Shop All Library Preparation Kits for Sequencing

SGS™ All Species ID Food DNA Analyser Kits (Thermo Scientific™)

Identify meat, plant or fish species present in all food sample types with ready-to-use DNA test kits, software and Ion Torrent NGS technology.

Ion AmpliSeq™ HD Library Kit (Ion Torrent™)

The Ion AmpliSeq HD Library Kit is designed for generation of amplicon libraries for use as part of the Ion AmpliSeq HD sequencing workflow. The kit is compatible with custom panels created using the Ion AmpliSeq Designer tool (www.ampliseq.com) and sequenced using an Ion GeneStudio S5 Series instrument. Ion AmpliSeq HD technology enables scalable polymerase chain reactions (PCRs) from 12- to 500-plex in a single well (1000-plex in two wells), with sample input amounts as small as 1 ng and a level of detection down to 0.1% depending on the sample source.

Key product features include:
• Custom design creation
• Ultra-high sensitivity detection
• Dual-barcoded sample multiplexing
• Bi-directional sequencing

Custom design creation
The Ion AmpliSeq Designer tool can now be used to create custom designs for use with Ion AmpliSeq HD technology. The designs are made-to-order and allow the user the flexibility of creating region designs, hotspot designs, or fusion designs. These designs are one- or two-pool designs and recommended for use with samples obtained from cfDNA , cfRNA, cfTNA, or FFPE.

Ultra-high sensitivity detection
Ion AmpliSeq HD technology is capable of ultra-high levels of detection down to 0.1%. These detection levels have been observed for cfDNA controls with known variants using an input amount of 20 ng. Levels of detection for other sample types, such as FFPE, will vary.

Dual-barcoded sample multiplexing
The Ion AmpliSeq HD Library Kit includes reagents for generating amplicons using Ion AmpliSeq HD primers, which are used to prepare libraries for sequencing. The libraries are dual-barcoded at the 5’ and 3’ ends using the Ion AmpliSeq HD Dual Barcode Kit 1-24, which enables the multiplexing of up to 24 samples in a single chip.

Bi-directional sequencing
The Ion AmpliSeq HD Library Kit also provides sequencing information from both strands. This enables better error correction and higher confidence in the quality of your sequence data.

Ion AmpliSeq™ HD Dual Barcode Kit 1-24 (Ion Torrent™)

The Ion AmpliSeq HD Dual Barcode Kit 1-24 provides a set of 24 unique dual-barcode primers designed and validated for optimal performance with Ion GeneStudio S5 series sequencers. This barcode kit enables up to 24 samples to be multiplexed on a single chip. The barcode kit is only compatible with the Ion AmpliSeq HD Library Kit and should not be used with any other library kit.

Key product features include:
• Enables multiplexing of up to 24 library samples on a single sequencing chip
• Dual barcoding at both the 5’ and 3’ end for enhanced sample tracking
• Barcodes have been sequence- and flow-optimized for equal representation of all barcodes within a pool
• Provided in a single-use 96-well plate for ease of use

Sample multiplexing
Sample multiplexing using the Ion AmpliSeq HD Dual Barcode Kit 1-24 allows for multiple samples to be run on the same chip, thus decreasing the amount of reagent used on a per sample basis.

Dual-barcoding
Use of dual-barcodes has been shown to provide greater confidence in sample tracking and enhances the ability to detect any cross-barcode events. The barcodes are added at the 5’ and 3’ ends as part of the library preparation protocol.

Sequence- and flow-optimized
The Ion AmpliSeq HD Dual Barcode Kit 1-24 contains primers with unique sequences that have been optimized to provide equal representation of all barcodes in a pool, with a minimum number of flows. This helps achieve economical multiplexed sequencing runs.

24 single-use dual-barcodes in a 96-well plate format
The dual barcodes come in a sealed 96-well plate. Spacing of the barcodes prevents cross-barcode mixing and enables easy access to individual barcodes. A single reaction is provided in each well, which prevents the contamination challenges faced when using multi-use tubes.

