cfDNA Pan-cancer Reference Standards

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

Twist cfDNA Pan-Cancer Reference Standard v2

The Twist cfDNA Pan-Cancer Reference Standard v2 is a meticulously engineered tool tailored for genomics professionals developing and validating NGS-based liquid biopsy assays. This reference standard provides a reliable and reproducible resource for detecting clinically relevant variants, enabling researchers to confidently evaluate assay performance at every stage. By integrating a wild-type (WT) cell-free DNA (cfDNA) background with synthetic oligonucleotides carrying mutant alleles, the material delivers exceptional precision and sensitivity.

Researchers can leverage this standard to define critical analytical parameters, including the Limit of Detection (LoD) and Limit of Blank (LoB), ensuring robust assay calibration and quality control. Ideal for both early-stage assay development and ongoing process monitoring, the Twist cfDNA Pan-Cancer Reference Standard v2 empowers genomics teams to accelerate liquid biopsy innovation while maintaining rigorous accuracy and reproducibility.

But... Why These Panels?

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

Download Product Sheet, Data Files & Detailed FAQs

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Data To Back This Up

Fragment Profile Comparison: Twist vs. Competitors

Twist cfDNA Pan-Cancer Reference Standard v2 closely mimics the fragment size distribution of native cfDNA, including distinct mononucleosomal and dinucleosomal peaks. When compared to competitor reference materials standardized for peak height, Twist’s standards provide a more biologically accurate representation of circulating cell-free DNA, supporting realistic assay development and reliable performance benchmarking.

Schematic of Synthetic Variant DNA Design

Twist’s synthetic variant DNA is engineered to tile across each genomic locus with extensive overlap, ensuring high coverage and diverse fragment representation. This design captures the variant in multiple positions relative to the DNA termini, providing realistic fragment diversity and enabling more accurate assay performance assessment.

Background Mutation Rate Comparison

Background mutation rate measures the occurrence of non-germline variants in duplex consensus reads from target-enriched wild-type samples. Analysis across Twist cfDNA Pan-Cancer Reference Standard v2, native cfDNA, competitors, and Twist v1 shows that v2 closely matches the low background error rate of native cfDNA. Its superior fidelity—lower than both v1 and competitor standards—is achieved through a high-precision production process, ensuring more reliable and accurate assay benchmarking.

INDEL Size Distribution

The Twist cfDNA Pan-Cancer Reference Standard v2 includes a wide range of insertion and deletion (INDEL) sizes, from deletions of 30 bp to insertions of 15 bp. Visualized as a histogram (bin width = 1), this distribution allows researchers to comprehensively evaluate INDEL detection performance across diverse fragment lengths. Single nucleotide variants (SNVs) are not included in this visualization, highlighting the standard’s focus on structural variant representation and assay sensitivity testing.

Variant Calling in Target Enrichment Workflows

Twist cfDNA Pan-Cancer Reference Standards deliver highly accurate variant detection across a range of variant allele frequencies (VAFs). Using a custom panel targeting 215 SNVs and sequencing to 80,000× raw coverage before UMI deduplication, the observed mean VAFs closely match the intended levels. This precision allows researchers to confidently benchmark and validate their NGS-based assays, ensuring reliable performance across the full spectrum of variant frequencies.

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.

NGS Portfolio

Custom Panels

Viral Panels

Methylation Detection

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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Custom Panels

Viral Panels

Methylation Detection

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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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Custom Panels

Viral Panels

Methylation Detection

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Exome Panels

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

About Twist Bioscience Alliance Panels

Twist Alliance Panels are a curated collection of high-quality, ready-to-use sequencing panels developed in partnership with leading scientific institutions. By combining Twist’s world-class oligonucleotide synthesis platform with our partners’ deep expertise, these panels provide comprehensive, validated coverage of clinically and scientifically relevant regions. Ready-made and scalable, they streamline workflows, save time and resources, and support research, clinical, and diagnostic applications—so your team can focus on discovery instead of design.

Exome 2.0

VCGS V2

Clinical Research

Mouse

Canine

Twist Alliance VCGS Exome v2

High-performance diagnostic exome panel for heritable diseases

When routine testing does not yield a diagnosis, DNA sequencing panels are often the next step—especially for suspected heritable conditions. Developed in collaboration between Victorian Clinical Genetics Services (VCGS) and Twist, the Twist Alliance VCGS Exome v2 provides comprehensive coverage of clinically relevant regions while maintaining high uniformity across the exome.

Key Features

Whole exome coverage (54.82 Mb) with enhanced capture of clinically significant genes (Mendeliome)
Dedicated coverage of pathogenic non-coding loci, ensuring clinically relevant variants outside traditional exons are captured
CNV detection backbone: probes across intergenic regions (~25 kb intervals) improve copy number variation calling
Highly uniform panel optimized for carrier screening, pre-natal, and post-natal testing

Probe Content

Component	Number of Probes
Twist Exome 2.0	427K
VCGS-curated content	101K
Total	528K

Ordering Options

111124 Twist Alliance VCGS Exome v2 – 54.82 Mb, 2 Reactions Kit

111126 Twist Alliance VCGS Exome v2 – 54.82 Mb, 12 Reactions Kit

111150 Twist Alliance VCGS Exome v2 – 54.82 Mb, 96 Reactions Kit

Twist Alliance Clinical Research Exome - 34.9 MB

Flexible exome panel for research and clinical discovery

Designed in collaboration with the Broad Institute Genomics Platform, the Twist Alliance Clinical Research Exome uses validated clinical patient data to provide comprehensive exome coverage. This panel enables efficient investigation of cancer, rare, and inherited disease-associated regions while maintaining high uniformity and throughput.

