Shop All Library Preparation Kits for Sequencing

Precision ID mtDNA Whole Genome Panel (Applied Biosystems™)

The Applied Biosystems Precision ID mtDNA Whole Genome Panel is an innovative next-generation sequencing (NGS) approach to mitochondrial DNA (mtDNA) analysis specifically developed for forensic applications. It is a 2-pool multiplex assay that targets the entire human mitochondrial genome (16,569 bp) (see figure below). Each pool contains 81 primer pairs, with minimal primer overlap between pools. This panel was constructed using a innovative tiling approach to obtain optimal coverage data from highly compromised, degraded samples such as hair shafts, teeth, and bones that uses massively parallel sequencing built on Ion AmpliSeq technology. This mtDNA tiling approach was also used to construct the Precision ID mtDNA Control Region Panel (Cat. No. A31443) which targets only the control region of the genome.

Simplicity
• Small amplicons enable better recovery of mtDNA genome with degraded samples
• As little as 2 pg of input
• Automated library and template preparation using the Ion Chef System
• Optimized analysis using Converge Software

Scalability
• Multiple chip formats to meet a range of sample throughput requirements
• Ability to multiplex up to 32 samples*

Speed
• Less than 45 minutes of hands-on time for a DNA-to-data targeted sequencing workflow*
• Total sample-to-data time of less than 2 days*

Mitochondrial DNA analysis is a key DNA detection method used by forensic scientists when samples such as teeth, bones, and hairs without a follicle (root) are collected from crime scenes, missing person remains, or disaster areas that have been exposed to high environmental stress where nuclear DNA is insufficient in quality and/or quantity. Balanced coverage is achieved using a small amplicon design (163 bp average amplicon length), optimized with the inclusion of degenerate primers that align with primer-binding SNPs in the Precision ID mtDNA Whole Genome Panel, which increases success with degraded and low template DNA samples. This panel can be used with all types of forensic samples, including ancient DNA remains as well as clinical research specimens.

Additionally, full automation of library and template preparation of the Precision ID mtDNA Whole Genome Panel using the Ion Chef System and sequencing on the Ion GeneStudio series systems can reduce variation observed with manual workflows (see figure below) and streamline user-instrument interaction with less than 45 minutes of hands-on time. The Converge NGS Analysis module automates mtDNA analysis, leveraging optimized base calling, phylogenetically-guided alignment, and quality filtering algorithms specific for the Precision ID mtDNA panels. Variant calling including, including heteroplasmy detection can be easily optimized within the software features. These solutions give forensic DNA laboratories the flexibility to detect variation within noncoding control sequences using the Precision ID mtDNA Control Region Panel or take advantage of the genetic diversity of full mtGenome sequence data using the Precision ID mtDNA Whole Genome Panel.

The Precision ID mtDNA Whole Genome Panel provides sufficient material to perform 96 reactions using the manual Precision ID Library kit (Cat. No. A26435) or 48 reactions using the automated Precision ID DL8 Library Kit (Cat. No. A33212).

*Using the Precision ID NGS System for Human Identification

Note: Precision ID mtDNA Whole Genome Panel, using the control region data for analysis, is approved for inclusion in the US National DNA Index System (NDIS) CODIS database.

Precision ID Library Kit (Ion Torrent™)

The Precision ID Library Kit is designed for rapid preparation of amplicon libraries using HID-Ion AmpliSeq ready-to-use panels, for sequencing on an Ion GeneStudio S5 sequencing system. This kit uses only certain components found in the Ion AmpliSeq™ Library Kit 2.0, that are needed for Precision ID applications, making the Precision ID Library Kit more customized and specific for forensic research use only.

Key features:

Simple protocol
• 96 well plate-based workflow allows easy sample management
• No library amplification with qPCR quantification

Ion AmpliSeq™ HiFi Master Mix
• Enables cleaner amplification for increased coverage uniformity
• Up to 3,072-plex PCR allows larger panel designs

Digestion reagent
• Cleaner digest allows for more efficient downstream sequencing

Benefits for HID applications:

• 1 ng of DNA input is recommended for the Precision ID panels
• Less components to help save time and money by preventing unnecessary waste

Scalable multiplex PCR reactions
The Precision ID Library Kit is built on Ion AmpliSeq chemistry, which enables scalable multiplex PCR reactions from 12- to 3,072-plex in a single well using just 1 ng of starting DNA. Ion AmpliSeq panels and primer pools allow highly multiplexed PCR amplification of thousands of genomic target regions, with superior coverage uniformity and specificity, without the need of a specialized microfluidics PCR platform. In addition, the primers contain proprietary modifications that enable removal of primer sequences during library preparation, for efficient target assessment during sequencing. Multiple primer pools can be used to create overlapping amplicons that enable complete coverage of large targets.

Barcoded library preparation
The Precision ID Library Kit includes reagents for generating amplicons with 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 and the IonCode™ Barcode Adapters 1-384 Kit. Barcoded libraries can be combined and loaded onto a single Ion chip to minimize the sequencing run time and cost and allow for accurate sample-to-sample comparisons.

Easy and flexible protocol
The Precision ID Library Kit uses a plate-based format for easier sample handling and tracking, and for compatibility with automation and high-throughput laboratories.

The resulting DNA libraries are ready for downstream template preparation for clonal amplification on an Ion Chef System, followed by sequencing on an Ion GeneStudio S5 sequencing system. Analysis is then performed using the Converge forensic software solution, allowing you to go from DNA to results in less than two days.

Oncomine™ Childhood Cancer Research Assay, Chef-Ready (Ion Torrent™)

The Ion Torrent Oncomine Childhood Cancer Research Assay consists of four pools of Ion AmpliSeq oligonucleotide primers and associated reagents to generate amplicon libraries for next-generation sequencing (NGS) on the Ion GeneStudio S5 platforms. The assay is designed to provide researchers with sensitive and comprehensive sample amplification of relevant DNA mutations and fusion transcripts associated with childhood and young adult cancers in a single NGS run. The panel is comprised of targets from 202 unique genes: 130 key DNA genes, 28 copy number variant targets, an expansive fusion panel of 90 driver genes with multiple partners, and 9 expression genes and controls. These cover the most relevant targets in the vast majority of all childhood and young adult oncology research samples.

This version of the assay is for automated library preparation using the Ion Chef System. For manual library preparation, see Cat. No. A36485.