Ion Xpress™ Barcode Adapters 1-96 Kit (Ion Torrent™)

The Ion Xpress™ Barcode Adapter 1-96 Kit provides an extensive set of 96 unique barcode adapters specifically designed and validated for optimal performance with the Ion Torrent PGM™ and Proton™ semiconductor sequencers. When used in combination with the Ion Xpress™ Plus Fragment Library Kit or the Ion Plus Fragment Library Kit, you may pool from 2 to 96 fragment libraries prior to emulsion PCR and then conduct multiplexed sequencing analysis, simplifying the next generation sequencing workflow for a wide range of applications, including targeted resequencing.

Key Product Features:

• Enables multiplexing of 96 fragment library samples on a single sequencing chip with the use of robust molecular barcodes
• Both sequence- and flow-optimized for equal representation all barcodes in a pool and more economical multiplexed sequencing runs
• Robust error correction built in by design for added confidence in sample identification

Multiplexing with Barcode Adapters Enables Higher Throughput
Multiplexing with barcoded libraries leads to more cost effective runs by permitting up to 96 samples per run, significantly decreasing the cost and handling requirements of emPCR, enrichment, and sequencing.

Sequence- and Flow-Optimized for Increased Performance and Efficiency
Barcode adapters contain sequences that are optimized to provide equal representation of all barcodes in a pool, require a minimum number of flows to interrogate, and require only 17 bases of adapter sequencing required which results in more economical multiplexed sequencing runs.

Robust Error Correction Built In by Design
Built-in error correction virtually eliminates the possibility of incorrect sample assignment.

For Research Use Only. Not for use in diagnostic procedures.

Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems (Applied Biosystems™)

Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems is a reagent component of the AB Library Builder™ System. This kit, along with separately purchased Agencourt® AMPure® Beads, allows for the creation of up to 13 RNA whole transcriptome libraries on the Library Builder™.
• Automation – reduce hands on time by 50% or more depending on the number of libraries
• Scalable – prepare up to 13 libraries per run, up to 26 libraries per day
• Integrated – compatible with the SOLiD® 4 System and 5500 Series Genetic Analysis Systems

Labor Saving Automation
The Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems when used with the AB Library Builder™ System automates the most labor-intensive parts of RNA whole transcriptome library preparation, helping to reduce hands-on time by at least 50%. The Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems contains enough reagents and materials to process up to 13 samples at a time.

Integrated RNA Library Preparation
The Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems, along with the AB Library Builder™ System, is an integrated solution comprising a predefined software protocol, plug-and-play cartridge format reagents, and instrument. These kits are all optimized and validated for RNA purification and RNA whole transcriptome library preparation with the 5500 and SOLiD® 4.

To further maximize automation consider using RNA purification protocols with the iPrep™ PureLink® Total RNA Kit, compatible with the Library Builder™ System.

For Research Use Only. Not for use in diagnostics procedures.

Ion Xpress™ Barcode Adapters 33-48 Kit (Ion Torrent™)

The Ion Xpress™ Barcode Adapters 33-48 Kit provides a set of 16 unique barcode adaptors specifically designed and validated for optimal performance with the Ion Torrent PGM™ and Proton™ semiconductor sequencers. When used in combination with the Ion Xpress™ Plus Fragment Library Kit or the Ion Plus Fragment Library Kit, this kit enables users to pool up to 16 fragment libraries prior to emulsion PCR and then conduct multiplexed sequencing analysis, simplifying the Ion semiconductor sequencing workflow for a wide range of applications, including targeted enrichment. Use of this kit with other Barcode Adapters kits allows pooling of up to 96 fragment libraries.

Key Product Features:

• Enables multiplexing of numerous fragment library samples on a single sequencing chip with the use of robust molecular barcodes
• Both sequence- and flow-optimized for equal representation all barcodes in a pool and more economical multiplexed sequencing runs
• Robust error correction built in by design for added confidence in sample identification

Multiplexing with Barcode Adaptors Enables Higher Throughput
Multiplexing with barcoded libraries leads to more cost effective runs by permitting up to 96 samples per run (16 with this kit), significantly decreasing the cost and handling requirements of emPCR, enrichment, and sequencing.

