DNA Synthesis: Tackling the Main Bottleneck in Biology Research

CLARA RODRÍGUEZ FERNÁNDEZ | November 18, 2019 | 4 views

A wave of new technologies to synthesize DNA faster, cheaper and more accurately could have a far-reaching impact across all areas of biology research. Ten years ago, Sylvain Gariel was working for the French oil company Total, engineering microorganisms to produce biofuels. It was tedious work. The advent of next-generation sequencing meant that a whole human genome could be read within one day instead of several years. So why not translate that principle into DNA synthesis? Gariel and two of his colleagues at Total started looking for a way to write DNA faster, cheaper and with fewer errors. In 2014, they founded DNAScript. The goal of this company based in Paris is to develop a brand new way of writing DNA that can replace traditional chemical synthesis.

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Igenbio, Inc.

Igenbio, Inc. (Integrated Genomics™), provides a full range of products and services to support research in microbial genomics, biochemistry and gene expression. These products and services are based on ERGO™, our web-based genome analysis platform.

OTHER ARTICLES

Advancement in Genomics Accelerating its Penetration into Precision Health

Article | April 19, 2020

Genomics is an interdisciplinary field of biology emphasizing the structure, editing, evolution, function, and mapping of genomes. It is creating deeper inroads across the precision health domain with the increasing introduction of advanced technologies such as quantum simulation, next-generation sequencing (NGS), and precise genome manipulation. As precision health focuses on providing the proper intervention to the right patient at the right time, genomics increasingly finds applications in human and pathogen genome sequencing in clinical and research spaces. Rising Hereditary Diseases Burden Paving the Way for Genomics in Precision Health In the last few years, a significant surge in the prevalence of diseases and ailments such as diabetes, obesity, baldness, and others has been witnessed across the globe. A history of family members with chronic diseases, such as cancer, diabetes, high blood pressure, hearing issues, and heart disease, can sometimes continue into the next generation. Hence, the study of genes is extensively being conducted for predicting health risks and early treatment of these diseases. It also finds use in CRISPR-based diagnostics and the preparation of precision medication for the individual. In addition, ongoing advancements in genomics are making it possible to identify different genetic traits that persuade people to more widespread diseases and health problems. The Emergence of Genomics Improves Disease Understanding Genomics refers to the study of the complete genetic makeup of a cell or organism. Increasing scientific research in the area substantially contributes to increasing knowledge about the human genome and assists in improving the ability to understand disease etiology, risk, diagnosis, treatment, and prevention. On account of these improvements, innovative genomic technologies and tools are being developed to enable better precision health not only for the individual but for various regional populations as well. The Way Forward With growing preference for personalized medicine and an increasing need for more accurate pathogen detection and diagnostics, genomics is gaining huge popularity across the precision health domain. Also, increasing research activities for developing novel high-precision therapeutics and rising importance of gene study in the prevention, diagnosis, and management of infectious and genetic diseases will further pave the way for genomics in the forthcoming years.

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Top 10 biotech IPOs in 2019

Article | April 13, 2020

The big question at the start of 2019 was whether the IPO window would stay open for biotech companies, particularly those seeking to pull off ever-larger IPOs at increasingly earlier stages of development. The short answer is yes—kind of. Here’s the long answer: In the words of Renaissance Capital, the IPO market had “a mostly good year.” The total number of deals fell to 159 from 192 the year before, but technology and healthcare companies were standout performers. The latter—which include biotech, medtech and diagnostics companies—led the pack, making up 43% of all IPOs in 2019. By Renaissance’s count, seven companies went public at valuations exceeding $1 billion, up from five the year before

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DIAGNOSTICS

Cell Out? Lysate-Based Expression an Option for Personalized Meds

Article | April 20, 2021

Cell-free expression (CFE) is the practice of making a protein without using a living cell. In contrast with cell line-based methods, production is achieved using a fluid containing biological components extracted from a cell, i.e., a lysate. CFE offers potential advantages for biopharma according to Philip Probert, PhD, a senior scientist at the Centre for Process Innovation in the U.K.