Features include:
• Simple, robust workflow that encompasses mutations and fusions in two DNA and two RNA pools in a single NGS run
• Excellent coverage of all relevant targets
• Multiplex up to eight samples on a single Ion 540 Chip
• Compatible with as little as 10 ng/pool input DNA or RNA per library from blood, bone marrow or FFPE samples
• Validated detection of somatic variants down to 5% allele frequency
• Simple and fast workflow produces targeted libraries in 3.5 hours typically
• For use on the Ion GeneStudio S5 Systems with manual or automated library preparation

The Oncomine Childhood Cancer Research Assay is a comprehensive, targeted NGS assay designed to assist researchers in the understanding of childhood and young adult cancer. The assay is a complete kit facilitating the amplification of multiple gene targets from FFPE, blood, or bone marrow samples with as little as 10 ng of input DNA or RNA per pool.

Leveraging the power of Ion AmpliSeq technology, this highly multiplexed NGS assay enables the generation of results from multiple samples in a single run. Designed for use on the Ion GeneStudio S5 sequencing systems, results are delivered in days rather than weeks. The assay is aligned with bioinformatics workflows within Torrent Suite and Ion Reporter analysis software that utilize optimized variant calling parameters for SNV, InDel, copy number variant, and fusion transcript detection. Samples can be processed quickly and easily, and variants detected and identified confidently.

Collibri™ ES DNA Library Prep Kit for Illumina Systems, with UD indexes (Set C, 49-72) (Invitrogen™)

The Invitrogen Collibri ES DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems.

The Collibri ES 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 preparation success
• Includes all necessary components in a single kit
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

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

The Collibri ES DNA Library Prep Kit is designed for fast and convenient library preparation from a wide range of inputs (1–500 ng) starting from intact DNA. Additionally, a PCR-free version is offered for inputs starting at 100 ng DNA. The entire library preparation protocol takes about three hours with a PCR 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 ES DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Genexus™ Library Strips 1 and 2-AS (Ion Torrent™)

The Ion Torrent Genexus Library Strips 1 and 2-AS kit for Ion AmpliSeq-based panels provides eight each of the strips required to perform automated library preparation using the Ion Torrent Genexus Integrated Sequencer. This kit, combined with Ion Torrent Genexus Barcodes 1-32 AS, 33-64 AS, or 65-96 AS, supports flexible, fully automated preparation and normalization of up to 32 single-pool Ion AmpliSeq libraries.

As part of the Genexus Integrated Sequencer workflow, the Genexus Library Strips 1 and 2-AS kit:
• Automates library preparation for 200–400 base-read Ion AmpliSeq libraries
• Supports intake variability of clinical research samples in a cost-effective manner
• Maximizes flexibility with the ability prepare one to 32 single-pool libraries per run
• Enables parallel processing of up to four compatible assays in a single run
• Delivers fast and simple instrument setup, with less than five minutes of hands-on time

The Ion Torrent Genexus Integrated Sequencer automates library preparation, sequencing, analysis, and reporting in a hands-off, walkaway workflow to deliver results in a single day. The innovative, multilane sequencing chip is designed to enable cost-effective processing of 1 to 32 single pool libraries.

IonCode Barcode Adapters, 385-768 (Ion Torrent™)

IonCode Barcode Adapters 385-768 are 384 unique barcode adapters designed for optimal performance with Ion Torrent semiconductor sequencers. This set includes IonCode Barcode Adapters 0501-0596, 0601-0696, 0701-0796, and 0801-0896. When used in combination with other IonCode barcode adapters and the AgriSeq HTS Library Kit, users can pool up to 768 amplicon libraries and then conduct multiplexed sequencing analysis, which helps increase lab efficiency and reduce sequencing costs per sample.

Key product features:
• Robust barcodes ligate efficiently and uniformly to generate balanced representation of libraries
• Unbiased performance enables identical genotypes independent of barcode used
• Robust error correction built in by design for added confidence in sample identification

Increase sample multiplexing without impacting data quality
Multiplexing with barcoded libraries enables more cost effective runs by permitting up to 768 samples per run, and helps significantly decrease the cost and handling requirements of sequencing. Each barcode was individually evaluated to verify no bias of sequence context representation. The barcodes were also screened for equivalent efficiency to verify balanced read depth between libraries. Regardless of the specific barcode used, AgriSeq targeted genotyping-by-sequencing (GBS) generates highly uniform libraries and concordant genotype calls (see figures below).

Precision ID IonCode™ Barcode Adapters 1–96 Kit in 96-Well PCR Plate (Applied Biosystems™)

The Precision ID IonCode Barcode Adapters 1–96 Kit in 96-Well PCR Plate provides a set of 96 unique barcode adapters specifically designed for optimal performance with Precision ID library kits and panels and Ion S5 or Ion S5 XL Systems. When used in combination with the Precision ID Library Kit, the Precision ID IonCode Barcode Adapters 1–96 Kit in 96-Well PCR Plate allows users to pool amplicon libraries prepared manually or with automation and conduct multiplexed sequencing analysis, thereby increasing lab efficiency and reducing sequencing costs per sample.

Key product features:
• Robust barcodes ligate efficiently and uniformly to generate balanced representation of libraries
• Unbiased performance helps ensure identical genotypes independent of barcode used
• Robust error correction built in by design for added confidence in sample identification

Increase sample multiplexing without impacting data quality
Multiplexing with barcoded libraries leads to more cost effective sequencing. Each barcode has been individually evaluated to help ensure no bias of sequence context representation. The barcodes were also screened for equivalent efficiency to enable balanced read depth between libraries.

Collibri™ ES DNA Library Prep Kit for Illumina Systems, with UD indexes (Set D, 73-96) (Invitrogen™)

The Invitrogen Collibri ES DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems.

The Collibri ES 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 preparation success
• Includes all necessary components in a single kit
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

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

The Collibri ES DNA Library Prep Kit is designed for fast and convenient library preparation from a wide range of inputs (1–500 ng) starting from intact DNA. Additionally, a PCR-free version is offered for inputs starting at 100 ng DNA. The entire library preparation protocol takes about three hours with a PCR 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 ES DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Oncomine Lung Cell-Free Total Nucleic Acid Research Assay (Ion Torrent™)

The Oncomine Lung cfTNA Research Assay is part of a complete solution to detect lung tumor-derived cell-free DNA and RNA (cell-free total nucleic acid; cfTNA) isolated from the plasma fraction of whole blood. It provides the reagents for library construction and a single pool of multiplex PCR primers for preparation of amplicon libraries from cfTNA obtained from the plasma fraction of a single 10 mL tube of whole blood.