Sequence- and Flow-Optimized for Increased Performance and Efficiency
Barcode adapters contain sequences that are optimized to provide equal representation of all barcodes in a pool, require a minimum number of flows to interrogate, and require only 17 bases of adaptor sequencing required which results in more economical multiplexed sequencing runs.

Robust Error Correction Built In by Design
Built-in error correction virtually eliminates the possibility of incorrect sample assignment.

For Research Use Only. Not for use in diagnostic procedures.

Collibri™ PCR-free PS DNA Library Prep Kit for Illumina Systems, with UD indexes (Set A, 1-24) (Invitrogen™)

The Invitrogen Collibri PCR-Free PS DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems. The kit is suitable for physically sheared (PS) genomes of all sizes and variable quality, including FFPE samples.

The Collibri PCR-Free PS DNA Library Prep Kit:
• Includes in-process visual feedback at every step of the process to confirm proper mixing of reagents for the highest chance of library prep success
• Includes all necessary components in a single kit
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Supports PCR-free protocols starting with as little as 500 ng of DNA
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PCR-Free PS DNA Library Kit contains inert dyes that provide visual feedback during library preparation: the reaction mixes change color in response to the addition of critical components at each step. The inert dyes do not interfere with enzymatic reactions and do not compromise sequencing results.

The Collibri PCR-Free PS DNA Library Prep Kit offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from inputs as low as 500 ng of physically sheared double-stranded DNA (see figure below). The entire library preparation protocol takes about two hours for the PCR-free workflow. The kit contains adapters with unique dual indexes (UDIs) or combinatorial dual indexes (CDs) that allow pooling of up to 24 or 96 different samples before the sequencing run.

Applications
The Collibri PCR-Free PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

MuSeek Library Preparation Kit, Ion Torrent compatible (Thermo Scientific™)

Thermo Scientific MuSeek Library Preparation Kit for Ion Torrent™ is designed for generation of high‐quality genomic DNA libraries for sequencing with the Ion Personal Genome Machine™ (PGM™) and Ion Proton™ systems. The fast protocol utilizes MuA transposase enzyme, which catalyzes simultaneous fragmentation of double-stranded target DNA and tagging the fragment ends with transposon DNA. In a subsequent PCR step the platform-specific adaptors are added using a robust and accurate Thermo Scientific Phusion™ High-Fidelity DNA polymerase. Starting with only 100 ng of the sample DNA the same protocol can be used to generate 100-400 bp insert libraries.

Highlights

Fast—generates NGS fragment library in less than 80 minutes
Convenient —no physical shearing, end-repair and ligation steps
Easy to use—same protocol for generating different length DNA fragment libraries

Applications

• DNA fragment library preparation for downstream use in next generation sequencing workflow.

Includes
• MuSeek Enzyme Mix
• MuSeek Fragmentation Reaction Buffer
• MuSeek Stop Solution
• Control DNA
• MuSeek Adaptor Addition Primer Mix
• MuSeek Adaptor Addition Reaction Buffer
• Phusion Hot Start II High-Fidelity DNA Polymerase
• MuSeek Sequencing Primer

Note: The kit is shipped on dry ice. Upon arrival, open the kit and place MuSeek Enzyme Mix for storage below -70°C, avoid repeated freeze-thaw cycles. The Stop Solution can be stored at room temperature, and the remaining kit components at -20°C.

Collibri™ Stranded RNA Library Prep Kit for Illumina™ Systems (Invitrogen™)

The Invitrogen Collibri Stranded RNA Library Prep Kit for Illumina Systems is designed for robust construction of cDNA libraries for strand-specific RNA sequencing on Illumina next-generation sequencing (NGS) systems. The kit brings together the superior features of SuperScript IV Reverse Transcriptase, Dynabeads magnetic particles, and Platinum SuperFi DNA Polymerase, enabling users to obtain high-quality sequencing-ready libraries.

