Author Archive for: Harshita

Qsep1

December 21, 2023/in BiOptic, Instruments, Partners/by Harshita Sharma

PRODUCTS

Qsep1

Smallest/portable-sized capillary electrophoresis Bio-Fragment Analyzer for DNA, RNA, and protein.

Ideal for small laboratories with low throughput needs (1~8 samples).

Supports Wi-Fi and cable connections, enhancing spatial flexibility.

Easy exchange of 10+ cartridges between various applications.

Quantitative method provides fragment size and concentration info in a single run.

Qsep1 is an automated Bio-Fragment Analyzer for DNA, RNA and protein fragments. Advantages of capillary electrophoresis are high resolution (1~4bp if less than 500bp), high sensitivity (5pg/μl) and significantly faster preparation and analysis time. Besides analyzing fragment sizes and concentrations, it is also suitable for quality control of next-generation sequencing (NGS).

Qsep1 is equipped with completed hardware and software and has fully functional remote access via cable/Wi-Fi. The system provides various kinds of applications such as RNA quality control with RNA Quality Number (RQN) provided, auto-distribution of NGS QC and quality control of gDNA with DNA Quality Number (DQN) provided. Qsep1 is a top choice for modern small laboratory.

Qsep series can not only replace the complicated and time-consuming gel preparation and analysis procedure, but increase the accuracy of analysis, elevate efficiency and reproducibility, and reduce the human error and costs.

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cfDNA Pan Cancer Reference standards

Viral Controls

December 20, 2023/in Partners, Synthetic Controls, Twist/by Harshita Sharma

PRODUCTS

Synthetic Viral Controls

Trusted Controls for Diverse Applications

In the wake of the global demand for diagnostic tests amid the Coronavirus pandemic, laboratories worldwide seek reliable tools for detecting SARS-CoV-2 and Respiratory viruses across various sample types. Our controls offer a trusted solution to address the expanding need for testing, ensuring accuracy and safety in a wide range of applications.

Ensuring Reproducible, High-Quality Results

Positive controls play a pivotal role in maintaining quality standards for diagnostic assays, spanning from development to day-to-day testing. These controls facilitate the verification and validation of diagnostic tests, supporting both next-generation sequencing (NGS) and reverse transcription polymerase chain reaction (RT-PCR) assays, ensuring reproducibility and reliability.

Safe and Effective Alternatives to “Live Virus”

Concerns regarding safety and security associated with controls based on viral nucleic acids extracted from infected patients or live virus cultures led us to develop synthetic controls through gene synthesis. These alternatives offer a safe and effective solution, allowing broader access to diverse strains while mitigating potential risks.

Flexible Formulations for Varied Needs

Tailor your approach with our flexible control formulations—Standard, Assay Ready, or Encapsulated. Whether in a frozen liquid, dried pellet, or encapsulated dried pellet form, our controls provide options for shipping, storage, and stability, meeting the unique requirements of your applications. Ambient shipping reduces costs and enhances accessibility for researchers globally, making our controls a reliable choice in the dynamic landscape of diagnostic testing.

RESPIRATORY VIRUS CONTROLS

Comprehensive Controls for Respiratory Virus Research

Twist’s Synthetic Respiratory Virus Controls encompass a wide spectrum of RNA and DNA viruses crucial for respiratory disease studies. Aligned with the Twist Respiratory Virus Research Panel (PN 103067), these controls seamlessly integrate into Twist Fixed Panel NGS workflows, as well as RT-PCR or qPCR experiments designed by users.

Navigating the Viral Landscape

Refer to the taxonomic tree in the accompanying figure for a visual representation of the viruses covered by Twist Respiratory Virus Controls. The table provides GenBank IDs, virus types, and lengths for each control, facilitating an in-depth understanding of the viral landscape. Custom synthesis options are also available—connect with your local sales representative for additional details.

Simplify Your Research Journey

For further information or to make a purchase, contact your local sales representative or conveniently “Buy Now.” Twist’s Synthetic Respiratory Virus Controls offer a robust foundation for respiratory virus research, enhancing the precision and reliability of your experiments.