Liquid biopsies offer several advantages over conventional solid tumor biopsies:
• Less invasive, enabling them to be taken at multiple time points to monitor progression of the cancer
• Lower cost
• Faster turnaround time from sample to results
• Better represent tumor heterogeneity

The Oncomine Lung cfTNA Research Assay enables the analysis of:
• Hotspot genes (SNVs) and short indels: ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROS1, and TP53 (~168 hotspots covered)
• Gene fusions: ALK, RET, ROS1
• MET exon 14 skipping
• Copy number gene (CNV): MET

These genes have been identified as frequently mutated in non-small cell lung cancer (NSCLC). Through the use of Tag Sequencing technology, low limits of detection (LOD) can be achieved for different variant types*:
• For SNVs/short indels, an LOD of 0.1% can be achieved with sensitivity of ~90% and specificity of >99%
• For fusions & MET exon skipping, an LOD of 1% can be achieved with sensitivity of >90% and specificity of >99%
• For MET CNV target, detection as low as 1.2-fold amplification can be achieved with sensitivity of >90% and specificity of >99%

The entire workflow from isolation of cfTNA using the MagMAX Cell-Free Total Nucleic Acid Isolation Kit to analysis of samples can be accomplished in just two days using the Ion S5 XL sequencing system.

Technology
cfDNA and cfRNA are 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 unique molecular tags to the gene-specific primers (figure below). After amplification, the tagged molecules are grouped based on the tags. Groups containing the same mutant variant 80% of the time or greater will be called positive. Using the Tag technology, groups that contain random errors generated through the library construction/sequencing process are removed.

Unlike other technologies with LODs of 1-5%, the Oncomine Lung cfTNA Research Assay has a flexible detection limit down to 0.1% for SNVs or one 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 cfTNA can be used, but the %LOD will be higher depending on the input amount.

Advantages:
• Optimized amplicon design for short cfDNA ensures highest possible capture rate
• Tag Sequencing technology minimizes false positives by removing randomly incorporated errors
• Optimized targeted assay design allows highly multiplexed next-generation sequencing (NGS), reducing
sequencing costs per sample
• Efficient 2-day workflow

Analysis of SNVs and short indels can be achieved using Torrent Suite Software 5.2 or higher. In order to analyze SNVs, short indels, fusion, and CNVs, Ion Reporter 5.6 (cloud- or server-based) is required.

Simplicity, speed, and scalability of TagSequencing technology
The Oncomine Lung cfTNA Research Assay enables cancer genetic studies from just 5 ng of input cfTNA for targeted library construction. The Oncomine Lung cfTNA Research Assay is compatible with FFPE samples for possible concordance studies. Total time to targeted libraries is just four hours. Scalability and flexibility are achieved using the Tag Sequencing Barcode Set 1-24 or 25-48 (Cat. Nos. A31830, A31847) for multiplexing barcoded samples on Ion S5 chips.

*Sensitivity and specificity for each variant type were determined using a collection of contrived positive samples and cfTNA isolated from normal healthy donors.

Genexus™ Library Strips 1 and 2-HD (Ion Torrent™)

The Ion Torrent Genexus Library Strips 1 and 2-HD kit for Ion AmpliSeq HD-based panels provides eight each of the strips required to perform automated library preparation using the Ion Torrent Genexus Integrated Sequencer. This kit, combined with Ion Torrent Genexus Barcodes 1-32 HD, supports flexible, fully automated preparation and normalization of up to 32 single-pool Ion AmpliSeq HD libraries.

As part of the Genexus Integrated Sequencer workflow, the Genexus Library Strips 1 and 2-HD kit:
• Automates library preparation for 200–400 base-read Ion AmpliSeq HD libraries
• Supports intake variability of clinical research samples in a cost-effective manner
• Maximizes flexibility with the ability prepare 1 to 32 single-pool libraries per run
• Enables parallel processing of up to four compatible assays in a single run
• Delivers fast and simple instrument setup, with less than five minutes of hands-on time

The Ion Torrent Genexus Integrated Sequencer automates library preparation, sequencing, analysis, and reporting in a hands-off, walkaway workflow to deliver results in a single day. The innovative, multilane sequencing chip is designed to enable cost-effective processing of 1 to 32 single pool libraries.

Oncomine™ Comprehensive Assay v3M (Ion Torrent™)

The Oncomine Comprehensive Assay v3 is a targeted, next-generation sequencing (NGS) assay that enables the detection of relevant SNVs, CNVs, gene fusions, and indels from 161 unique genes to help inform drug discovery research and clinical trial research programs. It provides the reagents for library construction and four pools—two DNA and two RNA—of multiplex PCR primers for preparation of amplicon libraries from formalin-fixed paraffin embedded (FFPE) tumor samples. Designed to help you go from hundreds down to a few relevant cancer drivers, this assay is part of a comprehensive workflow that enables NGS data analysis from as little as 10 ng of nucleic acid per pool. The assay is optimized for sequencing on the Ion S5 System with the Ion 540 Chip to enable up to 8 samples (7 samples and one no-template control) per run.

When combined with Oncomine Knowledge Reporter Software, you can create reports that align labels, guidelines, and clinical trials to your results so you can focus on key drivers of cancer in your research.

Key features of the assay are:
• Enables analysis of variants across 161 genes
• Detection of SNVs, CNVs, gene fusions, and indels
• Robust performance from as little as 10 ng per pool (40 ng total) isolated from FFPE samples including fine needle biopsies
• Characterized with molecular standards and controls
• Content driven by the Oncomine Knowledgebase and experienced scientists helps assure coverage of key targets aligned to published evidence

From sample to answer
The Oncomine Comprehensive Assay is part of an NGS workflow that helps researchers to filter variant results from hundreds to just a few key cancer driver variants. Enabled by Oncomine informatics, this filtering, as well as the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps you contextualize and interpret findings to move toward the answers you need.

