MGISP-Smart 8

RNA Sequencing

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

PRODUCTS

RNA Sequencing

Twist’s RNA sequencing workflows offer a complete NGS solution that produces uniform libraries for RNA sequencing.

Twist offers targeted and whole transcriptome workflows that reduce time at the bench and integrate with our current set of NGS reagents, including our target enrichment kits. Each workflow delivers high quality libraries ready for sequencing from a wide range of inputs and sample types, including translation research samples.

RNA Library Prep

Twist offers two comprehensive RNA sequencing workflows: Targeted RNA Sequencing and Whole Transcriptome Sequencing. The Targeted RNA Sequencing workflow involves creating custom panels to focus on specific RNA transcripts, utilizing streamlined library preparation kits, unique dual indices, molecular identifiers, optimized target enrichment, and a proprietary exon-aware panel design algorithm. This allows for sensitive and efficient sequencing, even with low-quality RNA from FFPE samples.

On the other hand, the Whole Transcriptome Sequencing workflow measures expression levels of various RNA species, including mRNA and lncRNA. It involves preparing libraries from total RNA extracted from both fresh and FFPE samples using Twist RNA Library Prep and Twist rRNA & Globin Depletion kit. This workflow enables RNA Library Preparation in less than 5 hours, providing a comprehensive view of the entire transcriptome. Two charts accompany the descriptions, detailing the targeted and whole transcriptome sequencing workflows.

RNA Exome

The collaboration of Twist RNA Exome, Twist RNA Library Prep, and Twist Target Enrichment forms a reliable toolkit for transcriptome sequencing, accommodating RNA from diverse sources, including FFPE samples. Notably, the RNA Exome enhances signal strength while requiring fewer sequencing reads, enabling the detection of low-expressing targets crucial for accurate transcriptional profiling. Its exon-aware design approach allows the identification of isoforms and junctions often overlooked in conventional methods, delivering precise and uniform sequencing reads tailored for analyzing protein-coding sequences within the human transcriptome.

Designed exclusively for the human transcriptome, the RNA Exome targets 35.8 Mb bases, 19,708 genes, and 63,215 isoforms using sequences from Gencode and RefSeq. With over a 1.8-fold enrichment compared to whole transcriptome sequencing, it features a target enrichment approach built for RNA, incorporating an exon-aware probe design for protein coding regions, fusions, and isoforms. This design not only ensures precision but also reduces reads per sample, facilitating efficient analysis of multiple samples. The RNA Exome is versatile, compatible with FFPE samples and low RNA input. In practical tests, it demonstrates the capability to detect more targets with fewer reads across a range of RNA inputs, including FFPE and universal human reference RNA, using libraries prepared with the Twist RNA Library Prep.

RNA Fusion

The Twist Alliance CeGaT RNA Fusion Panel Kit emerges as a crucial tool in the precise detection of gene fusions, particularly impactful oncogenic driver mutations in various cancer types. Rapid and accurate detection holds significant clinical implications, guiding treatment decisions effectively. This RNA-based enrichment panel stands out by offering an enhanced targeted and sensitive approach, surpassing traditional methods.

Curated in collaboration with CeGaT, a renowned genetic diagnostic and sequencing company in Europe, this panel encompasses 160 fusion genes associated with approximately 30 cancer types. Uniquely, it is designed not only for known gene fusions but also to unveil novel ones. The panel’s efficiency is amplified when used in conjunction with the Twist RNA Library Prep Kit, ensuring an end-to-end workflow with exceptional performance.

With an optimized design featuring 7394 probes and a breakpoint design for 66 genes, the panel excels in covering a diverse array of cancer types. The incorporation of Twist core enrichment technology further maximizes capture efficiency, instilling confidence in RNA gene fusion detection. This panel is particularly well-suited for screening oncology samples, providing critical insights for treatment decisions or uncovering novel fusions for tumor classifications.

*Note: The Twist Alliance CeGaT RNA Fusion Panel – 3 MB holds ISO-13485 certification, reinforcing its reliability in clinical applications.

