EasySeq NGS smMIP based capture

EasySeq NGS Targeted Capture Molecular Inversion Probes

Brand introduction

Technology of EasySeq NGS Targeted Capute

Using sequence capturing with single molecule Molecular Inversion Probes (smMIP), followed by a barcoding amplification step, the system enables sequencing of the targeted regions in a very simple, fast and robust workflow, and is enabling coverage with double probe tiling and independent reading of both strands.

The kits contain all reagents for a straightforward, one-step capturing and subsequently sample tagging for NGS sequencing. The resulting libraries are compatible with illumina® sequencing platforms.

Products

Available kits

EasySeq™ NGS Targeted Capture Kit for BRCA1/2 (24 samples)

EasySeq™ NGS Targeted Capture Kit for BRCA1/2 (96 samples)

EasySeq™ Predictive Analysis for Therapy in Cancer (PATH) kit, 96 samples

EasySeq™ Predictive Analysis for Therapy in Cancer (PATH) kit, 24 samples

EasySeq™ NGS Targeted Capture Kit HBOC 10 genes (24 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 10 genes (96 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 5 genes (24 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 5 genes (96 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 7 genes (24 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 7 genes (96 samples

May 26, 2021June 3, 2021

EasySeq NGS RC-PCR

EasySeq NGS Reverse Complement PCR

RC-PCR

Contamination Concerns?

Conventional Amplicon based methods for NGS target enrichment involve two PCR steps – one to amplify the regions of interest followed by a second PCR reaction to add adapter sequences for NGS. While these methods are well established there is always a high risk of cross contamination or carry-over from first to second rounds of amplification

Legal Notice:
RC-PCR is IP protected.
US Patent / WO Patent / EP Patent

Exclusive license granted to NimaGen B.V., Nijmegen, The Netherlands
by SALISBURY NHS FOUNDATION TRUST (SALISBURY, WILTSHIRE, GB)

It is strictly prohibited to use, produce, distribute, import, or sell RC-PCR based methods or kits without the patent owner’s written consent.

How it Works

Easy Handling

Just one Pre-PCR reaction setup, quick, easy and highly suited for automation

RC-PCR

Product generation is more target specific

Traditional PCR reactions have high concentrations of primer at the beginning of the reaction when the template availability is low.

In a RC-PCR the target specific primer is synthesized during the reaction and consequently more aligned with the target availability reducing the chance for dimerization and off target binding.

Multiplex Capabilities

Predesigned and custom panels available targeting up to 100 amplicons in a single closed tube reaction.

Solutions available and in development:

Human Sample tracking and ID kit for WGS/WES QC
Forensic Identification Kits
Crop Genotyping assays (GreenoType)
GMO detection kit
Meat detection kit (including speciate)
Pharmacogenetics (PGX)
Circulating Tumour DNA kit
Detection of aneuploidies

Products

EasySeq NGS RC-PCR products

EasySeq™ RC-PCR SARS CoV-2 (novel coronavirus) Whole Genome Sequencing kit (96 reactions).

PCR 2x Hotstart HiFi Mastermix, compatible with RC-PCR assays, 2.2 mL

Index Primer Plate U01 96 Unique Dual Indexes

Index Primer Plate U02 96 Unique Dual Indexes (#097-192)

Index Primer Plates U01 & U02

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U01

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U02

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U03

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U05

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U06

Human Identification and Sample tracking kit

May 26, 2021May 26, 2021

Magnet Plate

Alpaqua Magnet Plate

Portfolio

Alpaqua magnet for automation and manual use

Benefits of Ring Magnets

One dedicated magnet for each well means fewer edge effects and greater uniformity of results, improving subsequent resuspension and elution and offering near universal microplate compatibility.

Patented Spring Cushion Technology

Magnet plates with integrated spring cushion technology give way when tips come in contact with a well bottom, thus compensating for physical tolerances between labware and pipettors that can compromise precision aspiration.