The workflow has been adopted by large-scale national clinical trial research programs including NCI-MATCH (United States) and LC-SCRUM (Japan), and includes:
• Proven Ion AmpliSeq chemistry
• Automated library and template prep on the Ion Chef System
• Scalable sequencing on the Ion S5 Sytem
• Optimized Oncomine informatics

Multiple configurations
The Oncomine Comprehensive Assay v3 comes in the following configurations to match your laboratory needs:

Manual library preparation configuration:
Oncomine Comprehensive Library Assay v3M
This configuration contains all the reagents needed to prepare libraries for 24 or 96 samples:
    • Oncomine Comprehensive Panel v3M DNA—contains the DNA primer pools
    • Oncomine Comprehensive Panel v3M RNA—contains the RNA primer pools
    • Ampliseq Library Plus reagents—allow you to manually create your library
Ion Chef automated library preparation configuration:
Oncomine Comprehensive Library Assay v3C
This configuration contains all the reagents needed to prepare libraries for 32 samples:
    • Oncomine Comprehensive Panel v3C DNA—contains the DNA primer pools
    • Oncomine Comprehensive Panel v3C RNA—contains the RNA primer pools
    • Ion AmpliSeq Kit for Chef DL8 reagents—allows you to automate library prep on the Ion Chef System


IonCode Barcode Adapters, 0601-0696 (Ion Torrent™)

IonCode Barcode Adapters 0601-0696 are 96 unique barcode adapters designed for optimal performance with Ion Torrent semiconductor sequencers. When used in combination with other IonCode barcode adapters and the AgriSeq HTS Library Kit, users can pool up to 768 amplicon libraries and then conduct multiplexed sequencing analysis, which helps increase lab efficiency and reduce sequencing costs per sample.

Key product features:
• Robust barcodes ligate efficiently and uniformly to generate balanced representation of libraries
• Unbiased performance enables identical genotypes independent of barcode used
• Robust error correction built in by design for added confidence in sample identification
Increase sample multiplexing without impacting data quality
Multiplexing with barcoded libraries enables more cost effective runs by permitting up to 768 samples per run, and helps significantly decrease the cost and handling requirements of sequencing. Each barcode was individually evaluated to verify no bias of sequence context representation. The barcodes were also screened for equivalent efficiency to verify balanced read depth between libraries. Regardless of the specific barcode used, AgriSeq targeted genotyping-by-sequencing (GBS) generates highly uniform libraries and concordant genotype calls (see figures below).

SOLiD™ Fragment Library Construction Reagents (Applied Biosystems™)

The SOLiD™ Fragment Library Construction Reagents provide a fully optimized set of reagents to generate 10 fragment libraries using the SOLiD™ version 3 standard or express fragment library protocols. This kit replaces S3100105. Additional columns and gels recommended in the SOLiD™ version 3 and 3 plus protocol are available in the SOLiD™ Fragment Library Construction Kits. The SOLiD™ Fragment Library Oligo Kit or an equivalent alternative is also required to generate fragment libraries.

Ion Xpress™ Barcode Adapters 65-80 Kit (Ion Torrent™)

The Ion Xpress™ Barcode Adapters 65-80 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.

Genexus™ Controls (Ion Torrent™)

The Ion Torrent Genexus Controls kit provides library and template preparation controls for use with the Ion Torrent Genexus Integrated Sequencer. The kit offers greater experimental control and empowers you to assess sample quality, help save time and reagents, and maximize productivity. Each kit contains an Ion AmpliSeq-based Genexus Control Panel and a Genexus Control DNA, which can prepare up to 32 automated control libraries, as well as a Genexus Control Library, sufficient for four template preparations.

The Ion Torrent Genexus Integrated Sequencer automates library preparation, sequencing, analysis, and reporting in a hands-off, walkaway workflow to deliver results in a single day. The innovative, multilane sequencing chip is designed to enable cost-effective processing of 1 to 32 single pool libraries.

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.

Oncomine™ BCR IGH SR Assay, RNA (Ion Torrent™)

The Oncomine BCR IGH SR Assay, RNA, is a robust, targeted next-generation sequencing (NGS) assay designed for research in pharmacodynamics and biomarker analysis of immunotherapy, as well as infectious and autoimmune disease research. The assay kit includes a single pool of multiplex PCR primers, total RNA to cDNA synthesis kit, and AmpliSeq library reagents.

The Oncomine BCR IGH SR Assay, RNA, accurately identifies and measures clonal expansion of B lymphocytes using total RNA from bone marrow, whole blood, peripheral blood leukocytes (PBLs), peripheral blood mononuclear cells (PBMCs), and fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) research samples. The assay identifies unique B-cell clones through targeting of the highly diverse complementarity-determining region 3 (CDR3) of the B-cell receptor (BCR) immunoglobulin heavy (IGH) chain from mRNA template via Ion AmpliSeq multiplex framework 3 and joining gene primers. The nucleotide sequence of the IGH CDR3 region serves as a natural barcode to enable clone tracking and measurements of B cell clonal expansion and diversity for pharmacodynamics and vaccine biomarker research. IGH CDR3-region amino acid motifs may reveal signatures of B cell responses to defined antigens for use as future markers of autoimmune or infectious disease. RNA input improves detection of changes in plasmablast and plasma cell populations following immune challenge or administration of immunomodulatory agents. For DNA samples please see Cat. No. A45483.

Benefits of the Oncomine BCR IGH SR Assay with RNA input include:
• High sensitivity and exceptionally low limit of detection (LoD) for rare clone detection and tracking in research samples via dual-barcode indexing and high template capture efficiency of Ion AmpliSeq multiplex PCR
• Compatibility with a vast array of research sample types, including FFPE tissue, fresh-frozen (FF) tissue, bone marrow, whole blood, PBLs, and PBMCs
• Assay primers designed to amplify all variable and joining gene alleles in gold-standard IMGT database
• Ability to generate large libraries with minimal input requirement, facilitating detection of rare clones at a frequency of 10-6 from a single library preparation
• Efficient workflow using the Ion Chef templating system and Ion GeneStudio S5 system enabling library-to-results time within 48 hrs
• Flexible input requirements ranging from 25 ng to 2 µg
• Streamlined and user-friendly informatics solution with automated clonotyping, clonal lineage analysis, reporting of key repertoire features, and multi-sample analysis capability to enable longitudinal tracking in research samples
• Ultra-low substitution error rate minimizing artifacts arising from sequencing errors enabling highly accurate assessment of clonal heterogeneity in malignant B cell research samples of interest

The Oncomine BCR IGH SR Assay with total RNA input uses multiplex PCR primers to generate 90-bp amplicons that can be sequenced on all chip types supported by the Ion GeneStudio S5 sequencing systems, allowing you to pick the best multiplexing configuration for your unique sample batching needs and throughput requirements.