The Collibri Stranded RNA Library Prep Kit offers:
• Short, automation-friendly workflow. mRNA can be converted to sequencing-ready library within 4.5 hours.
• Inert dyes in the reagents that make it possible to see the progress of library generation without any negative effect on library quality
• Uniform transcript coverage and high transcript detection sensitivity
• High sensitivity of differential gene expression detectio
• >98% strand specificity
• Efficient detection of non-coding RNA

The Collibri Stranded RNA Library Prep Kit is designed for fast and convenient library preparation targeting insert sizes of ~150 bp for mRNA or whole transcriptome libraries with sample inputs of 1–25 ng of mRNA-enriched or ribo-depleted RNA. Single-tube adapter ligation and reverse transcription reactions, as well as magnetic bead-based library purification steps, enable completion of the entire workflow in approximately 4.5 hours. The kit is suitable for various quality RNA samples, including FFPE samples.

For maximum convenience, visual cues of process integrity are included throughout the library prep workflow. Monitor progress of library generation using visual feedback from dyes in critical reagents. The reaction mix changes color in response to the addition of critical components at each step to ensure that library preparation has the highest chance of success. The inert dyes do not interfere with enzymatic reactions and do not compromise sequencing results.

Full-length Illumina-compatible adaptors are introduced by PCR amplification using Platinum SuperFi DNA Polymerase to construct single-indexed libraries compatible with single-read or paired-end sequencing. The Collibri Stranded RNA Library Prep Kit contains 24 or 96 single-indexed barcoded PCR primers (i7) pre-mixed with a universal i5 primer that enables multiplexing of up to 96 libraries. Optimized cleanup steps efficiently remove residual primers and adapter/primer dimers while preserving high library yields.

A related product, the Collibri Library Quantification Kit is recommended for qPCR-based quantification of libraries before proceeding to sequencing.

Applications
The Collibri Stranded RNA Library Prep Kit is recommended for:
• Gene expression studies
• Alternative splicing analysis
• Non-coding RNA detection and discovery
• Gene fusion detection
• Detection of transcript isoforms

Ion Total RNA-Seq Kit for AB Library Builder™ System (Ion Torrent™)

The Ion Total RNA-Seq Kit for AB Library Builder™ System combines optimized reagents and protocols for automated preparation of representative cDNA libraries for strand-specific RNA sequencing of all types of RNA species on the Ion Personal Genome Machine (PGM™), Ion Proton™, and Ion GeneStudio™ systems. Either small RNA (such as microRNA) or whole transcriptome RNA samples can be prepared for next-generation sequencing.

The Ion Total RNA-Seq Kit for AB Library Builder™ System contains the same performance advantages as the manual Ion Total RNA-Seq Kit v2 with the convenience of protocol automation. The gel size selection step in the small RNA workflow and the filter cleanup steps have all been replaced with a magnetic bead-based method that reduces the total reaction time to approximately 6 hours. This automated workflow eliminates the hassles associated with manually producing RNA libraries for RNA expression analysis applications. This instrument and reagent combination provides researchers the ability to produce ~36 libraries in a typical work day for medium to high throughput sequencing labs.

The Ion Total RNA-Seq Kit for AB Library Builder™ System is designed to make cDNA library preparation for semiconductor sequencers simple, fast, and flexible. It can be used to generate a representative cDNA library from any type of RNA sample. The Ion Total RNA-Seq Kit for AB Library Builder™ System provides an automated total RNA library solution employing a common workflow for the discovery of small RNAs and isoforms, coding RNA, noncoding RNA, and alternative splice variants.

Additional Features of the New Ion Total RNA-Seq Kit for AB Library Builder™ System:

• Automated workflow—magnetic bead-based purification simplifies automation of library steps post RNA fragmentation
• Greater accuracy—SuperScript® III and Platinum® PCR SuperMix High Fidelity added for highest template fidelity
• Barcode compatible—works with Ion Xpress™ RNA-Seq Barcode 01-16 Kit for multiplexing

As with the manual Ion Total RNA-Seq Kit v2, the Ion Total RNA-Seq for AB Library Builder™ System:

• Preserves strand information—all mapped reads are aligned in the direction of transcription relative to the chromosomal strand
• Allows you to choose your workflow—interrogate either small RNA or the whole transcriptome
• Allows you to analyze any type of RNA—supports small RNA, rRNA depleted total RNA, and poly(A) RNA

