RNA Sequencing

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MRD Sequencing

January 23, 2024/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

MRD Sequencing

Minimal Residual Disease (MRD), characterized by a small number of lingering malignant cells post-treatment, poses a recurrence risk often undetectable by standard surveillance methods. Twist Bioscience’s MRD Rapid 500 Panel addresses this challenge by utilizing circulating tumor DNA for early detection. Leveraging Twist’s silicon-based DNA synthesis platform, this scalable solution offers rapid turnaround time (as few as 6 business days) with personalized variant profiles from whole-genome or whole-exome sequencing. The MRD panels, featuring 50 to 500 probes, provide comprehensive genomic insights, compatible with Twist’s NGS library preparation and hybrid capture workflow. This facilitates early intervention and enhances personalized medicine approaches in cancer recurrence monitoring.

Benefits

Unmatched Scalability and Speed:
Benefit from unparalleled scalability and efficiency as you capture variants of interest with panels ranging from 50 to 500 probes. Streamline your workflow by ordering up to 150 panels at a time, and experience the rapid shipment of panels within an impressive 6 business days.

Customized Panel Designs:
Tailor your panel designs to meet your specific needs using a variant target coordinate BED file. Improve capture performance by strategically filtering probe sequences over repetitive regions, leading to enhanced efficiency and significant cost savings on overall sequencing expenses.

Panel Information:
Leverage the advantages of a single plex for 12 tests, ensuring the detection of SNVs and small indels with high precision. Implement quality control through qPCR, and rest assured with ISO-13485 certification, signifying a commitment to reliability. Conveniently receive panels in Matrix Tubes, and benefit from designs supported against hg19 and hg38 reference genomes.

Lab Workflow:
Integrate seamlessly into your lab workflow with compatibility with Twist library preparation and hybridization workflows. Follow the recommended hybridization protocol, MRD Standard Hyb 2.0, ensuring not only efficiency but also a streamlined and harmonious laboratory process.

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Long Read Sequencing

January 23, 2024/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

Long Read Sequencing

Combine the precision of Twist target enrichment with the power of long read sequencing to efficiently explore crucial genomic regions at scale. Twist Alliance panels, both pre-designed and customizable, empower researchers to capture target regions in a cost-effective and high-throughput manner, ensuring exceptional performance.

Exceptional Performance: Elevate your sequencing endeavors with panels specifically crafted for long read sequencing. Probes are optimized for high uniformity and sequencing efficiency, ensuring balanced coverage even across challenging-to-sequence or difficult-to-map genomic regions.

Long Read Sequencing at Scale: Efficiently scale up your sequencing projects with a protocol optimized for long fragment enrichment. This approach allows you to pack more samples into a single sequencing run, making it possible to study targeted regions across large cohorts.

Accurate Variant Calling with Targeted HiFi Sequencing from PacBio: Leverage the accuracy of targeted HiFi Sequencing from PacBio for precise variant calling of SNPs, SVs, and indels. Benefit from unambiguous haplotype resolution and long-range phasing, ensuring reliable results. This approach is compatible with Sequel IIe and Revio Systems, providing versatility in sequencing platforms.

Twist Alliance Dark Genes Panel
Enables sequencing of genes that are difficult or impossible to fully sequence with short read technology.

Targets 389 genes (20 Mb)
Key targets include GBA, SMN1/2

Twist Alliance Long-Read PGx Panel
Focus on important genes in pharmacogenomics that are critical to drug metabolism and patient therapeutic response.

Targets 49 genes (2 Mb)
Key targets include CYP2D6, HLA-A, HLA-B

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Library Preparation

January 23, 2024/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

Library Preparation

Twist Library Preparation Kits offer a streamlined process for constructing high-quality DNA libraries in next-generation sequencing (NGS) applications. Tailored for whole genome sequencing and targeted enrichment, these kits simplify library preparation by combining multiple steps into a single reaction, enhancing efficiency and ensuring consistent results.

Two configurations are available to cater to different needs: Mechanical Fragmentation, designed for mechanically sheared gDNA, and Enzymatic Fragmentation, ideal for automated, high-throughput library preparation. Both configurations minimize artifacts, accommodate various DNA input types, and optimize sequencing of low-quality samples, with the Enzymatic Fragmentation offering tunable, reproducible fragment sizes while minimizing sequence bias and maximizing coverage depth.

