical researchers, that deliver affordable analysis solutions. Its integrated appliance solutions accelerate data-intensive genomic workflows and analysis, utilizing machine learning and AI. Founded in February 2015, the company has R&D operations in Milpitas, CA and Rochester, MN.

CompStor Novos is for research purposes only. CompStor Novos is a registered trademark of OmniTier, Inc.

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Somatic Variant Calling Is Added to OmniTier's CompStor Novos Genomics Analysis Appliance - Business Wire

The genomic subtype of a tumor may contribute to the level of circulating tumor DNA (ctDNA) shedding in patients with advanced nonsmall cell lung cancer (NSCLC), according to the results of a retrospective study reported in the Journal of Thoracic Oncology that could have implications for the clinical utility of ctDNA testing in early detection and disease monitoring.

The analysis included 144 patients with advanced NSCLC who had ctDNA testing performed at The University of Texas MD Anderson Cancer Center in Houston between November 2015 and July 2017. All patients had a computed tomography scan and brain magnetic resonance imaging to measure tumor burden within 30 days of ctDNA sampling. Genomic subtypes seen in the study population included TP53 mutation (53.5%), KRAS mutation (22.9%), EGFR mutation (39.6%), and ALK fusion (2.8%).

The analysis showed that ctDNA variant allele frequency (VAF) was significantly associated with tumor burden, as determined by CT volume (rho=0.34; P 0.0001) and metabolic tumor volume (rho=0.36; P =0.003).

While positive, the modest correlation observed between VAF and tumor burden in our cohort suggests that other factors also significantly impact ctDNA shedding, the study authors wrote.

All genomic subtypes assessed were found to have an association between ctDNA VAF and tumor burden. This association varied by genomic subtype. For example, tumors with KRAS mutations had the strongest association (rho=0.56; P 0.001) while tumors with EGFR mutations had the weakest (rho=0.24; P =0.077).

A multivariate analysis revealed that TP53 mutations (HR, 1.45; 95% CI, 1.16-1.80; P =0.001) and EGFR mutations (HR, 1.36; 95% CI, 1.08-1.71; P =0.009) were both independent predictors of elevated ctDNA shedding.

Among tumors with EGFR mutations, those that had EGFR copy number gain had a significantly higher ctDNA VAF compared with tumors without EGFR copy number gain (P 0.00001).

Visceral metastasis (hepatic, adrenal, renal, or splenic) was also an independent predictor of elevated ctDNA shedding (HR, 1.48; 95% CI, 1.16-1.91; P =0.002), as was tumor burden (HR, 1.00; 95% CI, 1.00-1.00; P <0.001), according to a multivariate analysis.

Our findings strongly suggest that ctDNA shedding is not only impacted by tumor burden but also by anatomic location and genomic subtype, the study authors concluded.

Disclosures: Some of the study authors disclosed financial relationships with the pharmaceutical industry and/or themedicaldeviceindustry. For a full list of disclosures, please refer to the original study.

Reference

Lam VK, Zhang J, Wu CC, et al. Genotype-specific differences in circulating tumor DNA levels in advanced NSCLC. J Thorac Oncol. Published online December 31, 2020. doi:10.1016/j.jtho.2020.12.011

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Tumor Genomic Subtype Might Influence Level of ctDNA Shedding in NSCLC - Cancer Therapy Advisor

The report by Zion Market Research titled How Will Global CRISPR Genome Editing Market React from 2021 Onwards?Research Reportpresents a profound comprehension regarding the functioning and expansion of theCRISPR Genome Editing Marketon a regional and global level. This analysis report is the collation of all the wide-ranging information relating to the market statistics during the recent years as well as forecasts for coming years. To begin with, the report comprises the major players actively participating and competing within the CRISPR Genome Editing Market; it entails several companies, manufacturers, suppliers, organizations, and so on. Thus, the report will assist in understanding the initiatives and approaches implemented by these players to create and reinforce their market presence. The thorough analysis presents a wide-ranging comprehension of the global market in a knowledgeable way. The client can merely point out the steps of the firm by having details regarding their global revenue, market share, price, production & capacity, and recent developments during the forecast period.