SARS-COV-2 CONTROLS

Elevating Quality Control with Twist Synthetic RNA Controls for SARS-CoV-2

Twist Bioscience offers synthetic RNA controls designed for diverse viral genomes, including SARS-CoV-2. With six non-overlapping 5 kb fragments transcribed into ssRNA, these controls provide over 99.9% genome coverage. Available in standard, Assay Ready, and Encapsulated Formats, they cater to various needs with concentrations tailored for flexibility.

Unique Stability in Encapsulated Controls

Twist’s Encapsulated Controls, sealed in a metal capsule around a desiccated pellet, ensure enhanced stability. With room temperature shipping and a five-year shelf life, these controls provide cost-effective and globally accessible solutions.

Contribution to Multiplex Assay Development

The Twist Assay Ready Synthetic SARS-CoV-2 RNA Control, developed with the US CDC, enables simultaneous testing for influenza A, B, and SARS-CoV-2. Originally designed for authorized laboratories, it is now available to customers outside the CDC.

Best Practices and Regulatory Considerations

For comprehensive guidance on storage and use of controls, refer to provided documents: Twist Assay Ready Synthetic Controls Storage and Use Document and Twist Sars-CoV-2 Encapsulated RNA Control Storage and Handling Guide.

Note: This product is authorized for emergency use by the FDA under an EUA for the detection of SARS-CoV-2 nucleic acid. The emergency use is limited to circumstances justifying the authorization.

MONKEYPOX CONTROLS

Twist Synthetic hMPXV Controls: Precision for Targeted Research

Twist’s Synthetic Human Monkeypox Virus (hMPXV) Controls, representing CB and WA clades, cover over 80% of the viral genome. Validated for custom assays and compatible with CDC-recommended PCR procedures, these controls, in two variants, offer precise tiling of the genome at 900bp intervals. With concentrations at approximately 100,000 copies/uL, they provide accuracy and reproducibility. Contact your local sales representative for more information.

Note: The Twist Synthetic hMPXV Controls are not ISO-13485 certified.

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Viral
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cfDNA Pan Cancer Reference standards

cfDNA Pan-cancer Reference Standards

December 20, 2023/in Partners, Synthetic Controls, Twist/by Harshita Sharma

PRODUCTS

Twist cfDNA Pan-cancer
Reference Standards

NGS-based liquid biopsy is a rapidly evolving application that requires accurate and precise reference standards. The Twist Pan-cancer Reference Standard is a high-quality, standardized control for use in the research and development of NGS-based liquid biopsy assays. This reference standard is ideal for establishing the analytical limit of detection (LoD) for specific cancer variants and as a control to track the quality of an NGS assay workflow and assess the fidelity of the assay process during research and development of such assays.

Comprehensive Detection of Cancer Variants

458 unique naturally occurring cancer variants

132 clinically relevant variants

Covers 84 different genes involved in cancer

Better Design of Background
DNA

Background DNA derived from human cfDNA samples

DNA size profile and post-sequencing profile mimic native cfDNA

Designed for Precision and Flexibility

Seven individual VAF percentages to choose from

Digital Droplet PCR verification of VAF percentages

Convenient test set of all VAF percentages available

About the Data

Comparison of Twist’s Reference standard and competitors

DNA analysis of the Twist cfDNA Pan-Cancer Reference Standard and competitors reference standards show that Twist more closely mimics native cell-free DNA providing a more true to life test result.

Post Sequencing Profile Comparison

Post sequencing library size distribution comparison between Twist and competitors show how similar Twist mimics native cfDNA samples including the jagged leading peaks.

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Custom Panels

December 20, 2023/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

NGS Custom Panels

Custom Panels

Twist Custom Panels can be designed and built to cover a wide range of panel sizes, target regions, and multiplexing requirements — all with the exceptional and consistent performance you’ve come to expect from Twist NGS solutions.

With our incredibly flexible design capabilities, you can easily expand or enhance content on your existing panel or blend together the content from multiple panels with the Twist Custom Blended Panels option. This unprecedented flexibility saves you time while guaranteeing high-quality performance and analysis.