Alpaqua Magnet Plate products

384 Post Magnet Plate

96M Magnum Plate

96R Ring Magnet Plate

96S Super Magnet Plate

Catalyst™ 48 Slotted Magnet Plate

Catalyst™ 96 Slotted Magnet Plate

Low Elution Magnet Plate

Magnum FLX™24

MAGNUM FLX™ Enhanced Universal Magnet Plate

Magnum-EX Universal Magnet Plate

MagPlate 24

MIDI Magnet™ - 24 Post Magnet Plate for AB-0859

PCR Strip Tube Adapter for A000400, A000380, A000550

Let us find your perfect match

Not sure which magnet plate is best for your specific application? We can help you find the best solution.

Are you looking for speed? Low elution volumes? Or using exotic PCR plates? Feel free to contact us with the requirements for your workflow!

May 20, 2021May 21, 2021

covid19

EasySeq™ RC-PCR SARS CoV-2 (novel coronavirus) Whole Genome Sequencing

Generate Whole Genome Sequencing data from cDNA, derived from Covid-19 positive tested patients.

Introduction

Info

The analysis and study of viral genomes is an essential epidemiological requirement to track the evolution of a virus, the origin of strains and their transmission during any epidemic or pandemic. Targeted Next Generation Sequencing (NGS) is a valuable tool for both detection and classification of viral genomes. The 2019 outbreak of the novel Coronavirus strain (SARS-CoV-2) is obviously unprecedented with over 26 million confirmed cases of the disease associated with SARS-CoV-2 (COVID-19) and sadly approaching 1 million of lost lives in a relatively short period of time. Therefore, the ability for public health professionals and researchers to monitor situations in the most efficient and streamlined manner possible is essential. As is the reassurance that testing methods are secure, and results are accurate.

RC-PCR, the next revolution in NGS Library Prep

– More efficient library prep: Up to 80% less hands-on time
– Combined Amplification and Indexing with RC-PCR
– Less Handling, Less Risk, Greater Sample Safety
– Easily adapted for Automation
– Single Click Analysis with virSEAK (JSI Medical Systems)

With the NimaGen EasySeq™ RC-PCR Library Preparation method the implementation of an NGS driven viral surveillance strategy could not be simpler or safer. Utilising patented RC-PCR technology, sequence ready libraries are generated from cDNA covering the entire 29.9Kb SARS-CoV-2 Genome with minimal hands-on time and just a single PCR for both amplification and indexing. Tiled RC-PCR primers and probes are provided in tubes, as well as 2 breakable 96 well plates which include UDI Indexes. Just add cDNA and the RC-PCR mastermix provided in the kit and load on to your PCR instrument. Post PCR all samples can be combined for pooled cleanup with the included Ampliclean Magnetic Bead Cleanup Kit and following standard quantification and QC checks your libraries are ready to sequence.

Video

Performance

Thanks to the improved reaction kinetics, intrinsic in the RC-PCR method, in combination with the well designed and balanced probe pools, the kit delivers clean data. Also, this allows for well balanced read distributions in order to make efficient use of the sequencer’s capacity. The method delivers a coverage of ~99% of the Covid Genome, and an on-target percentage of >90%. Thanks to the easy workflow, with just a few pipetting steps, this kit is the ideal solution for any virology lab, even without NGS experience. Our support team will get you up and running in no time.

Data Analysis

VirSEAK Analysis software

JSI medical systems GmbH in Germany developed a dedicated software tool for analyzing NGS data from the SARS-CoV-2 virus, with all needed settings ready installed.

Please contact JSI Medical Systems directly to learn about this software

Global GISAID data integrated

After the sequencing run ends, the generated fastq files can be imported into the JSI virSEAK software tool. virSEAK will automatically create a consensus sequence and alignment to the reference genome. It will show the claid where the sample belongs to and generate a .csv report of the mutations. Data will be compared to global databases (like GISAID) and you will be shown the subtype frequencies and distribution per country, as well as the evolution of the strain.

Results can be uploaded to the GISAID database with a single mouse-click in order to share the results with the global Covid community. It also provides an exportable consensus sequence for a more detailed analysis in local healthcare systems. For instance when investigating patient clusters or re-infections.