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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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purePlex™ DNA Library Prep Kit

January 17, 2024/in Low-pass Whole Genome Sequencing, Microbial Sequencing, Partners, SeqWell/by Harshita Sharma

PRODUCTS

purePlex™ DNA Library Prep Kit

A benefit to purePlex is that, because of its simplicity, users can quickly and seamlessly incorporate the kit with existing methods for high-throughput pipetting.

Speed, Performance, and Auto-Normalization with Unique Dual Indexes

2.5-hour workflow for 96 samples, 45 min. hands-on time
Auto-normalization of read counts and insert size over 10-fold input range
Unique dual indices included

Key Features

Fast, flexible workflow with no requirement for full plate processing
Auto-normalization reduces QC burden, improves data consistency
Early pooling for easier sample handling
Reduced GC bias compared to other transposase-based methods
Significant cost and plastics savings

purePlex™ DNA Library Prep Kit Workflow seqWell

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ExpressPlex™ Library Prep Kit

January 17, 2024/in Partners, Plasmid and Amplicon Sequencing, SeqWell/by Harshita Sharma

PRODUCTS

ExpressPlex™ Library Prep Kit

Designed for quick turnaround of plasmid, amplicon, or synthetic construct sequencing, ExpressPlex* is the fastest high-throughput library preparation kit available (based on total time to prepare 96 – 384 samples).

90-min workflow with 30-min or less hands-on
Fragmentation, barcoding, and amplification in 1 step
No primers/barcodes to buy
Virtually cross-talk free
Up to 6,144 samples prepped and sequenced in 24 hours
NEW: 384-well ultra-high throughput version available

*Patents Pending

Benefits of using ExpressPlex

ExpressPlex allows you to spend your time on data and results, not pipetting. There are solutions for low-, medium-, and high-throughput labs. For ultra-high throughput users, we now offer 384-well versions that will enable you to multiplex up to 6,144 samples in a single run.

Go from extracted samples to libraries on the sequencer in < 1/2 a day
Sequence more samples for less
Easily automate your protocol
Train any lab tech, minimize chance for error
Choice of 96 or 384-well versions to fit your workflow
Reduce labor while increasing efficiency
Decrease chance for errors via minimal handling steps
Everything included: no complex supply chain management of barcodes and primers

ExpressPlex 96-Well Workflow

ExpressPlex 384-Well Workflow

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Tagify

January 17, 2024/in Gene Editing QC, Partners, SeqWell/by Harshita Sharma

PRODUCTS

Tagify

Enable Gene Editing QC Applications with Tagify™ UMI Reagents

Methods such as CRISPR-Cas9 can exhibit unpredictability in both off- and on-target applications, but seqWell’s Tagify UMI tagging reagents ensure reproducibility, paving the way for the future of gene editing QC.

Writing the Future of Gene Editing QC

While genome editing tools like TALENs and ZFNs have transformed biomedical research, CRISPR-Cas9 stands out as a powerful tool since the early 2010s. The therapeutic potential of gene editing is immense, but to ensure precise edits, further research and the development of robust QC methods are essential. Transposase-based approaches, such as seqWell’s Tagify UMI reagents, offer a promising solution. Integrating Tagify UMIs with methods like UDiTaS™ can help establish QC benchmarks, contributing to the creation of safer and more effective gene editing techniques.

Ensure Consistency and Scalability

Georgia Giannoukos, Ph.D., Director of Next Generation Sequencing at Editas Medicine, emphasizes the use of seqWell’s custom Tagify reagent for UDiTaS. The consistent batches yield similar tagmentation profiles and editing results, with the flexibility to scale reactions from 96 to 384 wells. This adaptability has allowed the processing of thousands of reactions over a year, ensuring both consistency and scalability in gene editing applications.

Maximize Gene Editing QC with Tagify™ and ExpressPlex™ Library Prep Kit

By harnessing the synergies of Tagify and the ExpressPlex™ Library Prep Kit, researchers can achieve comprehensive gene editing quality control (QC). Tagify, incorporating UMIs, serves as a potent downstream QC method, enabling precise quantification of gene editing efficiency and fidelity at the on-target molecular level, ensuring accurate assessment post-editing.