Consistent Performance Across a Range of Panel Sizes and Target Regions

Design a Twist Custom Panel in minutes using a list of gene names or a target bed file. Regardless of panel size or target region, Twist Custom Panels consistently deliver excellent performance.

Robust Performance During Multiplex Target Enrichment

Twist Custom Panels deliver high-quality performance across 1-, 8-, and even 16-plex enrichment reactions:

High uniformity for all levels of multiplexing
High on-target rates do not vary with higher levels of multiplexing
Low duplication rates across all levels of multiplexing

Verified by NGS to Ensure Reproducibility from Lot to Lot

As demonstrated by NGS-based quality analysis, Twist Custom Panels demonstrate a low lot-to-lot variation. Every Twist Custom Panel is sequenced to ensure consistent quality and performance across all probes within a panel.

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Methylation

December 20, 2023/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

NGS Methylation Detection

NGS Methylation Detection System

The Twist NGS Methylation Detection System provides a robust, end-to-end sample preparation solution for identifying methylated regions in the human genome. The workflow employs a unique enzymatic process from New England Biolabs® that is much less damaging to DNA, alongside Twist‘s Custom Methylation Panel design.

Whether you are investigating cellular differentiation or screening liquid biopsies for cancer, the system offers the most efficient methylation detection available.

NEBNext® EM-seq™ Kit for Twist Targeted Methylation Sequencing

In partnership with New England Biolabs (NEB), Twist Bioscience offers a new methylation sequencing workflow that improves the quality of libraries and removes the need for damaging bisulfite treatment during prep.

The workflow features enzymatic conversion of unmethylated cytosines (see figure) to identify sites of methyl-cytosine (5mC) and hydroxymethyl-cytosine (5hmC).

Enzymatic conversion produces more intact libraries with better representation, and ultimately achieves more sensitive methylation detection. The library preparation system is suitable for whole genome sequencing and downstream enrichment with Twist Methylation Panels.

EM-seq conversion involves a series of enzymatic steps to convert unmethylated cytosines into uracils. The final result is the same as conventional bisulfite conversion, making EM-seq compatible with existing analysis pipelines that use Bismark and bwa-meth.

Twist Human Methylome Panel

The Twist Human Methylome Panel targets 3.98M CpG sites through 123 Mb of genomic content to target biologically relevant methylation markers. Expansive content makes this panel an ideal choice for investigators to explore the methylation fraction in a diverse range of applications from cancer metastasis, human development, and functional genomics.

The panel is optimized and validated for use with the Twist methylation detection system for a complete end-to-end workflow with industry leading performance. High capture efficiency increases the sensitivity of detection across the footprint of the epigenome while decreasing sequencing costs. The panel is ideal for screening cohort samples and differentially methylated region discovery.

Enhanced Coverage, Advantages, and High Performance: A Comparative Analysis with Microarrays

The Twist Human Methylome Panel offers comprehensive coverage of the genome, targeting 3.98 million CpG sites within 123 Mb of genomic content. It efficiently identifies 84% of CpG islands and covers an additional 105,288,339 bases of related regions. In comparison to average microarrays, the panel overcomes static content limitations and enhances coverage across the epigenome. Microarrays suffer from constraints in methylation detection at extreme ends due to background noise and saturation, whereas the Methylome Panel, utilizing hybrid-capture panels and Next-Generation Sequencing (NGS), provides expanded content, single-base resolution, and a higher dynamic range for more accurate detection of differentially methylated regions. The panel’s performance is notable, achieving 90% coverage at 30x depth, 95% on-target rates, and high uniformity with a fold 80 of 1.54. Its efficient capture metrics instill confidence in accurate methylation fraction detection while minimizing sequencing costs.

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Viral Panels

December 20, 2023/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

NGS Viral Panels

Comprehensive Viral Research Panel

The Twist Comprehensive Viral Research Panel is a highly versatile tool designed for comprehensive novel virus detection. It consists of 1,052,421 unique probes derived from reference sequences in databases like RefSeq, FluDB, and VIPR, covering a wide range of viral families affecting humans and animals. This panel can detect novel and evolved viral strains, including those related to specific outbreaks.