Product

EasySeq™ RC-PCR SARS CoV-2 (novel coronavirus) Whole Genome Sequencing kit (96 reactions).

SKU: RC-COV096

Format

Generate Whole Genome Sequencing data from cDNA, derived from Covid-19 positive tested patients.

Compatibility

Compatible with any low- and mid throughput illumina® NGS sequencer of the latest generations: iSeq®, MiniSeq®, MiSeq®, NextSeq®, in combination with 2×150 bp paired-end read chemistry.

Premium features

FAQ

Downloads

Premium features

FAQ

Downloads

Product Information	Variants	Cat.
EasySeq™ RC-PCR SARS CoV-2 (novel coronavirus) Whole Genome Sequencing kit (96 reactions).	96 reactions	SKU: RC-COV096
PCR 2x Hotstart HiFi Mastermix, compatible with RC-PCR assays, 2.2 mL	2 Tubes of 1.1 mL each	SKU: MMHS-25

May 19, 2021June 3, 2021

Next Generation Sequencing

Portfolio

Targeted library prep solutions

NimaGen offers different library prep kits for Illumina. All kits are based on our proprietary Reverse-Complement PCR or on the single-molecule Molecular Inversion Probe (smMIP) methods.

Reverse Complement PCR (RC-PCR) based assays:

Human Exome Sample Tracking SNP-ID kit
SARS-CoV-2 Whole Genome Sequencing kit
SARS-CoV-2 + Wintervirus detection kit, coming soon
IDseek Forensic STR, SNP-ID and Mitochondrial Sequencing kits
Bacterial and Fungal ID kits (16S / 18S)
GreenoType Plant Genotyping custom kits

1. EasySeq NGS RC-PCR

Reverse-Complement PCR: The only one-step library prep method on the market.

➼ The safest
➼ The fastest
➼ The simplest

2. EasySeq NGS smMIP based capture

Single-molecule targeted capturing, highly quantitative due to Unique Molecular Identifiers (UMI).

Products

EasySeq NGS RC-PCR products

EasySeq™ RC-PCR SARS CoV-2 (novel coronavirus) Whole Genome Sequencing kit (96 reactions).

PCR 2x Hotstart HiFi Mastermix, compatible with RC-PCR assays, 2.2 mL

Index Primer Plate U01 96 Unique Dual Indexes

Index Primer Plate U02 96 Unique Dual Indexes (#097-192)

Index Primer Plates U01 & U02

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U01

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U02

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U03

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U05

Two PCR plates, pre aliquoted with 4 uL Unique Dual Index Primers. Set U06

Human Identification and Sample tracking kit

Products

EasySeq NGS smMIP based capture products

EasySeq™ NGS Targeted Capture Kit for BRCA1/2 (24 samples)

EasySeq™ NGS Targeted Capture Kit for BRCA1/2 (96 samples)

EasySeq™ Predictive Analysis for Therapy in Cancer (PATH) kit, 96 samples

EasySeq™ Predictive Analysis for Therapy in Cancer (PATH) kit, 24 samples

EasySeq™ NGS Targeted Capture Kit HBOC 10 genes (24 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 10 genes (96 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 5 genes (24 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 5 genes (96 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 7 genes (24 samples)

EasySeq™ NGS Targeted Capture Kit HBOC 7 genes (96 samples

May 19, 2021April 11, 2023

Sanger Sequencing

NimaGen offers a complete portfolio of high-quality and cost-effective reagents and consumables for Applied Biosystems™ capillary electrophoresis based Genetic Analyzers: 3100, 3100 Avant 4, 3130 , 3130XL, 3500, 3500XL, 3730, 3730XL and SeqStudio™ Flex.