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Key players leveraging the business growth are

Editas Medicine, CRISPR Therapeutics AG, Horizon Discovery PLC., Sigma-Aldrich, Genscript, Sangamo BiosciencesInc., Lonza Group AG, Integrated DNA Technologies, New England Biolabs Inc, Origene Technologies Inc., Transposagen Biopharmaceuticals, Thermo Fisher Scientific, Caribou BiosciencesInc., Precision Biosciences, Cellectis, Intellia TherapeuticsInc., Novartis among others.

The research report includes the outline of the global CRISPR Genome Editing Market such as definition, classifications, and applications. Apart from this, it entails the comprehensive assessment of a number of factors like constraints, opportunities, drivers, challenges, and risk. Further, the global CRISPR Genome Editing Market is bifurcated on the basis of diverse parameters into respective segments as well as sub-segments. The report also encompasses the existing, previous, and likely growth trends within the market for each segment and sub-segment[Product, Applications, End-Users, and Major Regions]. Additionally, the market is also segregated based on regions[North America, Europe, Asia-Pacific, Latin America, The Middle East & Africa].along with detailed evaluation of their growth, key developments & strategies, opportunities, and the key patterns influencing the market expansion in those regions. The report will further also entail a particular part putting forth the changes and of the ongoing COVID-19pandemic. It comprises-depth market analysis rooted in the predictions of post-COVID-19 market circumstances together with data on the existing impacts on the CRISPR Genome Editing Marketof the pandemic.

Global CRISPR Genome Editing Market: Regional Segment Analysis

The research report also highlights the wide array of tactical steps, such as the latest business deals, joint ventures, partnerships, M&As, technological developments, and the launch of new products taking place in the market. In addition, it scrutinizes several patterns of the global CRISPR Genome Editing Market, entailing the rules, criteria, and policy deviations implemented by the private companies and government on the market over the last few years. As a final point, the analysis includes forecasts and historic data making it a beneficial asset for experts, industry executives, presentation, sales & product managers, consultants, and every other person or organization looking for essential market data and statistics.

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How Will Global CRISPR Genome Editing Market React from 2021 Onwards? The Courier - The Courier

A number of other previously identified strains have also been detected by whole genome sequencing, the ministry said.

The lineages are all consistent with overseas exposure, the ministry confirmed, reiterating that the 17 infections were detected due to routine testing in managed isolation facilities.

New Zealand has now recorded 29 cases of B.1.1.7, the mutated strain currently ravaging the United Kingdom, and seven infections of B.1.3.5.1, the South Africa variant.

"We expect we will continue to see both the UK variant and South Africa variant in positive cases in our managed isolation facilities here in New Zealand, as these forms of the virus become increasingly common around the world," the Ministry of Health said in Thursday's statement.

"All positive COVID-19 tests in New Zealand are sent to ESR to attempt whole genome sequencing as part of ongoing surveillance.

"This surveillance allows us to identify and better understand these variants in order to inform and refine our overall elimination strategy, in particular optimising our current stringent border processes including testing and regularly reviewing infection prevention procedures."

The healthcare department noted that further steps have been recently taken to strengthen New Zealand's border processes, including an additional test for returnees on arrival or day one of their stay in managed isolation. Pre-departure testing is now also required for all passengers planning to enter New Zealand, with the exception of travellers returning from Australia, Antarctica and the majority of the Pacific Islands.

On Wednesday, the Ministry of Health confirmed that six new imported cases had been detected in managed isolation facilities over the previous two days, including one who tested positive more than three weeks after arriving in the country. The person has been at the Jet Park Hotel, Auckland's quarantine facility, since the new year.

The ministry's next update is scheduled for 1pm on Friday, January 22.

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COVID-19: Genomic sequencing finds 17 of NZ's recent cases are the mutated UK, South African variants - Newshub