Small RNA Analysis
During small RNA library construction, the 3' and 5' adaptors are attached directionally and simultaneously. As a by-product of this step, an adaptor product may be formed without an RNA insert. This byproduct will amplify during first strand synthesis and PCR. If not removed, >50% of the reads will be the adaptor dimer. Historically, the only way to separate the adaptor dimer from the wanted small RNA-containing library fragments has been through gel size selection. The Ion Total RNA-Seq Kit for AB Library Builder™ System uses proprietary technology to inhibit cDNA synthesis of the adaptor byproduct, thus allowing cDNA separation with magnetic bead-based technologies. Total reaction time has been reduced to approximately 3 hours on the instrument. A separate Magnetic Bead Cleanup Module is included with the kit and additional modules may be purchased separately if needed.

Start with total RNA containing as little as 5–100 ng of miRNA, or RNA enriched for small RNA containing 1–100 ng of miRNA. The small RNA protocol provides guidance on whether to start with total RNA or RNA enriched for small RNA, based on the small-RNA content of your sample. Small RNA enrichment protocols are also provided.

Whole Transcriptome Analysis
The whole transcriptome protocol enables construction of strand-specific libraries in approximately 5 hours. Starting with as little as 100 ng of total RNA, construct a library from 1 ng of poly(A) RNA or 25 ng of rRNA-depleted RNA following the RNA enrichment and library generation protocols provided in the manual. Because the libraries are not limited to cDNA derived only from poly(A) RNA, Ion Total RNA-Seq Kit libraries support a more thorough investigation of transcriptome complexity, capable of characterizing known and undocumented transcripts, including alternative splice variants, fusion transcripts, and SNPs.

Preserve Strand Information
Unlike methods that ligate adapters to double-stranded cDNA, the Ion Total RNA-Seq Kit utilizes proprietary Ambion® technology to attach the adapters in a directional manner that preserves strand information in the resulting libraries. In addition, both the 3' and 5' adapters are attached simultaneously, reducing ligation and clean-up steps.Preserving strand orientation during library construction helps enable more accurate determination of the structure and expression level of transcripts, and can aid in the discovery of novel transcription regions from both the positive and negative genomic strands.

Ion AmpliSeq™ Library Kit Plus (Ion Torrent™)

The Ion AmpliSeq Library Kit Plus is designed for rapid preparation of amplicon libraries using Ion AmpliSeq panels. Ion AmpliSeq technology enables scalable, multiplex polymerase chain reactions (PCR) from 12- to 24,000-plex in a single well. Next-generation sequencing (NGS) libraries can be prepared using as little as 1 ng of starting material.

Key product features:
• Scalable and efficient library preparation
• Easy and robust protocol
• Barcoded sample multiplexing

Scalable and efficient library preparation
Using as little as 1 ng of starting material, highly multiplexed PCR amplification of thousands of genomic target regions yields superior coverage uniformity and specificity, without the need of a specialized microfluidics PCR platform. The primers contain proprietary modifications that enable removal of primer sequences during library preparation, thereby resulting in efficient target assessment during sequencing.

Easy and robust protocol
The Ion AmpliSeq Library Kit Plus uses a plate-based format for easier sample handling and tracking, and for compatibility with automation and high-throughput laboratories. The protocol is simple to use and enables high yield and uniformity, reliably and reproducibly. The resulting libraries are ready for downstream template preparation using the automated Ion Chef System (which also provides the option of automated library preparation using the Ion AmpliSeq Kit for Chef DL8) or the Ion OneTouch 2 System followed by sequencing. The intuitive Torrent Suite Software and optional Ion Reporter Software enables automation of data analysis.

Barcoded sample multiplexing
The Ion AmpliSeq Library Kit Plus includes reagents for generating amplicons using Ion AmpliSeq primers and preparing libraries from the resulting amplicons. The kit enables the preparation of barcoded libraries using Ion Xpress Barcode Adapters 1-96 kits or IonCode Barcode Adapters 1-384 kits. Barcoded libraries can be combined and loaded onto a single Ion chip to minimize the sequencing run time and cost, and to allow for accurate sample-to-sample comparisons.