Intro

Sanger Sequencing

Sanger Sequencing, also known as Capillary Electrophoresis (CE) sequencing, is a method of DNA sequencing, based on the selective incorporation of dideoxynucleotide chain terminators by DNA polymerase during in vitro DNA replication (cycle sequencing; the DNA polymerase adds four different nucleotides one by one onto a growing DNA template strand in a linear mode. Each incorporated nucleotide is identified by its fluorescent tag (dye). This extension continues until a particular nucleotide is incorporated. Because of the nucleotide’s dideoxy-configuration the polymerase cannot add any other base to this fragment and the extension is terminated. At the end of the selected number of cycles, numerous fragments with different lengths and one labelled nucleotide at the end are then generated. This dye terminator cycle sequencing is the modern variant of the dideoxy chain termination sequencing method first pioneered by Frederick Sanger and colleagues in 1977.

Important aspects in the Sanger Sequencing are the purification (clean-up) steps prior to loading for electrophoresis, and the use of high-quality reagents during all phases of the workflow. This will eliminate any interference, and will optimize conditions to produce high-quality peaks.

Automation of Sanger Sequencing has been made possible with the development of a variety of DNA sequencing instruments and platforms, such as Applied Bioystems® ABI Genetic Analyzers and SeqStudio™, and Promega Spectrum.

Since the introduction of massive parallel sequencing (MPS), or Next-Generation Sequencing (NGS), the Sanger Sequencing method remains in wide use, for smaller-scale projects, validation of NGS results and for obtaining especially long contiguous DNA sequence reads. While the Sanger method only sequences a single DNA fragment at a time, NGS is sequencing millions of fragments simultaneously (parallel) per sequencing run.

Portfolio

Recognized Premium Quality Reagents

NimaGen’s widely adopted range of Sanger Sequencing and Fragment Analysis reagents and consumables are compatible with the gold standard method for DNA analysis using Capillary Electrophoresis (CE). All reagents, including BrilliantDye™ Terminator Cycle Sequencing Kits, NimaPOP™ Polymers, and Red and Orange Fluorescent DNA Size Standards, are direct drop-in replacements 1:1 compatible with the complete range of 310, 3100, 3130, 3500, and 3730 Series Genetic Analyzers.

NimaGen’s, high-quality product brand portfolio includes:

Applied Biosystems and SeqStudio are trademarks of Applied Biosystems, LLC.

Products

Products for Clean-up and Capillary Electrophoresis

NimaPOP 7 for 3500 series (960 samples)

NimaPOP 7 for 3500 series (384 samples)

BrilliantDye™ Terminator 5X Sequencing Buffer (1 mL)

BrilliantDye™ Terminator 5X Sequencing Buffer (28 mL)

BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (24 rxn)

BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (1000 rxn)

BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (5000 rxn)

BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (25000 rxn)

BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (100 rxn)

BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (24 rxn)

BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (100 rxn)

BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (1000 rxn)

BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (5000 rxn)

BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (25000 rxn)

D-Pure™ DyeTerminator Cleanup kit, 5 mL

D-Pure™ DyeTerminator Cleanup kit, 50 mL

D-Pure™ DyeTerminator Cleanup kit, 500 mL

dGTP BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (100 rxn)

dGTP BrilliantDye™ Terminator (v1.1) Cycle Sequencing kit (1000 rxn)

dGTP BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (100 rxn)

dGTP BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (1000 rxn)

EasySeq™ PCR plates for BRCA1/2 (5 plates)

EasySeq™ PCR plates for BRCA1/2 (25 plates)

iX-Pure™ DyeTerminator Cleanup kit, 100 preps

iX-Pure™ DyeTerminator Cleanup kit, 1000 preps

iX-Pure™ DyeTerminator Cleanup kit, 2500 preps

iX-Pure™ DyeTerminator Cleanup kit, 40000 preps

NimaPOP 10X Running Buffer (with EDTA), 25 mL

NimaPOP 10X Running Buffer (with EDTA), 100 mL

NimaPOP 10X Running Buffer (with EDTA), 500 mL

NimaPOP 4 for 310 / 3100 series (5 mL Vial)

NimaPOP 4 for 310 / 3100 series (10 mL Vial)

NimaPOP 4 for 3130 series (5 mL Bottle)

NimaPOP 4 for 3130 series (10 mL Bottle)