The panel demonstrates success in detecting highly divergent viral sequences, such as the spike region of a newly discovered coronavirus and a segment from an H1N1 influenza outbreak. With a mismatch sensitivity defined through various tests, it can capture highly evolved viral sequences with over 99.8% coverage.

Furthermore, the Twist Comprehensive Viral Research Panel allows for the enrichment of novel viruses, showcasing its ability to capture sequences with up to 10% variation. It also supports multiplex detection of diverse viruses, making it suitable for metagenomic applications in various sample types. In a co-infection assay, the panel successfully captured four different virus types spiked into human RNA with high efficiency, demonstrating its multiplexing capabilities.

Respiratory Virus Research Panel

The Twist Respiratory Panel is a powerful tool designed for the detection of common human respiratory pathogens through a single test. It comprises 41,047 probes compiled from the GenBank database, allowing researchers to distinguish COVID-19 symptoms from those of other respiratory illnesses, whether influenza- or non-influenza-related. This panel facilitates high-resolution Next-Generation Sequencing (NGS) by enriching viral sequences, enabling the high-sensitivity detection of viral material, even in challenging samples, with more than 5000x enrichment. Post-enrichment, it achieves coverage of over 99.9% of the genome at 1X or greater.

The panel demonstrates its effectiveness in detecting viral standards from different viral families. Synthetic Viral Controls, when spiked into human carrier RNA, show significant enrichment, with over 70% of reads coming from viral genomes, representing at least a 2500-fold enrichment over the spiked-in content.

Furthermore, the Twist Respiratory Panel supports multiplexing for higher throughput and lower cost. Comparisons using multiplex and single-plex hybridization reactions at different viral titers show that 8-plex capture provides comparable efficient enrichment as a single-plex capture. This is demonstrated using the Twist Synthetic Viral Controls and the Twist Respiratory Virus Research Panel, showcasing the versatility and cost-effectiveness of multiplexing in this respiratory virus detection system.

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Exome Panels

December 20, 2023/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

Exome Panels

Exome 2.0

Twist Exome 2.0 is designed to detect rare and inherited diseases, as well as germline cancers. This panel’s high uniformity and low off-target rate deliver best-in-class sequencing efficiency, enabling quality data to be collected with less sequencing. With superior coverage of major genetic databases (RefSeq, CCDS, GenCode, Clinvar, ACMG73 and more) and the addition of clinically relevant non-coding pathogenic and likely pathogenic variants, Twist Exome 2.0 provides the value of multiple clinical panels all wrapped into one, easily customizable package.

Twist Alliance VCGS Exome - 40.1 MB

Victorian Clinical Genetics Services (VCGS) and Twist have collaborated to address the challenges physicians face in diagnosing heritable diseases when routine testing falls short. The result is the Twist Alliance VCGS Exome – 40.1 MB, a diagnostic panel drawing on VCGS’s extensive clinical genomics experience. This panel covers the entire exome, providing dedicated boosting of clinically relevant genes (Mendeliome), and is designed with special attention to additional coverage of clinically relevant loci beyond traditional gene coding regions.

The Twist Alliance VCGS Exome – 40.1 MB is a highly uniform panel, considered best-in-class, and aims to facilitate the identification of alleles linked to heritable diseases. Whether used for carrier screening or pre- and post-natal testing, this panel is intended to streamline the diagnostic process.

It’s important to note that the content of the Twist Alliance VCGS Exome – 40.1 MB has not been fully validated through the complete Twist workflow, and for guidance on assay set-up, contacting Twist Customer Support is recommended. Additionally, this panel is not ISO-13485 certified.

Twist Alliance Clinical Research Exome - 34.9 MB

The Twist Alliance Clinical Research Exome, developed in collaboration with the Broad Institute Genomics Platform, is a versatile tool designed for comprehensive exome sequencing.

Utilizing validated data from clinical patient samples, this panel is constructed on Twist’s flexible Next-Generation Sequencing (NGS) platform, allowing easy and rapid customization of content. It provides a thorough examination of the exome, with additional enrichment focusing on clinically relevant areas associated with cancer, rare diseases, and inherited conditions.