Learn more about the assay ›

Note: Information about data analysis using Ion Reporter Software v5.12 can be found in the User Guide below.

Collibri™ PCR-free PS DNA Library Prep Kit for Illumina Systems, with UD indexes (Set B, 25-48) (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

Ion GeneStudio™ S5 Food Protection System (Thermo Scientific™)

Identify species present in all food types using this next generation sequencing instrument as part of a NGS Workflow for Food Authenticity Workflow.

Oncomine™ Pan-Cancer Cell-Free Assay (Ion Torrent™)

The Oncomine Pan-Cancer Cell-Free Assay is part of a complete solution to detect multiple targets in tumor-derived DNA and RNA isolated from the plasma fraction of whole blood. The assay provides the reagents and a single pool of multiplex PCR primers for preparation of an amplicon library from cell-free total nucleic acid (cfTNA) obtained from the plasma fraction of a single 10-mL tube of whole blood. This library can then be used for highly multiplexed targeted next-generation sequencing (NGS).

Oncomine cell-free assay advantages:
• From a single tube of blood, generates an amplicon library from both DNA and RNA with a detection limit of 0.1% for SNVs
• Amplicon size optimized for short cfDNA, ensuring highest possible capture rate
• Tag Sequencing technology minimizes false positives by removing randomly incorporated errors
• Optimized targeted assay design allows highly multiplexed NGS, reducing sequencing costs per sample
• Two-day workflow from single 10-mL tube of blood to report; total time to targeted libraries is just four hours
• Enables cancer genetic studies from just 5 ng of input cfTNA
• Compatible with FFPE samples for possible concordance studies

The 52-gene panel includes:
• Hotspot genes (SNVs) and short indels: AKT1, ALK, AR, ARAF, BRAF, CHEK2, CTNNB1, DDR2,EGFR, ERBB2, ERBB3, ESR1, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MAP2K1, MAP2K2, MET, MTOR, NRAS, NTRK1, NTRK3, PDGFRA, PIK3CA, RAF1, RET, ROS1, SF3B1, SMAD4, SMO
• Gene fusions: ALK, BRAF, ERG, ETV1, FGFR1, FGFR2, FGFR3, MET, NTRK1, NTRK3, RET, ROS1
• MET exon 14 skipping
• Copy number genes (CNVs): CCND1, CCND2, CCND3, CDK4, CDK6, EGFR, ERBB2, FGFR1, FGFR2, FGFR3, MET, MYC
• Tumor suppressor genes: APC, FBXW7, PTEN, TP53

These genes have been identified as frequently mutated in multiple cancer types, including: bladder, brain and CNS, breast, cervical, colorectal, endometrial, esophageal, gastric, head and neck, kidney, liver, lung, melanoma, ovarian, pancreatic, prostate, sarcoma, and thyroid.

Detection limits:
• SNVs/short indels: a limit of detection (LOD) down to 0.1% allele frequency (AF) can be achieved with a sensitivity of >80% and specificity of >98%*
• TP53 whole-target SNVs/indels: 0.5% AF (looking at all bases within amplicons)
• Fusions and MET exon skipping: LOD down to 1% can be achieved
• CNV targets: detection as low as 1.4-fold change can be achieved

The MagMAX Cell-Free Total Nucleic Acid Isolation Kit (A36716) is highly recommended for isolation of both DNA and RNA from the plasma fraction of whole blood.

Scalability and flexibility are achieved using the Tag Sequencing Barcode Set 1-24 or 25-48 (Cat. Nos. A31830 & A31847 respectively) for multiplexing barcoded samples on the Ion S5 chips.

Analysis of SNVs and short indels can be achieved using Torrent Suite Software 5.2 or higher. In order to analyze SNVs, short indels, fusions, and CNVs, Ion Reporter Software 5.6 (cloud or server based) is required.

Technology
cfDNA and cfRNA are 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 unique molecular tags to the gene-specific primers. After amplification, the tagged molecules are grouped based on the tags. Groups containing the same mutant variant 80% of the time or greater will be called positive. Using this Tag technology, groups that contain random errors generated through the library construction/sequencing process are removed.

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

Liquid biopsies offer several advantages over conventional solid tumor biopsies:
• Liquid biopsy samples are less invasive enabling them to be taken at multiple time points to monitor progression of the cancer
• Lower cost compared to traditional tissue biopsies
• Faster turnaround time from sample to results
• Better represent tumor heterogeneity

*Sensitivity and specificity for each variant type were determined using a collection of contrived positive samples and cfTNA isolated from normal healthy donors.

Oncomine™ BRCA Research Assay, Manual Library Preparation (Ion Torrent™)

The Oncomine™ BRCA Research Assay consists of two pools of AmpliSeq™ oligonucleotide primers and associated reagents to generate amplicon libraries for next-generation sequencing (NGS) on Ion Torrent™ platforms. The assay is designed to provide sensitive and comprehensive sample amplification of all coding regions of the human BRCA1 and BRCA2 genes. This version of the assay is for manual library preparation. For automated library preparation using the Ion Chef™ System, please see Cat. No. A32841.

Features include:

• Validated for use on Ion 318 and Ion 530 chips
• Detects SNVs, InDels, and large exon/gene deletions/duplications
• Compatible with as little as 10 ng input DNA from formalin-fixed, paraffin-embedded (FFPE) tissue or blood samples
• Highly uniform coverage across all coding exons and splice sites for efficient sequencing and accurate analysis
• Optimized primer design and amplification chemistry enable highly specific target enrichment
• Validated detection of somatic variants to 5% and lower
• Simple and fast workflow produces targeted libraries in 3.5 hours typically

The Oncomine BRCA Research Assay is a complete kit facilitating the amplification of the entire exonic region of both BRCA genes from FFPE tissue or blood samples with as little as 10 ng of input DNA. Leveraging the power of Ion AmpliSeq technology, this highly multiplexed NGS assay enables the generation of results from multiple samples in a single run. Designed for use on either the Ion PGM™ or Ion S5™ sequencing systems, results are delivered in days rather than weeks. The assay is aligned with bioinformatic workflows within Torrent Suite™ and Ion Reporter™ analysis software that utilize optimized variant calling parameters for SNV, InDel, and large exon/gene deletion/duplication detection. Samples can be processed quickly and easily, and variants detected and identified confidently in either germline or somatic DNA analysis pipelines.