Ion Xpress™ Barcode Adapters 49-64 Kit (Ion Torrent™)

The Ion Xpress™ Barcode Adapters 49-64 Kit provides a set of 16 unique barcode adaptors specifically designed and validated for optimal performance with the Ion Torrent PGM™ and Proton™ semiconductor sequencers. When used in combination with the Ion Xpress™ Plus Fragment Library Kit or the Ion Plus Fragment Library Kit, this kit enables users to pool up to 16 fragment libraries prior to emulsion PCR and then conduct multiplexed sequencing analysis, simplifying the Ion semiconductor sequencing workflow for a wide range of applications, including targeted enrichment. Use of this kit with other Barcode Adapters kits allows pooling of up to 96 fragment libraries.

Key Product Features:

• Enables multiplexing of numerous fragment library samples on a single sequencing chip with the use of robust molecular barcodes
• Both sequence- and flow-optimized for equal representation all barcodes in a pool and more economical multiplexed sequencing runs
• Robust error correction built in by design for added confidence in sample identification

Multiplexing with Barcode Adaptors Enables Higher Throughput
Multiplexing with barcoded libraries leads to more cost effective runs by permitting up to 96 samples per run (16 with this kit), significantly decreasing the cost and handling requirements of emPCR, enrichment, and sequencing.

Sequence- and Flow-Optimized for Increased Performance and Efficiency
Barcode adapters contain sequences that are optimized to provide equal representation of all barcodes in a pool, require a minimum number of flows to interrogate, and require only 17 bases of adaptor sequencing required which results in more economical multiplexed sequencing runs.

Robust Error Correction Built In by Design
Built-in error correction virtually eliminates the possibility of incorrect sample assignment.

For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.

Oncomine™ Colon cfDNA Assay (Ion Torrent™)

The Oncomine™ Colon cfDNA Assay is part of a complete solution to detect colon (or other related gastro-intestinal) tumor-derived DNA (ctDNA) in cell-free DNA (cfDNA). It provides the reagents for library construction and a single pool of multiplex PCR primers for preparation of amplicon libraries from cfDNA obtained from the plasma fraction of a single tube of whole blood. The assay enables the analysis of single nucleotide variants and short indels that are frequently mutated in colon/gastro-intestinal cancers. Fourteen genes with >240 hotspots are covered (Genes: AKT1, BRAF, CTNNB1, EGFR, ERBB2, FBXW7, GNAS, KRAS, MAP2K1, NRAS, PIK3CA, MAD4, TP53, APC). Through the use of tag sequencing technology, a limit of detection (LOD) down to 0.1% can be achieved.

Note: Target and hotspot BED files and User Guide document for cfDNA Variant Analysis with Torrent Suite Software 5.2 can be found below under "Documents".

• Optimized short amplicon design for fragmented cfDNA (~170 bp in length)
• Detection of both single nucleotide variants (SNVs) and hotspot indels down to 0.1% LOD
• Very high sensitivity and specificity, enabling extremely low levels of detection with minimal false positives
• 6 samples can be run on an Ion 530™ Chip, reducing overall sequencing costs
• Efficient workflow, from a single tube of blood to results in just 2 days

Liquid biopsies offer several advantages over conventional solid tumor biopsies:
• Liquid biopsies are less invasive, enabling samples to be taken at multiple time points to monitor progression
• Lower cost compared to traditional tissue biopsies
• Faster turnaround time from sample to results
• More tumor heterogeneity captured

The entire workflow (figure below) from isolation of cfDNA using the MagMAX™ Cell-Free DNA Isolation Kit to analysis of samples can be accomplished in just 2 days using the Ion S5™ XL sequencing system.

Technology
ctDNA is found at extremely low concentrations in the plasma fraction of whole blood. Because of this low prevalence, a tag sequencing technology is utilized in this assay. The technology attaches a unique molecular tag to the gene-specific primers. The amplified products are then grouped into families containing the same tags. Families that contain the same mutant variant will be called with optimized Variant Caller settings for the Oncology-Liquid Biopsy application. Families that contain random errors, typically generated through the library construction/sequencing process, are identified and removed from variant calling.

