Led by CUNY SPH faculty Levi Waldron and Sehyun Oh, the project aims to enhance and expand the Bioconductor ecosystem, a cornerstone resource for statistical analysis and data management in cancer genomics research. The grant, totaling $5.2 million, will fund collaborative efforts with the Channing Division of Network Medicine at Mass General Brigham in Boston, the University of Colorado, and the University of Padova in Italy.

“This renewal represents a significant vote of confidence in our past 10 years of work and our ideas for the next five years,” said Dr. Waldron. “It will allow us to address the evolving challenges in cancer genomics, particularly in the realm of single-cell and spatial molecular profiling technologies.”

The project focuses on four main objectives: expanding infrastructure for multimodal experiments and spatial transcriptomics; transitioning to a federated, language-agnostic data-sharing system; creating curated and integrated data repositories; and developing comprehensive user training programs, including a cloud-based learning platform.

The authors aim to empower researchers with advanced tools and resources for cancer genomics research, potentially accelerating discoveries that could lead to improved cancer diagnostics and treatments.

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This collaboration between MGI and SeqOne encompasses three distinct initiatives:

Validating an end-to-end, automated, cost-effective solution for HRD signature with MGI DNBSEQ-G99

The collaboration between a Pathology Reference Lab in Spain, Agilent Technologies, MGI, and SeqOne aims to technically validate a routine workflow leveraging Agilent panels, Magnis lib prep automation, MGI DNBSEQ-G99, and SeqOne somaHRD, a clinically validated HRD signature solution, on 96 samples.

This end-to-end solution for pathology molecular labs will enable high-quality, efficient, and flexible HRD testing worldwide, including Genomic Instability score and BRCA testing.

Enabling and validating SeqOne tertiary analysis solution compatible with MGI Megabolt for Germline Panels, Whole Exome and Whole Genome

MegaBOLT bioinformatics analysis accelerator, self-developed and MPS-concentrated hardware accelerating system by MGI, is set to ensure seamless integration and compatibility with SeqOne’s AI-powered variants identification and analysis solution.

The collaboration aims to combine MegaBOLT and the SeqOne Platform to deliver a versatile, cost-effective, intuitive, and time-saving solution from sample to report, particularly attractive for high-throughput Human Genetics labs.

Validating SeqOne CE-IVD Platform for Germline and Somatic analysis for use with MGI sequencers in routine diagnostics

This technical validation project aims to evaluate the compatibility of the SeqOne Platform with MGI sequencing data. It will validate variant calling performances on a set of reference control samples in terms of QC, sensitivity and precision.

“We are thrilled to announce our collaboration with SeqOne. By combining MGI’s cutting-edge sequencing technology with SeqOne’s innovative genomic analysis Platform, we are poised to deliver real insights and solutions for personalized healthcare,” said Dr. Yong Hou, General Manager of MGI Europe and Africa. “This collaboration underscores our commitment to advancing genomic research and providing clinicians with the tools they need to offer tailored treatments to their patients.”

“This partnership with MGI strongly supports SeqOne’s mission to broaden access to sophisticated genomic analysis, aiming to improve healthcare outcomes,” said Martin Dubuc, CEO, SeqOne. “Molecular laboratories globally are exploring how MGI’s sequencing and bioinformatics technologies can advance next-generation sequencing (NGS) research and diagnostics. We are eager to integrate SeqOne’s CE-IVD Platform with MGI’s offerings, enhancing the quality, sensitivity, and precision of bioinformatic analyses.”

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The new solution consists of an automated full-process product portfolio designed for large-scale molecular breeding genotyping of agricultural diploid species. The full workflow covers extraction, library preparation, sequencing, and SNP & InDel calling.

The new MGIEasy Large-scale PCR-Free FS Library Prep Set for Low-pass WGS, available in two specifications, 96RXN and 384RXN, is designed specifically for Low-pass WGS applications with a new plate-based library preparation reagent module. Compared with common PCR-free library preparation sets on the market, this kit cuts the purification step and completes library construction in three easy steps, reducing the time and consumables required.

In combination with MGI’s advanced automation platforms, the Low-pass WGS solution breaks through the limit on throughput as seen in ordinary library preparation. It utilizes the fewer number of automated tools to match ultra-high throughput, as while maintaining a high degree of automation. As a result, large-scale library preparation can be done in a short time, at low cost, and with great automation friendliness.