Key Features

Comprehensive exome coverage (34.9 Mb) with flexibility for content customization using Twist’s NGS platform
Supplemental enrichment of clinically relevant coding and non-coding regions, including cancer-associated loci and rare disease genes
High uniformity probes allow cost-efficient per-sample processing and high throughput—successfully applied to >250,000 samples at the Broad Institute
Validated design for research and clinical discovery

Panel Content Highlights

Component	Description
Twist Core Exome	Standard exome coverage
Mitochondrial Genome	Full coverage of mitochondrial DNA
ACMG73 Genes	Clinically actionable targets
OMIM & COSMIC Regions	Supplemental coverage of disease- and cancer-associated loci
Broad-defined Targets	Additional validated coding and non-coding regions

Ordering Options

104032 Twist Alliance Clinical Research Exome – 34.9 MB, 2 Reactions Kit

104033 Twist Alliance Clinical Research Exome – 34.9 MB, 12 Reactions Kit

104034 Twist Alliance Clinical Research Exome – 34.9 MB, 96 Reactions Kit

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.

Get a complete overview of Twist Alliance Panels, including panel coverage, workflow efficiency, and application scope. For guidance on selecting or integrating these panels into your research or diagnostic operations, Decode Science provides personalized support and local assistance.

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.

CNV Backbone Spike-in Panels

RNA Sequencing

MRD Sequencing

Long Read Sequencing

Library Preparation

Other Panels

Custom Panels

Methylation

Viral Panels

Exome Panels

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 Software Portfolio

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 Software Portfolio

STOmics Offline Software

STOmics Cloud

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Stereo-seq Transcriptomics for Large Chip Designs

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

PRODUCTS

Stereo-seq Transcriptomics for Large Chip Designs

STOmics Stereo-seq Transcriptomics for Large Chip Designs (LCD) pioneers the whole transcriptome study for entire tissue sections. Stereo-seq for Large Chip Designs is firstly offered to the market – 1cm x 2cm, 2cm x 2cm, 2cm x 3cm. Compatible for all species (FF samples), it enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view.

Stereo-seq Transcriptomics for Large Chip Designs Workflow

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STOmics Kits Portfolio

Stereo-seq Transcriptomics solution

Stereo-seq Transcriptomics mIF solution

Stereo-seq Transcriptomics H&E solution

Stereo-seq Transcriptomics for Large Chip Designs

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Stereo-seq Transcriptomics H&E solution

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

PRODUCTS

Stereo-seq Transcriptomics H&E solution

Unlock the potential of integrating tissue phenotyping and spatial heterogeneity profiling of molecular information. By incorporating H&E-stained tissue morphological information, Stereo-seq Transcriptomics H&E solution will better assist with tissue type identification, profiling of specific tissue regions of interests (ROIs), and conducting downstream differential analysis between selected ROIs.

Stereo-seq Transcriptomics H&E solution workflow

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STOmics Kits Portfolio

Stereo-seq Transcriptomics solution

Stereo-seq Transcriptomics mIF solution

Stereo-seq Transcriptomics H&E solution

Stereo-seq Transcriptomics for Large Chip Designs

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Stereo-seq Transcriptomics mIF solution

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

PRODUCTS

Stereo-seq Transcriptomics mIF solution

STOmics Stereo-seq Transcriptomics Set for Chip-on-a-slide enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view. Stereo-seq Transcriptomics Solution utilizes DNB patterned array chips loaded with spatially-barcoded probes that capture and prime poly-adenylated mRNA from tissue sections in situ. Each cDNA synthesized from mRNA captured on a particular spot is linked to its spatially-barcoded probe, allowing subsequent gene expression mapping of a tissue section following sequencing and visualization analysis using the StereoMap visualization platform.

Stereo-seq Transcriptomics mIF solution workflow

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STOmics Kits Portfolio

Stereo-seq Transcriptomics solution

Stereo-seq Transcriptomics mIF solution

Stereo-seq Transcriptomics H&E solution

Stereo-seq Transcriptomics for Large Chip Designs

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Author Archive for: Harshita

About Harshita Sharma

Entries by Harshita Sharma

Comprehensive Detection of Cancer Variants

Better Design of Background DNA

Designed for Precision and Flexibility

Unlock instantly with few steps.

Chris Wicky

NGS Custom Panels

Exceptional, Reliable Performance

Panel Blending

Simple Design

Scalable Panels

Chris Wicky

NGS Methylation Detection

Have a question?

NGS Viral Panels

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Key Features

Probe Content

Ordering Options

Key Features

Panel Content Highlights

Ordering Options

Chris Wicky

STOmics Offline Software

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STOmics Cloud

Data Analysis

Data Visualization

Data Storage

Data Sharing

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Stereo-seq Transcriptomics for Large Chip Designs

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Stereo-seq Transcriptomics H&E solution

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Stereo-seq Transcriptomics mIF solution

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Better Design of Background
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