Library Preparation Workflow

The Twist Library Preparation Kits provide a comprehensive solution for the entire library preparation workflow, encompassing crucial steps such as end repair, dA-tailing, adapter ligation, and library amplification. Both kits offer versatility in adapter choices, allowing the use of either full-length or universal adapters based on specific application requirements.

For the Enzymatic Fragmentation Kit, additional functionality includes the incorporation of enzymes for the fragmentation of genomic DNA (gDNA) samples. This feature enhances the kit’s capability for high-throughput library preparation.

The accompanying chart illustrates a robust library construction process by utilizing Twist Universal Adapters for insert ligation and UDI primer PCR amplification. This approach ensures a streamlined and efficient workflow, producing libraries suitable for a diverse range of applications.

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Other Panels

January 3, 2024/in NGS, Partners, Twist/by Harshita Sharma

PRODUCTS

Other Panels

Mitochondrial Panel

The mitochondrial genome encodes factors critical to energy production, which directly affects the energy state of the cell, tissue, and human individual. Pathogenic mutations of Mitochondrial DNA (mtDNA) are often implicated in a group of complex human diseases which can be difficult to diagnose such as metabolic & neurologic disorders as well as cancer. Interrogation of the human mitochondrial genome by targeted Next Generation Sequencing (NGS) can help investigators shed light on the genetic mechanism behind mitochondrial disorders.

The Twist Mitochondrial Panel is a fixed content panel designed to cover all 16,659 base pairs (bp) and 37 genes of the mitochondrial genome. This panel can be used as a standalone panel or as a spike-in with Twist’s Human Core Exome, Comprehensive Exome as well as Twist’s Custom Panels. Providing industry-leading coverage, uniformity, and flexibility, the Twist Mitochondrial Panel can help investigators enrich for, sequence, and analyze mtDNA variants contributing to disease including incidences of heteroplasmy.

Twist Alliance Diversity SNP Panel

Historical genotyping tools have long grappled with biases toward a limited number of ethnicities, resulting in underrepresentation of significant portions of the global population. Traditional platforms, like microarrays, exacerbate this issue by offering fixed content updated only periodically. To address these inefficiencies and promote equity, researchers can turn to target capture-based Next-Generation Sequencing (NGS) workflows with probe panels designed for diversity and flexibility.

Twist’s expanding Targeted Genomic Block Sequencing (GBS) portfolio includes the Twist Diversity SNP Panel, offering a flexible, ethnicity-neutral gold standard for genotyping. This panel can be used independently or as a spike-in with the Twist Human Comprehensive Exome panel. Its customizable design allows for additional probes to cover specific regions of interest, all synthesized on Twist’s DNA synthesis platform.

Developed in collaboration with the Regeneron Genetics Center, the Twist Diversity SNP Panel seamlessly integrates into existing fully automated exome processing workflows, providing base calls and imputed variants. Genotype imputations can be calculated using open-source tools, with an imputation guide available from Twist Customer Support for those starting with imputation analysis tools.

Note: While the Diversity SNP panel content has not been fully validated through the complete Twist workflow, users are encouraged to contact Twist Customer Support for recommendations on assay set-up.

Twist Alliance Pan-cancer Methylation Panel - 1.5 MB

Methylation sequencing plays a crucial role in detecting and tracing the origins of cancer cells, offering sensitivity in unraveling complex methylation patterns. The Twist Alliance Pan-cancer Methylation Panel – 1.5 MB, a collaborative effort between Twist and AnchorDx, is tailored to focus on cancer-specific methylation patterns across 31 different cancers. This custom target enrichment panel provides deep coverage of clinically relevant targets, enabling the study of methylation patterns crucial for early cancer detection and diagnosis, especially from tumor and liquid biopsy samples.

Constructed with Twist’s state-of-the-art oligonucleotide synthesis platform, the panel boasts high on-target rates and uniformity. It has undergone validation with the Twist Methylation workflow, utilizing liquid biopsy samples from breast cancer, colorectal cancer, and non-small cell lung cancer. The panel design, based on the TCGA database, covers 31 cancer types and 47 disease entities, featuring 13,090 probes targeting approximately 126k CpG sites. Notably, around 74% of the 12k differentially methylated regions (DMRs) overlap with CpG islands, showcasing the panel’s comprehensive coverage.