For sequencing, the product bundles for high throughput and medium throughput Low-pass WGS feature the ultra-high-throughput DNBSEQ-T7 sequencer and the versatile DNBSEQ-G400 benchtop sequencer respectively, empowering large-scale agricultural genomics research projects in a short time.

The initial workflow released includes a pig reference panel and a data analysis software that has been based on GLIMPSE2, allowing users to perform pig genotyping without having to build their own database. Free format conversion service is also available for users with an existing reference panel to be compatible with the analysis software.

“Since genome selection was widely used in agricultural breeding, genotyping tools went through several iterations, sequencing technology gradually shows its irreplaceable advantages,” said Duncan Yu, President of MGI. “Low-pass WGS has been applied in both animal and plant breeding, but not without implementation challenges. Our new total solution for large-scale pig breeding addresses these user pain points and promises flexible automation needs, simplified library preparation, high throughput sequencing, and efficient data processing.”

Bolstered by MGI’s powerhouse instruments, this agricultural Low-pass WGS solution has a daily throughput of 96 to 1,536 samples and annual throughput of 24,000 to 384,000 samples (based on the 1.0X depth of a pig genome and an average sample data output of 3G). It has also obtained high-accuracy SNP results from 0.5~1X Low-pass in pig ear tissue samples, demonstrating 98.4% consistency with the SNP array and 98.1% with 50X WGS. Together with MGI’s self-developed MegaBOLT bioinformatics analysis accelerator, it can analyse 192 pig 1.0X samples daily, and approximately 1,536 per day with ZBOLT Pro.

Compared to traditional genotyping by microarray, MGI’s new solution offers genome-wide data at the same cost but captures a broader range of genetic variation, enhances the discovery of new variants, and increases the statistical power of genome-wide studies, all while eliminating high design and start-up costs associated with microarrays. The dynamic features of this solution enable continuous updates and optimizations in genomic analyses.

“As a provider of core tools in life science, MGI is committed to providing agricultural scientists and breeders with high-quality, convenient, and reliable genome products, while actively driving the growth of agricultural research and industry,” added Yu.

The Low-pass WGS product and workflow will be available for orders starting on June 30th. For further information on MGI’s latest whole workflow agricultural large-scale Low-pass WGS solution, please visit mgi-tech.com.

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Complete Genomics, a pioneering genomic sequencing company, today announced the May 22 opening of its Customer Experience Center (CEC) demonstration lab near Boston’s biotech hub.

The new lab, located in Framingham near Boston, is Complete Genomics’ first footprint on the East Coast and is expected to enable faster service and support to East Coast customers. Current and prospective customers in Boston and the greater northeast will be able to experience Complete Genomics’ DNBSEQ workflows including next-generation sequencing platforms, sample prep automation systems and bioinformatics products.

“The opening of our Boston Customer Service Center is the latest example of Complete Genomics’ commitment to serve our U.S. customer base. Last week, we celebrated the creation of our first U.S.-based supply chain with the opening of a new $3.2 million manufacturing facility at our San Jose, Calif. headquarters which will be online later this year,” said Dr. Radoje (Rade) Drmanac, Co-Founder and Chief Scientific Officer of Complete Genomics.

In addition to an introduction to Complete Genomics and its DNBSEQ sequencing platforms, the event will feature an introduction to the STOmics Stereo-seq technology and a DNBSEQ User Experience Workshop on how to optimize DNBSEQ-G99*, G400*, and T7* sequencers for research projects. A mini symposium will feature several Complete Genomics’ ecosystem partnerships centered around DNBSEQ technologies. Speakers from seqWell, Inc., Fluent Biosciences and Velsera, Inc., all headquartered in the Boston area, will present their product solutions and ongoing collaboration with Complete Genomics, aiming for expanded product accessibility to accelerate genomics research.

DNBSEQ sequencing platforms to be featured during the opening event include the flagship DNBSEQ-T7*, the G99*and the E25*. Also featured will be the high-throughput automated sample prep system SP-960 and the eight independent channel pipetting robot SP-Smart 8. The day will wrap up with a tour of the demo lab followed by a cocktail and networking reception. Transportation will be provided from Boston and Cambridge to the lab in Framingham.

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Genomics solutions provider Integrated DNA Technologies (IDT) and Bio-IT company Molecular Health have entered into a global multi-year agreement, starting in the U.S., to integrate their next generation sequencing (NGS) capabilities. The partnership pairs IDT’s Archer NGS research assay platform with Molecular Health’s variant annotation and reporting software to equip molecular researchers with tertiary analysis for their NGS data, maximizing lab efficiency and streamlining genomics data workflows to accelerate cancer discoveries. The collaboration also extends access to research customers in the genomic profiling space through IDT’s nationwide footprint.