Simultaneously, the ExpressPlex™ Library Prep Kit serves as an innovative upstream QC method, allowing users to verify the DNA sequence of reagents before initiating the gene editing process.

When utilized in tandem, with ExpressPlex upstream and Tagify downstream, researchers create a robust QC framework, effectively sandwiching the gene editing process between two reliable checkpoints. This approach proves valuable when QC activities span different labs within the same company, promoting a streamlined workflow and reproducible results.

Explore the synergistic potential of this powerful combination in more detail in our latest blog.

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plexWell LP 384

January 17, 2024/in Low-pass Whole Genome Sequencing, Microbial Sequencing, Partners, SeqWell/by Harshita Sharma

PRODUCTS

plexWell LP 384

The plexWell™ LP 384 kit is engineered for low-pass whole genome library preparation and sequencing, utilizing the enhanced plexWell workflow. The kit includes major reagents essential for library preparation, featuring Magwise™ paramagnetic beads (DNA polymerase not included). This kit allows efficient library preparation for more than one 96-well plate of samples and normalizes input DNA over a wide range of 5-25 ng.

plexWell™ LP 384 (Low-Pass Whole Genome) Highlights:

NGS multiplexed library generation kit designed for Illumina® platforms.
Features assay-ready 96-well fully-skirted low-profile PCR plates in sets of 4 (4 x 96).
Provides 2,304 (96 x 24) unique barcode combinations.
Includes 6 sets of 4 pool barcodes (PB Set A, B, C, D, E, or F).

Recommended Application: Ideal for low-depth whole genome/GBS (Genotyping by Sequencing) coupled with imputation and analysis software for comprehensive genomic studies.

plexWell™ Library Prep Workflow:

plexWell™ Library Prep Chemistry:

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plexWell

January 17, 2024/in Microbial Sequencing, Partners, Plasmid and Amplicon Sequencing, SeqWell/by Harshita Sharma

PRODUCTS

plexWell

plexWell 96

The plexWell™ 96 (PW096) kit streamlines NGS multiplexed library generation for Illumina® platforms, housed in an assay-ready 96-well fully-skirted low-profile PCR plate. The kit includes major reagents, featuring Magwise™ paramagnetic beads (DNA polymerase not included), facilitating efficient library preparation for one 96-well plate inputs. Notably, it offers normalization of input DNA over a broad range of 3-30 ng, with a cost-saving volume-based pricing structure that can reduce total lab costs by 30-50%.

Key Features:

Comprehensive kit with Magwise™ beads.
Efficient library prep for one 96-well plate.
Normalization of input DNA (3-30 ng).
Volume-based pricing for cost savings.

Recommended Applications: Ideal for large-scale full-length viral surveillance, Synthetic Construct Sequencing (Amplicons, Plasmids, BACs, etc.), microbiome screening, microbial whole-genome sequencing, scRNA-seq (single-cell RNA sequencing), and low-depth whole-genome/GBS (genotyping by sequencing).

plexWell 384

The plexWell™ 384 (PW384) kit is a comprehensive solution for NGS multiplexed library generation on Illumina® platforms. Each kit includes major reagents, featuring Magwise™ paramagnetic beads (DNA polymerase not included), essential for efficient library preparation for more than one 96-well plate of samples. This kit offers normalization of input DNA across a wide range of 3-30 ng, with a cost-saving volume-based pricing structure, reducing total lab costs by 30-50%.

Key Features:

Comprehensive kit with Magwise™ paramagnetic beads.
Efficient library prep for more than one 96-well plate.
Normalization of input DNA (3-30 ng).
Cost-saving volume-based pricing.

Recommended Applications:

Large-scale full-length viral surveillance.
Synthetic Construct Sequencing (Amplicons, Plasmids, BACs, etc.).
Microbiome screening.
Microbial whole-genome sequencing.
scRNA-seq (single-cell RNA sequencing).
Low-depth whole-genome/GBS (genotyping by sequencing).

plexWell™ Library Prep Workflow:

plexWell™ Library Prep Chemistry:

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