It’s essential to note that the Twist Alliance Pan-cancer Methylation Panel – 1.5 MB does not carry ISO-13485 certification.

Twist Alliance CNTG Exome - 41 MB

The Twist Alliance CNTG Exome – 41 MB, developed through collaboration between CENTOGENE and Twist, serves as a powerful tool for addressing the challenges associated with the diagnosis of rare diseases. Rare diseases often pose difficulties for physicians, leading patients on prolonged diagnostic journeys. DNA sequencing panels, such as this collaboration, offer comprehensive solutions, providing answers and resolutions for patients undergoing these diagnostic odysseys.

As a leader in rare disease diagnostics, CENTOGENE leverages its expertise in conjunction with Twist’s advanced omics technology to design target enrichment capture panels. The Twist Alliance CNTG Exome – 41 MB ensures highly uniform coverage of the entire exome, including full coverage of the mitochondrial genome. This panel significantly enhances diagnostic yield compared to standard whole exome sequencing, addressing a broad spectrum of disorders encompassing over 7,000 rare diseases.

The panel comprises a total of 483,000 probes, with components such as the Twist Human Comprehensive Exome (396.1K probes), Twist Mitochondrial Panel (139 probes), Twist Alliance Centogene Rare Disease Panel (78.8K probes), and Centogene Spike-In (7.8K probes). Notably, the Twist Alliance CNTG Exome – 41 MB does not carry ISO-13485 certification, emphasizing its designation for research use only and not for diagnostic procedures.

Twist Alliance CNTG Rare Disease Panel - 7.6 MB

The Twist Alliance CNTG Rare Disease Panel, designated for research use only and not for diagnostic procedures, focuses on providing a more streamlined solution for researchers targeting rare diseases. With over 2,500 relevant genes associated with rare diseases, this panel ensures comprehensive coverage, encompassing ≥99.5% of targeted regions within the CNTG Exome footprint.

Containing 78.8K probes, the Twist Alliance CNTG Rare Disease Panel is designed to detect genes linked to various conditions, including rare treatable diseases, early onset childhood disorders, cardiac disorders, neurodegenerative diseases, skeletal abnormalities, and metabolic disorders. This lightweight tool offers researchers the flexibility to capture crucial rare disease coverage without the full exome footprint.

It’s important to note that the Twist Alliance CNTG Rare Disease Panel-7.6MB does not carry ISO-13485 certification, emphasizing its specific designation for research purposes.

Twist Alliance CNTG Hereditary Oncology Panel - 0.2 MB

The Twist Alliance CNTG Hereditary Oncology Panel, expressly designed for research use only and not intended for diagnostic procedures, focuses on providing a targeted solution for identifying genetic predisposition to hereditary tumors. This panel includes 72 carefully selected cancer-associated genes and covers ≥99.5% of targeted regions.

With applications ranging from identifying genetic predispositions in breast cancer to gastrointestinal tumors, Li-Fraumeni syndrome, MEN1, MEN2, paragangliomas, and more, the Twist Alliance CNTG Hereditary Oncology Panel offers a specialized tool for researchers delving into the genetic underpinnings of hereditary cancers.

It’s essential to note that the Twist Alliance CNTG Hereditary Oncology Panel- 0.2MB does not carry ISO-13485 certification and is exclusively designated for research purposes.

Twist Human Ancient DNA Panel

The Ancient Human DNA Panel, a collaborative effort with David Reich’s lab at Harvard University, is designed for studying genetic variation in ancient DNA specimens, typically obtained from bones and teeth. Targeting 1.35 million SNPs, this panel includes a subset covering all 1.23 million polymorphic sites in the human genome published in Fu et al. Nature 2015. This ensures compatibility with published data on numerous ancient individuals, fostering broad comparability.

Developed using Twist’s double-stranded capture probes and hybridization capture reagents, the panel demonstrates high genome coverage and reduced allelic bias. This optimization, as highlighted in Rohland, Mallick et al. Genome Research 2022, enables genome-scale data at significantly reduced sequencing costs compared to shotgun sequencing, thanks to the highly efficient enrichment of human DNA fragments.