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Closing bacterial genomes from the human gut microbiome using long-read sequencing

Article | February 12, 2020

In our lab, we focus on the impact of the gut microbiome on human health and disease. To evaluate this relationship, it’s important to understand the particular functions that different bacteria have. As bacteria are able to exchange, duplicate, and rearrange their genes in ways that directly affect their phenotypes, complete bacterial genomes assembled directly from human samples are essential to understand the strain variation and potential functions of the bacteria we host. Advances in the microbiome space have allowed for the de novo assembly of microbial genomes directly from metagenomes via short-read sequencing, assembly of reads into contigs, and binning of contigs into putative genome drafts. This is advantageous because it allows us to discover microbes without culturing them, directly from human samples and without reference databases. In the past year, there have been a number of tour de force efforts to broadly characterize the human gut microbiota through the creation of such metagenome-assembled genomes (MAGs)[1–4]. These works have produced hundreds of thousands of microbial genomes that vastly increase our understanding of the human gut. However, challenges in the assembly of short reads has limited our ability to correctly assemble repeated genomic elements and place them into genomic context. Thus, existing MAGs are often fragmented and do not include mobile genetic elements, 16S rRNA sequences, and other elements that are repeated or have high identity within and across bacterial genomes.

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Spotlight

Igenbio, Inc.

Igenbio, Inc. (Integrated Genomics™), provides a full range of products and services to support research in microbial genomics, biochemistry and gene expression. These products and services are based on ERGO™, our web-based genome analysis platform.

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MEDICAL

Spotlight Therapeutics Raises $36.5 Million Series B to Advance a Pipeline of Cell-Targeted In Vivo CRISPR Gene Editing Biologics

Spotlight Therapeutics | March 22, 2022

Spotlight Therapeutics, Inc. (“Spotlight”), a biotechnology company applying new insights to develop cell-targeted in vivo CRISPR gene editing biologics, today announced a $36.5M Series B financing to fuel a drive toward the clinic. The financing round was co-led by new investors GordonMD Global Investments and EPIQ Capital Group, with participation from Magnetic Ventures, as well as existing investors GV (formerly Google Ventures) and Emerson Collective and other investors. Craig Gordon, M.D., Founder, CEO and CIO of GordonMD Global Investments, joins the Company’s Board of Directors. Spotlight's proprietary technology platform, TAGE (Targeted Active Gene Editors), is a new class of biologics; highly engineered, modular programmable CRISPR effectors designed to target and edit selected cell types in vivo. This approach circumvents the complexity of packaged viral, viral-like, and nanoparticle delivery systems, opens the door to expanded applications, and holds the promise of increasing patient access. We are excited to help Spotlight advance its pioneering work, which shows promise for cell-targeted delivery of CRISPR effectors in vivo. Spotlight’s TAGE platform could enable significant expansion of CRISPR medicines to a wide range of diseases." Dr. Gordon. This Series B funding is a crucial milestone as we advance our lead first-in-class immuno-oncology (IO) program and progress our pipeline of programs in IO, ophthalmic diseases and hemoglobinopathies,It will enable us to execute our development plan, leveraging Spotlight’s unique cell-targeted in vivo delivery approach, as we aspire to unlock the full potential of gene editing and enable effective one-and-done medicines for patients.” Mary Haak-Frendscho, Ph.D., President and CEO of Spotlight Therapeutics. About Spotlight Therapeutics Established in mid-2018, Spotlight Therapeutics is a privately held biotechnology company advancing a pipeline of cell-targeted in vivo CRISPR gene editing therapies. Spotlight's proprietary technology platform TAGE (Targeted Active Gene Editors) is a new class of biologics, CRISPR effectors engineered for direct delivery in vivo, to achieve cell-selective therapeutic genome editing. Spotlight's pipeline is advancing its modular programmable CRISPR effectors towards clinical studies in immuno-oncology, ophthalmic diseases and hemoglobinopathies. The company is headquartered in Hayward, California.