NimaPOP 6 for 310 / 3100 series (5 mL Vial)

NimaPOP 6 for 310 / 3100 series (10 mL Vial)

NimaPOP 6 for 3130 series (5 mL Bottle)

NimaPOP 6 for 3130 series (10 mL Bottle)

NimaPOP 7 for 3130 series (5 mL Bottle)

NimaPOP 7 for 3130 series (10 mL Bottle)

NimaPOP 7 for 3730 series (28 mL Bottle)

NimaPOP 7 for 3730 series (10 x 28 mL Bottles)

ReCAP™ Capillary Regeneration Kit for 3130 series

ReCAP™ Capillary Regeneration Kit for 3730 series

Seq-DI Formamide 25 mL

Seq-DI Formamide 250 mL

May 12, 2021May 12, 2021

ZYMO RESEARCH RELEASES OPEN-SOURCE BIOINFORMATICS PIPELIN

ZYMO RESEARCH RELEASES OPEN-SOURCE BIOINFORMATICS PIPELINE FOR SARS-COV-2 VARIANT DETECTION IN WASTEWATER

EARLY RELEASE OF THE VIRSIEVE™ BIOINFORMATICS PIPELINE WILL PROMOTE COLLABORATION IN ENVIRONMENTAL SARS-COV-2 RESEARCH

Zymo Research releases the VirSieve™ Open-Source Bioinformatics Pipeline source code to the environmental microbiology community to promote global collaboration and support for the detection of SARS-CoV-2 variants in wastewater.

Zymo Research has released the VirSieve™ Bioinformatics Pipeline source code to the environmental microbiology community to promote global collaboration and support for the detection of SARS-CoV-2 variants in wastewater. VirSieve™ is an automated computational pipeline that analyzes sequencing reads from the SARS-CoV-2 virus in wastewater samples to better understand viral variants present in monitored communities. By rating the confidence interval in observed viral mutations, the software has the potential to significantly increase the accuracy of analyzing any changes in the viral genetic material.

According to the Centers for Disease Control and Prevention, while the deployment of vaccines has had a tremendous positive impact on curbing the SARS-CoV-2 pandemic within the USA, new viral strains are still emerging. Some of these strains, e.g., B.1.1.7, are classified as “variants of concern” due to evidence of increased spread, pathogenicity, or vaccine evasion. Wastewater Next-Gen Sequencing is emerging as the most viable solution for near real-time community surveillance.

Viral sequencing from wastewater is difficult due to fragmentation and degradation of the viral RNA, often resulting in sequencing errors that ultimately manifest as false mutations. VirSieve™ can identify these false variants and mark them as being low or no confidence, allowing researchers to filter mutations with a higher degree of support. Zymo Research also provides DNA/RNA Shield™, a reagent that safeguards viral RNA from further degradation after inactivation of any virus for safe, ambient temperature collection and transportation of wastewater samples.

“Zymo Research has previously developed public software tools like the Zymo Research Transmit Program, an open-source client for submitting COVID-19 test results through the CalREDIE public health reporting system,” said Dr. Michael Weinstein, Director of Laboratory Information Systems, and Project Lead on the VirSieve™ Pipeline project at Zymo Research. “VirSieve™ is part of Zymo Research’s ongoing effort to provide maximum support to pandemic response efforts around the globe. We feel VirSieve™ has the potential to be used not only for tracking variant strains of the SARS-CoV-2 virus in wastewater, but other viruses as well, for future public health efforts.”

“Getting accurate variants from clinical samples or sewage is key to proper placement of a viral strain in the context of all other viral variants and informing pathogen tracking efforts,” said Dr. Christopher Mason, who is a paid speaker for Zymo Research, is the co-director of the WorldQuant Institute for Quantitative Prediction and a professor of physiology and biophysics at Weill Cornell Medicine.

For more information about the VirSieve™ Pipeline visit Zymo Research’s website or contact us via email at customerservice@biolinkk.com.

IRVINE, Calif., (May. 11, 2021)

For more information about Zymo Research’s COVID-19 products, check out the following links: