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Cancer Genome Sequencing Rise in Trends In the relentless pursuit of understanding and combatting cancer, the field of genomics has undergone a transformative journey. Today, let's explore the groundbreaking advancements in Cancer Genome Sequencing technology, specifically delving into the strides made by Second and Third Generation Technology Platforms. Get PDF In Your Mailbox: https://lnkd.in/daPZQ2nj 1. #SecondGeneration Technology Platforms: Second-generation sequencing technologies marked a turning point in cancer genomics, allowing for faster and more cost-effective #DNA sequencing. Platforms like Illumina's sequencing technology became synonymous with high-throughput capabilities, enabling researchers to analyze the genetic blueprint of cancer cells with unprecedented precision. This advancement facilitated large-scale genomic studies, uncovering critical insights into the intricate genomic alterations underlying various types of cancer. 2. #ThirdGeneration Technology Platforms: The advent of Third Generation Technology Platforms ushered in a new era of cancer genome sequencing, characterized by innovations that addressed limitations observed in earlier technologies. Companies like Pacific #Biosciences and #Oxford Nanopore Technologies pioneered single-molecule sequencing, enabling longer reads and the ability to capture complex genomic structures. This evolution proved instrumental in deciphering intricate aspects of cancer genomes, including structural variations and dynamic changes within tumor cells over time. Key Market Player:  Agilent Technologies GE Healthcare Life Sciences Johnson & Johnson LI-COR Biosciences (Lincoln, NE) Beckman Coulter (Fullerton, CA) Integrated DNA Technologies Microchip Biotechnologies #CancerResearch #GenomeSequencing #PrecisionMedicine #MedicalInnovation #HealthTech #CancerGenomics #SecondGenSequencing #ThirdGenSequencing #diagnosticsandbiotech #diagnostic #biotech #healthcareadvancements

Aventa Genomics Announces Launch of Aventa FusionPlus, the First 3D Genomics Clinical Test for Patients with Solid Cancers We are excited to introduce Aventa™ Genomics, LLC, a clinical laboratory launched through a joint venture between Arima Genomics, Inc. and Protean BioDiagnostics. Matching the right molecular test with the right patient is crucial for effective treatment . The Aventa FusionPlus test incorporates 3D genomics technology to identify novel breakpoints and fusion partners, improving upon conventional testing methods like FISH and RNA sequencing. With the ability to detect previously missed biomarkers, our hope is that no cancer patient will be left behind. https://lnkd.in/evwryrcM #AventaGenomics #CancerTesting #PrecisionMedicine #nopatientleftbehind #NGS #solidtumors #science #molecularcharacterization #genefusions #precisionmedicine #oncology #HiC #structuralvariants #genomics Visit us at www.aventagenomics.com or reach out to [email protected] to learn more!

#cancerresearch #oncology #tumormicroenvironment #genetics https://lnkd.in/g4hxgTrP Abstract Single-cell and spatial technologies that profile #gene #expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.

It's that time of year, reflecting on highlights of 2023 - one of these was the Nanopore Day, Bay Area. Over 250 delegates registered and the quality of the talks was mind-blowing. There were many clear examples of improved insight and outcomes for patients in Human, Cancer and Infectious Disease, all of them showing the importance of data missing from legacy short-read platforms and what to expect from the new normal. What You're Missing Matters - #WYMM. "This is not a long-read technology it’s a new generation of sequencing technology." Telomere-to-telomere human genome assemblies using only Oxford Nanopore sequencing - Karen Miga, University of California. Ultra-Rapid Nanopore Whole Genome Sequencing for Critically Ill Patients - John Gorzynski, Stanford University. Single molecule cancer genomics from individual cell mutation detection and engineering to cell free tumor detection - Hanlee Ji, Stanford University. scTaILoR - single cell targeted isoform long-read sequencing improves .sensitivity for isoform and variant detection - Ashley Byrne, Genentech. Applications of CZ ID -- a free, open source, cloud-based metagenomics tool for researchers - Katrina Kalantar, Chan Zuckerberg Initiative. Julie Collens, Brian Fritz, Sara Agee Le, James Brayer, Shivani Chinnappan, Darrell Joyce II, MBA, PMP, Martin Stern, Jonathon Foos, Satu Strandman, Daniel Garalde, Anna Maria Niewiadomska, Ph.D., Androo Markham, Yan Yang, John Beaulaurier, Scott Hickey, Joseph Guillory.

🔬 Exploring the Power of RNAscope™ Advanced Cell Diagnostics Division of Bio-Techne in Laboratories: Unveiling Cutting-Edge Insights into Gene Expression 🧬 In the realm of molecular biology and biomedical research, precision and accuracy are paramount. This is where innovative technologies like RNAscope™ step in, revolutionizing the way we study gene expression with unprecedented specificity and sensitivity. RNAscope™, a game-changing RNA in situ hybridization (ISH) assay, offers a remarkable window into the intricate world of RNA molecules within cells and tissues. Its ability to detect and visualize individual RNA molecules with single-molecule resolution provides researchers with a powerful tool to unravel the mysteries of gene expression patterns. 🔍 Benefits of RNAscope™: 1️⃣ High Specificity: RNAscope™ enables precise localization of RNA targets within complex biological samples, even in the presence of abundant background signals. 2️⃣ Sensitivity: With its unparalleled sensitivity, RNAscope™ can detect low-abundance RNA transcripts, allowing researchers to explore gene expression dynamics with unmatched accuracy. 3️⃣ Versatility: From basic research to clinical diagnostics, RNAscope™ finds diverse applications across various fields, including oncology, neuroscience, developmental biology, and infectious diseases. 🌟 Key Applications of RNAscope™: 🔬 Cancer Research: Unravelling the molecular landscape of tumours and identifying novel biomarkers for diagnosis and targeted therapies. 🧠 Neuroscience: Mapping gene expression patterns in the brain to understand neurodevelopmental disorders and neurological diseases. 🔬 Infectious Diseases: Studying host-pathogen interactions and viral RNA localization to develop effective antiviral strategies. 🌱 Developmental Biology: Investigating gene expression dynamics during embryonic development and tissue regeneration. 📚 Highlighting Cutting-Edge Research: Recently, ground-breaking research titled "Species-specific gene expression profiling of PDX tumors and humanized mice by RNAscope™ ISH" has shed light on the intricate interplay between tumor microenvironments and therapeutic responses. This study exemplifies the power of RNAscope™ in unravelling complex biological phenomena and guiding personalized treatment strategies. 🤝 Let's Connect and Explore the Possibilities: Interested in harnessing the full potential of RNAscope™ in your research endeavours? I invite you to connect with me for a discussion on how RNAscope™ can elevate your studies and accelerate scientific discoveries. #RNAscope #MolecularBiology #BiomedicalResearch #GeneExpression #PrecisionMedicine #ScientificInnovation

"Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics." Interesting study using whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis to study the breast cancer tumor microenvironment, by Amanda Janesick, PhD and larger team. Also, I hope everyone celebrating the Christmas holiday today gets to enjoy the time off with friends, family and loved ones! https://lnkd.in/eZy9PD3V

Unique opportunity to contribute moving ahead cancer vaccine approaches in fields never evaluated so far, and translates your expertise in discovery science into patient care

Workflow download - Nanopore single-cell transcriptomics: Obtaining full-length isoforms from single cells with nanopore sequencing Characterisation of transcriptomic differences between individual single cells, or spatially across tissues, has provided insight into how the genome is utilised for specialised functions, such as neurological disorders and cancer. However, the majority of these studies recover limited isoform and single nucleotide polymorphism (SNP) content due to the limited read length of short-read sequencing. With the latest nanopore sequencing technology, it is now simple to get isoform-level expression from full-length cDNAs at the throughput needed to analyse thousands of cells. RNA from single cells can be prepared using the 10x Genomics microfluidics-based Chromium platform, which produce barcoded, full-length cDNA from individual cells. Nanopore sequencing is compatible with the 10x Genomics sample preparation approach and can be used to sequence full-length transcripts and splice variants, providing detail on isoform diversity and isoform switching, such as during development. In addition, long nanopore reads enable the detection of both SNPs for RNA-based genotyping and gene fusions that are often associated with cancer. Here, we present a complete workflow for single-cell transcriptome analysis from 10x Genomics cDNA, with library prep in approximately three hours. https://lnkd.in/dBztGrAE

Decoding Cancer Complexity with TruSight Oncology 500 ctDNA v2 (#TSO500ctDNA) The #TruSight_Oncology 500 ctDNA v2 by Illumina is a pivotal innovation in precision oncology. This assay empowers clinicians and researchers to delve into the genetic underpinnings of cancer with accuracy and depth that was once unimaginable. 🔬 Technical Precision The assay's sensitivity is a testament to its technical prowess, capable of detecting ctDNA concentrations as low as 0.2% allele frequency. This is crucial for early #detection and #monitoring of minimal residual disease (#MRD), where ctDNA fragments are often scarce. 🧬 Bioinformatics Backbone The bioinformatics pipeline is integrated within the TruSight Oncology 500 ctDNA v2 workflow. It employs sophisticated #algorithms to ensure the accuracy of #variant_calling, minimizing false positive and negative calls. 📊 Workflow Integration The workflow is streamlined for efficiency, from sample preparation to data analysis. It begins with the extraction of ctDNA from #plasma, followed by #NGS library preparation with unique indexes to prevent sample-to-sample contamination. #Sequencing is performed with high fidelity by #NovaSeq6000Dx platform. 🧪 Clinical Parameters at a Glance - Sample Input: as low as 20 ng of ctDNA - Panel Size: targets 523 genes to assess DNA variants across major variant classes (SNV, MNV, indels, CNV, and gene rearrangements), plus critical immuno-oncology gene signatures (TMB, MSI) - Indexes: utilizes unique dual indexes for up to 384 samples, mitigating index hopping and ensuring sensitive and accurate detection - Turnaround Time: rapid results, from sample to report, in less than four days 🌐 From Data to Decision The true power of the TruSight Oncology 500 ctDNA lies in its ability to transform #complex_genomic datasets into clinically relevant reports. The data output is not just a list of mutations; it's a comprehensive profile that informs #treatment pathways and #therapeutic_decisions. The TruSight Oncology 500 ctDNA is a window to #precision_medicine, offering a non-invasive yet comprehensive view into the molecular landscape of cancer. For more information, visit 👉 https://lnkd.in/d-K-RjVM or contact GeneTiCA Group. We are on your side.

In their 2024 Nature Communications article, Jonathan Mitchell et al. introduce a computational method for assessing tumor-in-normal contamination (TINC) in whole-genome sequencing. Addressing a key challenge in cancer genomics, TINC enhances the accuracy of detecting tumor-specific genetic variants by analyzing variant allele frequencies to quantify tumor cell presence in normal samples. Validated against Genomics England's data, TINC offers a robust tool for improving cancer genomic analyses and clinical decision-making. #cancer #bioinformatics https://lnkd.in/gGiQwnc2