It’s important to note that the Twist Alliance Ancient Human DNA Panel is not ISO-13485 certified, emphasizing its exclusive use for research purposes.

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Custom Panels

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

PRODUCTS

NGS Custom Panels

Twist Custom NGS Target Enrichment Panels - Precision Panels, Distributed by Decode Science

Twist Bioscience’s custom target enrichment panels are designed using a silicon-based DNA synthesis platform that produces highly accurate, reliable probes for next-generation sequencing (NGS). These panels can be tailored to suit a wide variety of applications, from small and highly focused panels targeting specific regions to large and complex designs that span broad genomic areas, making them suitable for almost any sequencing project. The combination of advanced design algorithms, proprietary synthesis processes, and a streamlined production pipeline ensures that each panel delivers uniform coverage, reduced off-target effects, and consistent, high-quality performance across sequencing platforms.

Another advantage of Twist’s approach is the flexibility it provides. Researchers can expand existing panels, update or enhance them with new content, or even combine multiple designs into blended panels to support evolving project needs. Turnaround times are fast, and the resulting panels are built to maintain accuracy and reproducibility, ensuring dependable results even in demanding research environments.

Exceptional, Reliable Performance

Twist’s double-stranded DNA probes undergo NGS-based quality control to ensure balanced representation and minimise dropout

Panel Blending

Easily combine two or more panels into a single design, either in your own lab or through Twist’s streamlined blending service.

Simple Design

Submit specifications online and benefit from Twist’s advanced design algorithms that optimize every panel for accuracy and efficiency.

Scalable Panels

From 100 probes to one million, Twist custom panels can be tailored to projects of any size while maintaining consistency and precision.

As the official distributor for Twist Bioscience in Australia and New Zealand, Decode Science makes accessing these panels straightforward. Our role is to connect your lab with Twist’s advanced technologies, ensuring you get the right custom panel solution for your sequencing projects—delivered locally with support when you need it.

Nucleic Acid Panel Designs

DNA

Twist Bioscience’s custom DNA target enrichment panels provide advanced solutions for a variety of sequencing applications. Using proprietary strategies such as probe shifter technology, these panels deliver precise, consistent coverage and high-performance results tailored to specific biological targets.

RNA

Twist Bioscience’s RNA custom target enrichment panels are designed to capture and enrich cDNA libraries for next-generation sequencing (NGS). Using innovative strategies such as exon-aware probe placement, these panels provide precise, high-performance coverage to maximize transcriptional insights from your RNA sequencing experiments.

Methylation

Twist Bioscience’s methylation target enrichment panels are designed to capture libraries prepared to reveal DNA methylation patterns. Using a unique design approach with four probe species per target—fully methylated and unmethylated, sense and antisense—these panels deliver uniform coverage while preserving accurate methylation signatures for reliable NGS analysis.

Featured Resources

FAQs

What is the standard probe length in a custom panel?

Custom panels typically use probes that are 120 base pairs (bp) long. Twist also offers alternative lengths—such as 80 bp or 100 bp—depending on your experimental needs, but all probes within a single panel are uniform in length.

Can target enrichment panels be customized for gene fusions and SNPs?

Yes. Twist custom panels can be designed for a variety of targets, including gene fusions, single nucleotide polymorphisms (SNPs), viruses, microsatellite instabilities (MSIs), structural variants, copy number variants (CNVs), and insertion/deletion events (InDels).

Can Twist design panels for targeted methylation (bisulfite) sequencing?

Yes. Twist offers custom panels specifically for targeted methylation sequencing, optimized to capture methylation patterns with high accuracy.

Are Twist target enrichment probes double-stranded?

Yes, all Twist target enrichment probes are double-stranded DNA, ensuring stable hybridization and reliable performance.

How is the quality of Twist probes ensured?

Twist performs NGS-based quality control by sequencing the probes to verify their representation within the pool, ensuring consistent and uniform performance across the panel.

Ready To Order?

As the official distributor for Twist Bioscience in Australia and New Zealand, Decode Science makes accessing these panels straightforward. Our role is to connect your lab with Twist’s advanced technologies, ensuring you get the right custom panel solution for your sequencing projects—delivered locally with support when you need it.

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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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