BRCA1 and BRCA2 genes are tumor suppressor genes that code for proteins that are vital components of the homologous recombination pathway of DNA damage repair. BRCA mutations resulting in the deficiency of either gene have been shown to result in inefficient activation of this function and are linked to hereditary predisposition to cancer. Errors in the coding sequence of BRCA genes have been detected in germline and somatic mutations and also occur in tumor samples.

Oncomine™ Breast cfDNA Research Assay v2 (Ion Torrent™)

The Oncomine Breast cfDNA Assay v2 is part of a complete solution to detect breast 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 10 mL tube of whole blood.

Liquid biopsies offer several advantages over conventional solid tumor biopsies:
• Less invasive, enabling them to be taken at multiple time points to monitor progression of the cancer
• Lower cost
• Faster turnaround time from sample to results
• Better represent tumor heterogeneity

The Oncomine Breast cfDNA Assay v2 enables the analysis of:
• Hotspot genes: AKT1, EGFR, ERBB2, ERBB3, ESR1, FBXW7, KRAS, PIK3CA, SF3B1, TP53 (~152 hotspots)
• Copy number genes (CNVs): CCND1, ERBB2, FGFR1
• Full length genes: TP53 (~80% coverage)

These genes have been identified as frequently mutated in breast cancer. Through the use of Tag Sequencing technology, low limits of detection (LOD) can be achieved for different variant types*:
• For SNVs/short indels, an LOD of 0.1% can be achieved with sensitivity of ~80% and specificity of >99%
• For detection of TP53 mutations, an LOD of 0.5% can be achieved
• For ERBB2 and FGFR1 CNV targets, detection as low as 1.2-fold amplification can be achieved and for CCND1 CNV target, detection as low as 1.4-fold amplification can be achieved with sensitivity of >90% and specificity of >99%

The entire workflow (figure below), from isolation of cfDNA using the MagMAX Cell-Free DNA Isolation Kit (Cat. No. A29319) to analysis of samples, can be accomplished in just two days using the Ion S5 XL sequencing system.

Technology
cfDNA (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 unique molecular tags to the gene-specific primers (figure below). After amplification, the tagged molecules are grouped based on the amplified tags. Groups containing the same mutant variant 80% of the time or greater will be called positive. Using the Tag technology, groups that contain random errors generated through the library construction/sequencing process are removed.

Unlike other technologies with LODs of 1–5%, the Oncomine Breast cfDNA Assay v2 has a flexible detection limit of 0.1% for SNVs or one 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, but the %LOD will be higher depending on the input amount (figure below).

Advantages:
• Optimized amplicon design for short cfDNA ensures highest possible capture rate
• Optimized targeted assay design allows highly multiplexed next-generation sequencing (NGS), reducing sequencing costs per sample
• Efficient workflow in just two days

Analysis of SNVs and short indels can be achieved using Torrent Suite Software 5.2 or higher. In order to analyze SNVs, short indels, and CNVs, Ion Reporter 5.6 (cloud- or server-based) is required.

Simplicity, speed, and scalability of Tag Sequencing technology
The Oncomine Breast cfDNA Assay v2 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. Additionally, the Oncomine Breast cfDNA Assay v2 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 Sets 1-24 (Cat. No. A31830) or 25-48 (Cat. No. A31847) for multiplexing barcoded samples on Ion S5 chips.

*Sensitivity and specificity for each variant type were determined using a collection of contrived positive samples and cfDNA isolated from normal healthy donors.

Ion Torrent™ Dual Barcode Kit 1-96 (Ion Torrent™)

The Ion Torrent Dual Barcode Kit 1-96 provides 96 unique dual-matched barcode adapters specifically designed to enable optimal performance of amplicon libraries and Ion semiconductor sequencers. When used in combination with Ion AmpliSeq and Oncomine assays, the kit enables users to pool up to 96 amplicon libraries to conduct multiplexed sequencing analysis, thereby increasing lab efficiency and reducing sequencing costs per sample. The barcode adapters are provided in 96-well plate format.

Features of the Ion Torrent Dual Barcode Kit 1-96 include:
• Enables multiplexing of numerous amplicon library samples on a single sequencing chip with the use of robust molecular barcodes to identify very rare clones with high accuracy
• Both sequence- and flow-optimized for equal representation of all barcodes in a pool and more economical multiplexed sequencing runs
• Robust error correction built in by design for added confidence in sample identification

Higher throughput and variant calling of rare clones
Multiplexing with dual-barcoded libraries enables cost-effective runs by permitting up to 96 samples per run, significantly decreasing the cost and handling requirements of sequencing. Each barcode was individually tested to minimize representation bias and provides superior sensitivity in detecting low-frequency clones with high accuracy.

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 and require a minimal number of flows to interrogate, resulting in more economical multiplexed sequencing runs.

Robust error correction built in by design
Built-in error correction increases the accuracy of sample assignment.

Oncomine™ Myeloid Research Assay (Ion Torrent™)

The Ion Torrent Oncomine Myeloid Research Assay consists of three pools of AmpliSeq oligonucleotide primers and associated reagents to generate amplicon libraries for next-generation sequencing (NGS) on Ion Torrent platforms. The assay is designed to provide sensitive and comprehensive sample amplification of relevant DNA mutations and fusion transcripts associated with myeloid disorders in a single NGS run. The panel is comprised of 40 key DNA genes and a broad fusion panel of 29 driver genes to cover the most relevant targets in major myeloid disorders: acute myeloid leukemia (AML), myeloid dysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML).

This version of the assay is for manual library preparation. For automated library preparation using the Ion Chef System, please see Cat. No. A32841.