“NGS remains a critical research tool used to understand the biology and pathology of cancer,” said Steve Wowk, Vice President/General Manager, Gene Reading Business Unit at IDT. “As the pace of innovation drives the cancer research community’s understanding of how biomarkers are associated with the onset, progression and treatment of disease, their research now requires more complete tools inclusive of high-performance chemistries along with the ability to manage and annotate an ever-expanding biomarker knowledgebase. Our partnership with Molecular Health reflects another step toward our goal of delivering on our customers’ needs and solving their problems by equipping them with a more efficient path to advance genomic discoveries through NGS in support of the fight against cancer.”

The rapid discovery of variants that impacted the scientific field over the past five years has generated increased market demand for large targeted NGS panels, and scientists are now focused on harnessing the volume of information that these assays provide. Since the acquisition of Archer NGS research assays in 2022, IDT has been innovating on the Archer NGS platform, as reflected by this strategic partnership and three new cancer-focused product releases in 2023, including the launch of new automation-friendly liquid reagents, and RNA- and DNA-based research assays aimed at comprehensive profiling inclusive of complex genomic signatures. This continued expansion of IDT’s NGS tools portfolio has been critical for researchers looking to advance cancer discoveries.

“Cancer and other diseases can be caused by inherited or acquired genetic conditions. Understanding the consequences of mutations requires precise data generation and analysis,” said Friedrich von Bohlen, PhD, CEO of Molecular Health. “The combination of IDT’s and Molecular Health’s NGS products and expertise enables high-quality, end-to-end integration plus a deep understanding of sequencing data. Our proprietary Dataome knowledge base allows clients to go beyond the generation of genomic data. It provides contextualization of variants to unlock the value of the data for researchers in the growing field of molecular profiling and discovery.”

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“We’re thrilled to open our Oxford laboratory, which allows us to bring state-of-the-art NGS technology to UK researchers,” said Dr Ginger Zhou, President of Azenta’s Multiomics business unit.  “This new facility not only strengthens our global footprint but also offers researchers access to local experts and cutting-edge resources. The Oxford team comprises some of the best minds in the field, all with deep roots in the local scientific community.”

The opening event, held on April 25, 2024, featured a ribbon-cutting ceremony, a lab tour, and a celebratory reception with key stakeholders, including members of the local scientific community, distinguished guests, and Azenta executives.

Dr David Buck, Director of Lab Services Oxford added, “This new lab represents our commitment to supporting UK researchers by delivering high-quality data faster, advancing research and development in critical fields such as diabetes, infectious diseases, Alzheimer’s and more. We’re excited about the energy, engagement, and collaboration with the scientific community, and we look forward to contributing to their success.”

“Having an amazing genomics facility like the one Azenta has opened at our doorstep, allows us to work faster, achieving more in less time, with higher accuracy and for an effective cost.  This helps us enhance discovery in medical research to patient benefit.” Said Dr. John Todd, Professor of Precision Medicine at the University of Oxford, who attended the opening event.

The Oxford Genomics Laboratory was created with customer convenience in mind.  It offers a network of GENEWIZ collection points plus free-of-charge, same day dry ice sample collection in Oxford, and Cambridge, streamlining the sample submission process for researchers. The lab provides a comprehensive suite of NGS services; library preparation, sequencing, bioinformatics analysis with UK based data storage, plus soon to be, a range of DNA/RNA extraction capabilities, all backed by experienced Ph.D.-level study managers who guide projects from conception to delivery.

GENEWIZ from Azenta is equipped with the latest, cutting-edge NGS platforms globally to enable service users to stay at the forefront of scientific innovation.  Some of these platforms include:  Illumina NovaSeq X Plus, PacBio Revio, Oxford Nanopore Technologies GridION, PromethION 2 Solo, 10x Genomics Chromium X, Nanostring GeoMx^® & nCounter^®, and Olink^® Protein Biomarker Detection.

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“Over the past three decades, sequencing technologies have evolved drastically. It feels like every month, a new sequencing method is developed,” says Michael Becich, Cache CEO. “With the democratization of sequencing, laboratories are struggling to store and manage a growing number of crucial molecular samples—and their accompanying data—in a compliant manner. As artificial intelligence continues driving the field forward, the need for standards and scalable capabilities in an evolving multi-omic landscape has never been greater.”