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MEDICAL

TGen Selects MemVerge to Accelerate Idiopathic Pulmonary Fibrosis Research Discovery with Big Memory Technology

MemVerge | March 21, 2022

MemVerge™, the pioneers of Big Memory software, today announced that TGen, the Translational Genomics Research Institute, an affiliate of City of Hope, has selected MemVerge Memory Machine Big Memory virtualization software to accelerate time to discovery for Idiopathic Pulmonary Fibrosis (IPF), a disease which affects 100,000 people annually in the U.S. Using MemVerge technology, TGen is able to dramatically speed analytical processing by nearly 36% for single-cell RNA sequencing. As a nonprofit medical research institute, TGen researchers process single-cell RNA sequences to characterize cell transcriptomic profiles. The process can take up to six and a half hours to analyze a matrix of 30,000 genes by 114,000 cells. With consistently growing datasets, this processing time was preventing a desired time to discovery. The data required for analysis was simply too large to retain in traditional memory, and scaling capacity with dynamic random-access memory (DRAM) was too costly. TGen has instead deployed memory virtualization technology from MemVerge which virtualizes both DRAM and PMem (persistent memory) memory technologies, to increase the memory pool available for processing without requiring more high-cost DRAM. The solution further speeds TGen's genomics sequencing analysis with Memory Machine ZeroIO in-memory snapshots which capture multi-terabyte data sets at any point for rapid reloads at each stage of processing. The ZeroIO snapshot service is 1,000 times faster than the fastest storage snapshot to SSD and enables TGen to run processing workflows in parallel. This ensures that in the event of a system crash, in-memory snapshots are available to instantly re-start long running jobs without lengthy reloading. By utilizing the snapshotting and cloning capabilities of Memory Machine, we were able to parallelize the processing workflow, As a result, we can now save nearly 36% of computational time while also taking advantage of the big memory nodes. This will save a lot of time in downstream analysis." Glen Otero, Ph.D., Vice President of Scientific Computing at TGen. MemVerge Memory Machine has quickly resulted in research value for TGen, We have removed performance barriers from their research process so that they are able to perform vital, life-saving, research faster than ever possible. Now TGen is expanding the use of Big Memory technology across other research use cases where results and discoveries can produce findings for a healthier tomorrow." Jonathan Jiang, COO of MemVerge. MemVerge Memory Machine makes 100% use of available memory capacity while providing new operational capabilities to memory-centric workloads. Memory Machine answers the need for a modern in-memory computing model to support emerging applications that require real-time analytics, true in-memory computing, and fault-tolerant memory persistence to speed massive processing workloads. About MemVerge MemVerge is pioneering Big Memory Computing and Big Memory Cloud technology for the memory-centric and multi-cloud future. MemVerge® Memory Machine™ is the industry's first software to virtualize memory hardware for fine-grained provisioning of capacity, performance, availability, and mobility. On top of the transparent memory service, Memory Machine provides another industry first, ZeroIO™ in-memory snapshots which can encapsulate terabytes of application state within seconds and enable data management at the speed of memory. The breakthrough capabilities of Big Memory Computing and Big Memory Cloud Technology are opening the door to cloud agility and flexibility for thousands of Big Memory applications.

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MEDICAL

Duke Researchers Identify Genetic Mechanism in Brain Lesion Formation Using Single-Cell DNA Sequencing from Mission Bio