Features include:
• Simple, robust workflow that encompasses mutations and fusions in two DNA and one RNA pool in a single NGS run
• Excellent coverage of challenging targets such as CEBPA and FLT3-ITDs
• Multiplex up to four samples on a single Ion 318 chip or twelve on an Ion 530 chip
• Compatible with as little as 10 ng/pool input DNA or RNA per library from blood or bone marrow samples
• Validated detection of somatic variants down to 5% allele frequency
• Simple and fast workflow produces targeted libraries in 3.5 hours typically
• For use on the Ion PGM and Ion S5 systems with manual or automated library preparation
• Compatible with the Oncomine Knowledgebase Reporter for variant annotation

The Oncomine Myeloid Research Assay is a comprehensive, targeted NGS assay designed to assist hematologists in the understanding of myeloid cancer. The assay is a complete kit facilitating the amplification of multiple gene targets from blood or bone marrow samples with as little as 10 ng of input DNA or RNA per pool. Leveraging the power of Ion AmpliSeq technology, this highly multiplexed NGS assay enables the generation of results from multiple samples in a single run. Designed for use on either the Ion PGM or Ion S5 sequencing systems, results are delivered in days rather than weeks. The assay is aligned with bioinformatics workflows within Torrent Suite and Ion Reporter analysis software that utilize optimized variant-calling parameters for SNV, InDel, and FLT3 large internal tandem duplication (ITD) detection. Variants can be annotated in the Oncomine Knowledgebase Reporter to generate a sample-specific report. Samples can be processed quickly and easily, and variants detected and identified confidently.

Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (Ion Torrent™)

The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit enables the simultaneous measurement of the expression levels of over 20,000 human RefSeq genes in a single assay. Providing the ability to work directly with low input levels of total RNA derived from challenging samples such as formalin-fixed paraffin-embedded (FFPE) tissue or other samples with degraded RNA, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit is ideal for those interested in obtaining comprehensive, highly sensitive, and easily obtained gene expression measurements from a wide range of RNA sources. For automated library production, see the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-ready Kit.

The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit offers:
• Flexible, straightforward library preparation – start with as little as 10 ng of total RNA from FFPE samples, cells, or other sources
• Representation of over 20,000 human RefSeq genes
• Wider dynamic range and improved detection sensitivity compared to conventional microarray analysis
• A complementary software plug-in for automated sequencing analysis that provides gene quantitation and reporting as well as quality control metrics
• Compatibility with Ion Xpress™ Barcode adapters allowing for multiplexed sequencing

Wider dynamic range for enhanced performance
With a wider dynamic range and improved gene detection compared to conventional microarray analysis, the Ion AmpliSeq Transcriptome™ Human Gene Expression Kit provides a clear solution to researchers needing enhanced performance for their gene expression needs. A simple workflow allows for sample-to-gene quantitation in less than 2 days, helping to reduce workload and increase throughput.

Straightforward library preparation and multiplex sequencing
Starting with as little as 10 ng of total RNA, libraries can be prepared in approximately 7 hours with only one hour of hands-on time. Total RNA is first processed with the included SuperScript® VILO™ cDNA Synthesis kit, and the resulting cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all genes.

The resulting libraries are ready for downstream template preparation using the Ion OneTouch™ 2 System or Ion Chef™ System and sequencing on the Ion Proton™ sequencing system. Libraries can be barcoded for multiplexing, allowing for flexibility, helping to reduce cost, and increase throughput, with the recommended 16 libraries per Ion 550 Chip and 8 libraries per Ion 540 or Ion PI chip. Other multiplexing options are also possible, depending on the experimental design and desired level of sensitivity.

Automatic data analysis with Torrent Suite™ plug-in
Using the complementary analysis plug-in available with Torrent Suite™ software, gene quantitation information is automatically compiled, minimizing the requirement for costly computational resources and bioinformatics expertise to process raw sequencing data into meaningful information. An easy to interpret, highly portable table is produced containing all genes interrogated and their respective expression levels, output that may be used with a variety of existing software applications for downstream analysis of microarray or next-generation sequencing data.

Learn more about the Ion AmpliSeq Transcriptome Human Gene Expression Kit ›

Note: Libraries made from this protocol yield fragments suitable for 200-base read sequencing.

Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Ion Torrent™)

The new Ion Xpress™RNA-Seq Barcode 1-16 Kit provides a set of 16 unique barcode primers for sequencing RNA on the Ion Torrent PGM™semiconductor sequencer. When used in combination with the Ion Total RNA-Seq Kit v2, the Ion Xpress™RNA-Seq Barcode 1-16 Kit enables users to pool up to 16 fragment libraries prior to template preparation and then conduct multiplexed sequencing analysis, simplifying the Ion semiconductor sequencing workflow for small and whole transcriptome RNA.

Features and Benefits:
• Efficient multiplexing-enables multiplexing of up to 16 fragment libraries on a single sequencing chip
• Both sequence- and flow-optimized for equal representation of all barcodes in a pool
• Multiplexing decreases the cost and the handling requirements of template preparation and sequencing
• Robust error correction built in by design for added confidence in sample identification

Efficient Multiplexing with Barcode Primers Enables Higher Throughput Sample Sequencing
Multiplexing with barcoded libraries leads to more cost-effective runs by permitting up to 16 samples per run, significantly decreasing the cost and handling requirements of template preparation and sequencing.

Sequence- and Flow-Optimized for Increased Performance and Efficiency
Barcode primers contain sequences that are optimized to provide equal representation of all barcodes in a pool, require a minimum number of flows to interrogate, and necessitate only 20 bases of barcode and adaptor sequencing, which results in more economical multiplexed sequencing runs.

Robust Error Correction Built In By Design
Built-in error correction significantly minimizes the possibility of incorrect sample assignment.

The Ion Xpress™ RNA-Seq Barcode 01-16 Kit is designed to create 10 multiplexed libraries per barcode or a total of 160 multiplexed libraries.

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

Genexus™ Barcodes 1-96 AS (Ion Torrent™)

The Ion Torrent Genexus Barcodes 1-96 AS kit provides one each of Ion Torrent Genexus Barcodes 1-32 AS, 33-64 AS, and 65-96 AS. When used in conjunction with Ion Torrent Genexus Library Strips 1 and 2-AS, it supports flexible, fully automated preparation and normalization of up to 96 Ion AmpliSeq libraries. Each plate is filled with 32 dried-down, single-use barcodes and covered with a pierceable foil seal, eliminating the risk of cross contamination between wells. The barcodes can be flexibly utilized in increments of 1 to 32, until all barcodes are exhausted. For Ion AmpliSeq HD-based assays, choose Ion Torrent Barcodes 1-32 HD.