Genetic materials, like DNA and RNA, play a fundamental role in disease biology, therapeutic targeting, and clinical diagnostics. However, growing demands across clinical and research applications challenge laboratories around the globe. Most of the ongoing capital-intensive laboratory infrastructure needed to maintain samples, such as freezers, relies on finite grant funding or falls outside of testing reimbursement.

Cache is transforming sample management infrastructure by preserving precious biomolecules at room temperature, future-proofing samples in a more efficient footprint for discovery and validation for decades to come. Through its innovative chemistry, hardware, and software, Cache offers a scalable and sustainable system to secure and share multi-omic datasets, enabling the next generation of longitudinal and cross-sectional studies.

“Nucleic acids are the core information carriers of our cells, recording our genetic lineage, developmental histories, and environmental exposures relating to cancer, aging, and inherited disorders,” says Mark Bathe, PhD, professor of Biological Engineering at MIT and Cache co-founder. “Cache is transforming our ability to harness this information.”

After securing an exclusive license to their intellectual property from MIT, Cache was awarded an SBIR grant from the National Science Foundation (press release). In less than a year, with this pre-seed funding, the team has made tremendous progress and has moved its operations to the San Francisco Bay Area.

In addition, Illumina Accelerator backed Cache with in-kind support, including lab space and access to sequencing capabilities (press release), which Cache used to run extensive concordance analyses and validate its technology using gold-standard genomic reference materials.

Cache is now partnering with a growing number of academic medical centers, commercial labs, and biobanks worldwide. The team recently presented findings from their collaboration with the University Health Network on FFPE tumor-derived samples at the American College of Medical Genetics & Genomics (ACMG) and the International Society for Biological and Environmental Repositories (ISBER) annual meetings (article).

Founders and Team

In addition to Becich and Bathe, Cache was co-founded by James Banal, who earned his PhD in chemistry at the University of Melbourne and has received international recognition for his work in biochemistry, solar engineering, and quantum computing.

Bathe and Banal co-invented the core technology, which grew out of research they conducted while Banal was a postdoctoral scholar in the Bathe lab at MIT. The lab explores using nucleic acids as programmable nanomaterials. Bathe also co-founded Kano Therapeutics, which is developing a single-stranded DNA (ssDNA) manufacturing platform for gene and cell therapies.

Cache’s CEO is Michael Becich, a bioengineer from Stanford and MS/MBA candidate from Harvard Business School who has worked in bioinformatics, assay development, digital health, and venture capital. While in Boston, Becich and Banal spent several months launching Cache through Nucleate. The team is joined by pathology and laboratory medicine industry veteran Heather E. Williams, PhD, Cache’s COO. She is a clinical laboratory geneticist who conducted an ABMGG fellowship at New York Presbyterian-Columbia University Medical Center and has an executive MBA from Yale SOM.

Scientific advisors include Paul Blainey, George Church, and Jeremiah Johnson, all faculty at MIT or Harvard. The team recently assembled a clinical advisory board with experts in biobanking, sequencing, and bioethics.

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Bruker Corporation (Nasdaq: BRKR) today announced that it has closed its asset acquisition of the business of NanoString Technologies, Inc., headquartered in Seattle, Washington, a leading provider of life-science research solutions for spatial transcriptomics and gene expression analysis.

Under the asset purchase agreement, Bruker has now acquired substantially all of the assets and rights associated with NanoString’s business, including the nCounter^®, GeoMx^®, CosMx and AtoMx product lines, for approximately $392.6 million in cash, and the assumption of certain liabilities. In 2023, NanoString generated revenues of approximately $168 million.

NanoString’s innovative platforms and leading solutions for spatial transcriptomics and gene expression analysis have been critical in enabling scientists and medical researchers to advance vital discovery, translational, and pre-clinical disease research, leading to over 7,000 peer-reviewed publications. The products and organizational infrastructure of NanoString and Bruker are highly complementary, and under Bruker’s ownership, the combined organization will leverage each other’s strengths to continue to innovate and support the discovery and translational research communities with a broad set of leading solutions, ushering in the single cell and spatial biology revolution.

“We have a proven track record in successfully integrating and nurturing our acquired businesses for growth and increased profitability, while preserving their cutting-edge R&D. We are excited to carry forward all the NanoString product lines which are so important for science and medical research,” commented Dr. Mark R. Munch, President of the Bruker NANO Group. “NanoString’s innovative platforms are complementary to Bruker’s high-performance CellScape spatial proteomics platform and contribute further to Bruker’s leadership in the post-genomic era.”