Mission Bio | March 15, 2022

Mission Bio, the pioneer in high-throughput single-cell DNA and multi-omics analysis, announced new findings by Daniel Snellings from the lab of Douglas Marchuk, PhD, at Duke University School of Medicine using single-cell DNA sequencing to identify genetic mechanisms leading to the development of cerebral cavernous malformations (CCMs). The study, published today in the journal Nature Cardiovascular Research, is the latest demonstration of how Mission Bio's Tapestri Platform is allowing researchers to probe new aspects of biology at a single-cell resolution not possible with bulk sequencing. Dr. Marchuk is Professor of Molecular Genetics and Microbiology at Duke. CCMs, a blood vessel abnormality that can lead to brain hemorrhages, have long been associated with developmental venous anomalies (DVAs), a typically benign but irregular vascular arrangement often found near sporadic CCMs – though researchers had yet to prove a link. In the paper, Snellings and colleagues sequenced DNA from three CCM patient samples to see if somatic mutations in MAP3K3 or PIK3CA – common in patients with CCMs – co-existed in the same cells. Single-cell DNA sequencing with Tapestri found co-occurring mutations in the cells of all three samples, a pattern that could not be determined by bulk sequencing. Further, the group found that the CCMs and the associated DVAs harbored identical mutations in PIK3CA, but that mutations in MAP3K3 were only found in the CCMs. Because of the pattern of PIK3CA and MAP3K3 co-occurrence in CCMs, the team could assess the temporal pattern of genetic mutations associated with disease progression. They determined that DVA is the first lesion to occur, and that CCM development happens only after acquisition of an activating MAP3K3 mutation in a cell of the existing DVA.sazsz It was surprising to find that something as common as DVAs—which are present in up to 16% of people—could be caused by a cancer driver mutation. This explains why sporadic CCMs are often found in the vicinity of a DVA, and may explain why other diseases like pontine gliomas are also found near DVAs." Snellings. Tapestri is regularly deployed in cancer research to detect somatic mutations in clonal populations as a way of tracking tumor development, and the researchers adapted that methodology to evaluate the relationship between DVAs and CCMs. Since DVAs are not regularly biopsied, the researchers also confirmed the presence of circulating mRNAs in patients with both CCM and DVA related to this biological pathway, in plasma – a first step toward establishing a biomarker for CCM risk in patients with DVAs. We expect this research will have a meaningful impact for patients at risk for developing spontaneous cerebral cavernous malformations, which can lead to strokes or even death, This paper is a powerful new demonstration that there are many disease areas where single-cell DNA sequencing is helping elucidate the mechanisms of disease development, and identifying potential targets for diagnostics or therapeutics." Yan Zhang, PhD, CEO of Mission Bio. About Mission Bio Mission Bio is a life sciences company that accelerates discoveries and cures for a wide range of diseases by equipping researchers with the tools they need to better measure and predict our resistance and response to new therapies. Mission Bio's multi-omics approach improves time-to-market for new therapeutics, including innovative cell and gene therapies that provide new pathways to health. Founded in 2014, Mission Bio has secured investment from Novo Growth, Cota Capital, Agilent Technologies, Mayfield Fund, and others. The company's Tapestri platform gives researchers around the globe the power to interrogate every molecule in a cell together, providing a comprehensive understanding of activity from a single sample. Tapestri is the only commercialized multi-omics platform capable of analyzing DNA and protein simultaneously from the same sample at single-cell resolution. The Tapestri Platform is being utilized by customers at leading research centers, pharmaceutical, and diagnostics companies worldwide to develop treatments and eventually cures for cancer.

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MEDICAL

Spotlight Therapeutics Raises $36.5 Million Series B to Advance a Pipeline of Cell-Targeted In Vivo CRISPR Gene Editing Biologics