Leveraging the exceptional uniformity of Twist NGS probes, the assay achieves cost and throughput efficiency. The Broad Institute Genomics Platform has already processed over 250,000 samples, showcasing the panel’s effectiveness and keeping the institute at the forefront of exome sequencing.

The panel’s design encompasses the Twist Core exome, the mitochondrial genome, and validated coding and non-exonic regions of interest, including ACMG73 genes, supplemental coverage of OMIM and COSMIC regions, and specific targets defined by Broad. It offers a comprehensive solution for a range of research applications.

Important to note, the content of the Twist Alliance Clinical Research Exome – 34.9 MB has not been fully validated through the complete Twist workflow. For guidance on assay set-up, users are advised to contact Twist Customer Support. Additionally, this panel is not ISO-13485 certified.

Mouse Exome Panel

The mouse is an extremely important model system for studying genetic variation, tumor mutations, and phenotypic outcomes as well as the therapeutic effect of pharmaceutical agents. As genetic variant databases are continuously updated, the Twist Mouse Exome panel is thoughtfully designed and built from the most current databases. When combined with Twist’s expanding portfolio of library preparation and enrichment reagents, the complete toolset allows researchers to achieve industry-leading coverage across target regions while optimizing sequencing cost and sample throughput.

Twist Alliance Canine Exome - 40.5 MB

Understanding the genetic variations among dog breeds is crucial for unraveling the genetic regulation of traits and understanding the basis and progression of diseases in dogs. Comprehensive gene panels, such as exomes, play a pivotal role in enhancing veterinary diagnostics and associated clinical medicine. These Next-Generation Sequencing (NGS) panels, like the Twist Alliance Canine Exome developed in collaboration with the Broad Institute’s Karlsson lab, are essential tools for advancing canine genomic research. They contribute to improved understanding of canine cancers and potential therapeutics.

The Twist Alliance Canine Exome panel is designed to achieve the following objectives:

Covers coding exons of canine genes.
Facilitates comparative genomic studies between canine and human genomes.
Includes regions of known importance in human cancers.
Allows for cost-effective deep sequencing.

Furthermore, canine genomic research has demonstrated benefits for human medical research, revealing genetic similarities between human and canine tumors, such as Copy Number Variations (CNVs), differential gene expressions, and structural chromosome abnormalities. This interdisciplinary approach underscores the potential for insights gained in canine genetics to contribute to advancements in human medicine.

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STOmics Offline Software

December 13, 2023/in STOmics Software/by Harshita Sharma

PRODUCTS

STOmics Offline Software

Spatial Omics Analysis Suite Overview: ImageStudio, SAW, and StereoMap

ImageStudio:

ImageStudio is a SpatioTemporal omics offline image processing software.
It assesses image quality, focusing on sharpness and track lines, determining suitability for downstream data analysis.
The manual adjustment module addresses scenarios beyond the software’s capabilities.

SAW (Stereo-seq Analysis Workflow):

SAW integrates Stereo-seq spatial group gene expression analysis tools.
It reduces and visualizes spatial expression information from sequencing data on microarrays.
Spatial expression matrices generated by SAW are suitable for downstream analysis.

StereoMap:

StereoMap is a high-definition visual desktop software designed for Stereo-seq data analysis results.
It visualizes STOmics’ SpatioTemporal omics technologies, allowing further exploration through various tools.
GEF matrix, image RPI and IPR data, and clustering results from SAW can be displayed in StereoMap.

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STOmics Offline Software

STOmics Cloud

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STOmics Cloud

December 13, 2023/in STOmics Software/by Harshita Sharma

PRODUCTS

STOmics Cloud

STOmics Cloud is a spatial-temporal data analysis platform for managing and analyzing multi-omics data. The platform is centered around projects, enabling users to seamlessly integrate data and tools into their projects, ensuring traceable analysis processes, reproducible results, knowledge sharing, and project collaboration. Additionally, STOmics Cloud offers a user-friendly portal interface, providing code-free data analysis, high-resolution visualization, and personalized analysis services.

What You Can Achieve

Data Analysis

Data Visualization

Data Storage

Data Sharing

STOmics Cloud Workflow

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STOmics Cloud

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