Confirming Bruker’s April 22^nd press release, Bruker expects the NanoString business to be near break-even by 2026 with resumed revenue growth, margin improvements, and transaction synergies, including public company costs, which are not assumed in this asset deal. As a preliminary estimate, for the remainder of 2024, the transaction is expected to be dilutive to Bruker’s non-GAAP EPS by $0.15 to $0.20. Due to significant business disruption and uncertainty, Bruker is not yet in a position to give financial guidance on the NanoString business for 2024, but Bruker expects to add this business to Bruker’s guidance by 2025 and beyond.

Brad Gray, NanoString CEO, added: “We are proud to have pioneered spatial biology and built an enterprise with compelling solutions that advance scientific and medical research. Bruker will provide a great home for our talented team who will continue to serve NanoString’s current and future customers in our mission to map the universe of biology.”

Morgan, Lewis & Bockius LLP and Goldman Sachs & Co. LLC are serving as legal and financial / strategic advisors, respectively, to Bruker. NanoString is represented by Willkie Farr & Gallagher LLP as counsel, AlixPartners LLP as restructuring advisor and Perella Weinberg Partners L.P. as restructuring investment banker.

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Under this agreement, MiLaboratories will grant exclusive rights to its innovative RNA kits immune sequencing technology to Miltenyi Biotec. This technology has been instrumental in advancing research and development in the field of immunology and personalized medicine. Miltenyi Biotec will leverage its global reach and expertise in biotechnology to produce and commercialize these kits, making them widely available to researchers and clinicians worldwide.

A cornerstone of this partnership is the integration of MiLaboratories’ renowned software solutions, MiXCR and Platforma, into Miltenyi Biotec’s offerings. These software platforms are leaders in next-generation sequencing (NGS) data analysis, providing powerful, user-friendly tools for genomic data interpretation. Customers purchasing RNA kits from Miltenyi Biotec will now benefit from seamless access to MiXCR and Platforma, enhancing their research capabilities and efficiency.

“This partnership is a significant milestone in our mission to accelerate the development of next-generation therapies,” said Stan Poslavsky, CEO of MiLaboratories. “By combining our innovative RNA technologies and software platforms with Miltenyi Biotec’s manufacturing and commercial strengths, we are poised to make a substantial impact in the field of genomics and personalized medicine.”

Jürgen Schmitz, Managing Director at Miltenyi Biotec, added, “We are thrilled to partner with MiLaboratories, a company that shares our commitment to advancing human health. Their RNA kits technology for immune sequencing complements our molecular analysis product portfolio perfectly. Moreover, their software solutions will offer our customers unparalleled support in data analysis. Together, we are building the future for next-generation therapies.”

This partnership is expected to accelerate the pace of discovery and development in the field of genomics, offering researchers and clinicians new tools to explore the complexities of genetic information and foster the development of innovative therapies.

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CancerVision and RareVision mark a significant leap forward in genetic diagnostics as they capture not only commonly known mutations, but also rare and complicated mutations that are often missed by other types of genetic testing like traditional panel sequencing and whole exome sequencing.

The clinical use of whole genome sequencing has relatively been limited due to cost and technology barriers. Inocras’s patent protected technology and proprietary bioinformatics pipelines have made it possible to interpret vast whole genome data into actionable insights at a cost comparable to standard panel sequencing. This advancement promises more personalized treatment for cancer and rare disease patients, aiming to resolve issues of delayed diagnosis and over- or under-treatment.

Inocras CEO, Jehee Suh, remarks, “We are proud of the comprehensiveness and depth of clinical insights that CancerVision and RareVision will deliver, offering patients and providers a superior alternative to what’s available today.”

The debut of these two products is complemented by Inocras’s innovative service digital platform. Beyond whole-genome testing, patients gain access to genetic counseling services and support for clinical trial matching, all delivered through seamless end-to-end digital experiences – from requesting an order to receiving test results.

Moreover, the platform extends its benefits to healthcare providers with digital solutions that streamline the processes and provide real-time visibility into the status of requests. This integrated approach reflects Inocras’s commitment to delivering holistic and user-friendly healthcare solutions, empowering both patients and providers.

“Our vision is to make whole-genome insights accessible and understandable to all”, says Jehee Suh, emphasizing the importance of the platform’s introduction alongside flagship diagnostics products. “This milestone solidifies our position as the whole-genome precision health leader.”

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