Spotlight Therapeutics | March 22, 2022

Spotlight Therapeutics, Inc. (“Spotlight”), a biotechnology company applying new insights to develop cell-targeted in vivo CRISPR gene editing biologics, today announced a $36.5M Series B financing to fuel a drive toward the clinic. The financing round was co-led by new investors GordonMD Global Investments and EPIQ Capital Group, with participation from Magnetic Ventures, as well as existing investors GV (formerly Google Ventures) and Emerson Collective and other investors. Craig Gordon, M.D., Founder, CEO and CIO of GordonMD Global Investments, joins the Company’s Board of Directors. Spotlight's proprietary technology platform, TAGE (Targeted Active Gene Editors), is a new class of biologics; highly engineered, modular programmable CRISPR effectors designed to target and edit selected cell types in vivo. This approach circumvents the complexity of packaged viral, viral-like, and nanoparticle delivery systems, opens the door to expanded applications, and holds the promise of increasing patient access. We are excited to help Spotlight advance its pioneering work, which shows promise for cell-targeted delivery of CRISPR effectors in vivo. Spotlight’s TAGE platform could enable significant expansion of CRISPR medicines to a wide range of diseases." Dr. Gordon. This Series B funding is a crucial milestone as we advance our lead first-in-class immuno-oncology (IO) program and progress our pipeline of programs in IO, ophthalmic diseases and hemoglobinopathies,It will enable us to execute our development plan, leveraging Spotlight’s unique cell-targeted in vivo delivery approach, as we aspire to unlock the full potential of gene editing and enable effective one-and-done medicines for patients.” Mary Haak-Frendscho, Ph.D., President and CEO of Spotlight Therapeutics. About Spotlight Therapeutics Established in mid-2018, Spotlight Therapeutics is a privately held biotechnology company advancing a pipeline of cell-targeted in vivo CRISPR gene editing therapies. Spotlight's proprietary technology platform TAGE (Targeted Active Gene Editors) is a new class of biologics, CRISPR effectors engineered for direct delivery in vivo, to achieve cell-selective therapeutic genome editing. Spotlight's pipeline is advancing its modular programmable CRISPR effectors towards clinical studies in immuno-oncology, ophthalmic diseases and hemoglobinopathies. The company is headquartered in Hayward, California.

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MEDICAL

TGen Selects MemVerge to Accelerate Idiopathic Pulmonary Fibrosis Research Discovery with Big Memory Technology

MemVerge | March 21, 2022

MemVerge™, the pioneers of Big Memory software, today announced that TGen, the Translational Genomics Research Institute, an affiliate of City of Hope, has selected MemVerge Memory Machine Big Memory virtualization software to accelerate time to discovery for Idiopathic Pulmonary Fibrosis (IPF), a disease which affects 100,000 people annually in the U.S. Using MemVerge technology, TGen is able to dramatically speed analytical processing by nearly 36% for single-cell RNA sequencing. As a nonprofit medical research institute, TGen researchers process single-cell RNA sequences to characterize cell transcriptomic profiles. The process can take up to six and a half hours to analyze a matrix of 30,000 genes by 114,000 cells. With consistently growing datasets, this processing time was preventing a desired time to discovery. The data required for analysis was simply too large to retain in traditional memory, and scaling capacity with dynamic random-access memory (DRAM) was too costly. TGen has instead deployed memory virtualization technology from MemVerge which virtualizes both DRAM and PMem (persistent memory) memory technologies, to increase the memory pool available for processing without requiring more high-cost DRAM. The solution further speeds TGen's genomics sequencing analysis with Memory Machine ZeroIO in-memory snapshots which capture multi-terabyte data sets at any point for rapid reloads at each stage of processing. The ZeroIO snapshot service is 1,000 times faster than the fastest storage snapshot to SSD and enables TGen to run processing workflows in parallel. This ensures that in the event of a system crash, in-memory snapshots are available to instantly re-start long running jobs without lengthy reloading. By utilizing the snapshotting and cloning capabilities of Memory Machine, we were able to parallelize the processing workflow, As a result, we can now save nearly 36% of computational time while also taking advantage of the big memory nodes. This will save a lot of time in downstream analysis." Glen Otero, Ph.D., Vice President of Scientific Computing at TGen. MemVerge Memory Machine has quickly resulted in research value for TGen, We have removed performance barriers from their research process so that they are able to perform vital, life-saving, research faster than ever possible. Now TGen is expanding the use of Big Memory technology across other research use cases where results and discoveries can produce findings for a healthier tomorrow." Jonathan Jiang, COO of MemVerge. MemVerge Memory Machine makes 100% use of available memory capacity while providing new operational capabilities to memory-centric workloads. Memory Machine answers the need for a modern in-memory computing model to support emerging applications that require real-time analytics, true in-memory computing, and fault-tolerant memory persistence to speed massive processing workloads. About MemVerge MemVerge is pioneering Big Memory Computing and Big Memory Cloud technology for the memory-centric and multi-cloud future. MemVerge® Memory Machine™ is the industry's first software to virtualize memory hardware for fine-grained provisioning of capacity, performance, availability, and mobility. On top of the transparent memory service, Memory Machine provides another industry first, ZeroIO™ in-memory snapshots which can encapsulate terabytes of application state within seconds and enable data management at the speed of memory. The breakthrough capabilities of Big Memory Computing and Big Memory Cloud Technology are opening the door to cloud agility and flexibility for thousands of Big Memory applications.