Unlike other technologies with LODs of 1-5%, the Oncomine Colon cfDNA Assay has a flexible detection limit down to 0.1% or 1 mutant copy in a background of 1,000 wild-type copies. To achieve 0.1% LOD, 20 ng of input cfDNA is required. Lower amounts of cfDNA can be used (down to 1 ng), but the LOD will be higher depending on the input amount.

Simplicity, speed, and scalability of tag-sequencing technology
The Oncomine Colon cfDNA Assay enables cancer genetic studies from just 1 ng of input cfDNA for targeted library construction. The cfDNA assay uses standard PCR equipment and two simple PCR reactions, one to attach the unique molecular tags and the second to amplify the library, for high multiplex PCR-based target selection with no need for extensive capital investment. Additionally, the Oncomine Colon cfDNA Assay is compatible with FFPE samples for possible concordance studies. Total time to targeted libraries is just 3.5 hours. Scalability and flexibility are achieved using the Tag Sequencing Barcode Set 1-24 (Cat. No. A31830) or Taq Sequencing Barcode Set 25-48 (Cat. No. A31847) for multiplexing barcoded samples on Ion S5 chips.

Learn more about Oncomine cfDNA Assays >

Collibri™ PCR-free PS DNA Library Prep Kit for Illumina Systems, with CD indexes (Invitrogen™)

The Invitrogen Collibri PCR-Free PS DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems. The kit is suitable for physically sheared (PS) genomes of all sizes and variable quality, including FFPE samples.

The Collibri PCR-Free PS DNA Library Prep Kit:
• Includes in-process visual feedback at every step of the process to confirm proper mixing of reagents for the highest chance of library prep success
• Includes all necessary components in a single kit
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Supports PCR-free protocols starting with as little as 500 ng of DNA
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PCR-Free PS DNA Library Kit contains inert dyes that provide visual feedback during library preparation: the reaction mixes change color in response to the addition of critical components at each step. The inert dyes do not interfere with enzymatic reactions and do not compromise sequencing results.

The Collibri PCR-Free PS DNA Library Prep Kit offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from inputs as low as 500 ng of physically sheared double-stranded DNA (see figure below). The entire library preparation protocol takes about two hours for the PCR-free workflow. The kit contains adapters with unique dual indexes (UDIs) or combinatorial dual indexes (CDs) that allow pooling of up to 24 or 96 different samples before the sequencing run.

Applications
The Collibri PCR-Free PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Oncomine™ Tumor Mutation Load Assay, manual library preparation (Ion Torrent™)

The Oncomine Tumor Mutation Load Assay is a targeted next-generation sequencing (NGS) assay that provides an assessment of tumor mutation load and mutation signatures in a simple workflow. The assay provides reagents for library construction from two pools of multiplex PCR primers for preparation of amplicon libraries from formalin-fixed paraffin-embedded (FFPE) tumor samples without the need for a matched normal sample, using 10 ng of DNA per primer pool. This assay is designed to facilitate successful selection and identification of samples most likely to derive responses in cancer immunotherapy research.

Features:
• Enables accurate quantitation of somatic mutations to assess tumor mutation load
• Single tumor sample workflow reduces the need for a matched normal sample
• Efficient amplification from challenging samples with AmpliSeq technology
• Streamlined analysis with feature-rich visualization
• Efficient multiplexing of up to eight samples per Ion 540 Chip on the Ion S5 Systems

The Oncomine Tumor Mutation Load Assay, Manual Library Preparation, includes panel primers and reagents for library construction sufficient for 24 samples. The libraries are compatible with automated template preparation and chip loading on the Ion Chef System. For automated library preparation using the Ion Chef System, please see Cat. No. A37910.

From sample to answer
The Oncomine Tumor Mutation Load Assay comes with optimized informatics and visualization software that provides a sample-to-answer solution. Run metrics can be assessed using a Torrent Suite plugin. The Ion Reporter analysis workflow utilizes a custom variant calling and germline variant filtering algorithm to accurately estimate somatic variants in cancer research samples. A detailed report is provided that includes the normalized mutation load (mutations/MB) and mutation signatures of the somatic variants, including percentage of mutations consistent with UV damage, tobacco smoke damage, de-amination, and specific substitutions.

Learn more about Oncomine Oncology ›