Read More

MEDICAL

Duke Researchers Identify Genetic Mechanism in Brain Lesion Formation Using Single-Cell DNA Sequencing from Mission Bio

Mission Bio | March 15, 2022

Mission Bio, the pioneer in high-throughput single-cell DNA and multi-omics analysis, announced new findings by Daniel Snellings from the lab of Douglas Marchuk, PhD, at Duke University School of Medicine using single-cell DNA sequencing to identify genetic mechanisms leading to the development of cerebral cavernous malformations (CCMs). The study, published today in the journal Nature Cardiovascular Research, is the latest demonstration of how Mission Bio's Tapestri Platform is allowing researchers to probe new aspects of biology at a single-cell resolution not possible with bulk sequencing. Dr. Marchuk is Professor of Molecular Genetics and Microbiology at Duke. CCMs, a blood vessel abnormality that can lead to brain hemorrhages, have long been associated with developmental venous anomalies (DVAs), a typically benign but irregular vascular arrangement often found near sporadic CCMs – though researchers had yet to prove a link. In the paper, Snellings and colleagues sequenced DNA from three CCM patient samples to see if somatic mutations in MAP3K3 or PIK3CA – common in patients with CCMs – co-existed in the same cells. Single-cell DNA sequencing with Tapestri found co-occurring mutations in the cells of all three samples, a pattern that could not be determined by bulk sequencing. Further, the group found that the CCMs and the associated DVAs harbored identical mutations in PIK3CA, but that mutations in MAP3K3 were only found in the CCMs. Because of the pattern of PIK3CA and MAP3K3 co-occurrence in CCMs, the team could assess the temporal pattern of genetic mutations associated with disease progression. They determined that DVA is the first lesion to occur, and that CCM development happens only after acquisition of an activating MAP3K3 mutation in a cell of the existing DVA.sazsz It was surprising to find that something as common as DVAs—which are present in up to 16% of people—could be caused by a cancer driver mutation. This explains why sporadic CCMs are often found in the vicinity of a DVA, and may explain why other diseases like pontine gliomas are also found near DVAs." Snellings. Tapestri is regularly deployed in cancer research to detect somatic mutations in clonal populations as a way of tracking tumor development, and the researchers adapted that methodology to evaluate the relationship between DVAs and CCMs. Since DVAs are not regularly biopsied, the researchers also confirmed the presence of circulating mRNAs in patients with both CCM and DVA related to this biological pathway, in plasma – a first step toward establishing a biomarker for CCM risk in patients with DVAs. We expect this research will have a meaningful impact for patients at risk for developing spontaneous cerebral cavernous malformations, which can lead to strokes or even death, This paper is a powerful new demonstration that there are many disease areas where single-cell DNA sequencing is helping elucidate the mechanisms of disease development, and identifying potential targets for diagnostics or therapeutics." Yan Zhang, PhD, CEO of Mission Bio. About Mission Bio Mission Bio is a life sciences company that accelerates discoveries and cures for a wide range of diseases by equipping researchers with the tools they need to better measure and predict our resistance and response to new therapies. Mission Bio's multi-omics approach improves time-to-market for new therapeutics, including innovative cell and gene therapies that provide new pathways to health. Founded in 2014, Mission Bio has secured investment from Novo Growth, Cota Capital, Agilent Technologies, Mayfield Fund, and others. The company's Tapestri platform gives researchers around the globe the power to interrogate every molecule in a cell together, providing a comprehensive understanding of activity from a single sample. Tapestri is the only commercialized multi-omics platform capable of analyzing DNA and protein simultaneously from the same sample at single-cell resolution. The Tapestri Platform is being utilized by customers at leading research centers, pharmaceutical, and diagnostics companies worldwide to develop treatments and eventually cures for cancer.

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