As part of the Genexus Integrated Sequencer workflow, the Genexus Barcodes 1-96 AS kit:
• Automates library preparation for 200–400 base-read Ion AmpliSeq libraries
• Supports intake variability of clinical research samples in a cost-effective manner
• Maximizes flexibility with the ability prepare 1 to 32 single-pool libraries per run
• Enables parallel processing of up to four compatible assays in a single run
• Delivers fast and simple instrument setup, with less than five minutes of hands-on time

The Ion Torrent Genexus Integrated Sequencer automates library preparation, sequencing, analysis, and reporting in a hands-off, walkaway workflow to deliver results in a single day. The innovative, multilane sequencing chip is designed to enable cost-effective processing of 1 to 32 single pool libraries.

Ion AmpliSeq™ Library Kit 2.0 (Ion Torrent™)

The Ion AmpliSeq™ Library Kit 2.0 is designed for rapid preparation of amplicon libraries using Ion AmpliSeq™ panels.

Scalable Multiplex PCR Reactions
The Ion AmpliSeq 2.0 technology enables scalable multiplex PCR reactions from 12- to 24,000-plex in a single well using just 10 ng of starting DNA. Ion AmpliSeq panels and primer pools allow highly multiplexed PCR amplification of thousands of genomic target regions, with superior coverage uniformity and specificity, without the need of a specialized microfluidics PCR platform. In addition, the primers contain proprietary modifications that enable removal of primer sequences during library preparation, for efficient target assessment during sequencing. Multiple primer pools can be used to create overlapping amplicons that enable complete coverage of large targets. Ion AmpliSeq™ Custom Primer Pools are designed via the Ion AmpliSeq™ Designer Tool, available at www.ampliseq.com.

Barcoded Library Preparation
The Ion AmpliSeq Library Kit 2.0 includes reagents for generating amplicons with 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 allow for accurate sample-to-sample comparisons.

Easy and Flexible Protocol
The Ion AmpliSeq Library Kit 2.0 uses a plate-based format for easier sample handling and tracking, and for compatibility with automation and high-throughput laboratories. The library preparation uses very small quantities of starting material per PCR. The resulting DNA 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.

5500 SOLiD™ Fragment Library Barcode Adaptors 1-16 (Applied Biosystems™)

The 5500 SOLiD™ Fragment Library Barcode Adaptor Kit provides a complete set of 96 unique barcode adaptors and primers for cost-effective next generation sequencing of fragment libraries on the 5500 Series Genetic Analysis Systems. When used in combination with the 5500 SOLiD™ Fragment Library Core Kit, the 5500 SOLiD™ Fragment Library Barcoding Kit enables users to pool up 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 enrichment

Key Product Features:
• Efficient multiplexing—enables multiplexing of up to 96 fragment or paired-end library samples on a single flow chip with the use of robust molecular barcodes.
• Cost effective runs—allows more samples per run, significantly decreasing the cost and handling requirements of ePCR, enrichment, and deposition.
• Consolidated 5500 SOLiD sampling—enables pooling of samples prior to emulsion PCR (ePCR) and sequencing on the 5500 Series Genetic Analysis Systems.
• Versatile sequencing—substantially benefits applications such as whole genome sequencing of small genomes or targeted resequencing of enriched samples.

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

Oncomine™ Focus Assay, 318 Solution (Ion Torrent™)

The Oncomine Focus Assay is a targeted next-generation sequencing (NGS), multi-biomarker assay that enables the detection of variants across 52 cancer-relevant genes from DNA and RNA in a single workflow. The assay provides reagents for library construction and two pools—one DNA and one RNA—of multiplex PCR primers for preparation of amplicon libraries from formalin-fixed paraffin embedded (FFPE) tumor samples. Using as little as 10 ng of nucleic acid per primer pool, the assay enables analysis of hotpots, SNVs, indels, CNVs, and gene fusions in a single sequencing run.

The Oncomine Focus Assay, 318 Solution, includes all necessary reagents and consumables for library construction, template preparation with the Ion OneTouch 2 System, and sequencing on the Ion PGM System. Select™ reagents and consumables are manufactured to rigorous standard in our ISO 13485-compliant facility. For a kit that includes only the panel primers and Select reagents for library construction and normalization, please see the Oncomine Focus Library Assay, Select Library. For a kit with higher sample scalability and flexibility, please see the Oncomine Focus Assay, AmpliSeq Library.

From sample to answer
The Oncomine Focus Assay, Select Library, is part of an NGS workflow that helps researchers filter variant results from hundreds to just a few key cancer driver variants. Enabled by Oncomine informatics, this filtering, as well as the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps you contextualize and interpret findings to move toward the answers you need.

Learn more about Oncomine Focus Assay and Oncomine oncology >

Oncomine Focus Assay, Chef-Ready Library (Ion Torrent™)

The Oncomine Focus Assay is a targeted next-generation sequencing (NGS), multi-biomarker assay that enables you to detect variants across 52 cancer-relevant genes from DNA and RNA in a single workflow. It provides reagents for library construction and two pools—one DNA and one RNA—of multiplex PCR primers for preparation of amplicon libraries from formalin-fixed paraffin embedded (FFPE) tumor samples. Using as little as 10 ng of nucleic acid per primer pool, the assay enables analysis of hotpots, SNVs, indels, CNVs, and gene fusions in a single workflow. For a kit that includes reagents for manual library preparation, please see the Oncomine Focus Assay, AmpliSeq Library.

The Oncomine Focus Assay, Chef-Ready Library, is for the Ion Chef System and Ion GeneStudio S5 System workflow. It contains all the reagents needed to prepare libraries for 32 samples:

Oncomine Focus Assay, DNA Chef-Ready panel—contains the DNA primer pool
Oncomine Focus Assay, RNA Chef-Ready panel—contains the RNA primer pool
Ion AmpliSeq Kit for Chef DL8 reagents—allows you to automate library prep on the Ion Chef System

From sample to answer
The Oncomine Focus Assay is part of an NGS workflow that helps researchers filter variant results from hundreds to just a few key cancer driver variants. Enabled by Oncomine Informatics, this filtering, as well as the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps you contextualize and interpret findings to move toward the answers you need.Learn more about Oncomine Focus Assays and Oncomine Oncology.

Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Ion Torrent™)

The Ion AmpliSeq Transcriptome Mouse Gene Expression Assay allows simultaneous gene expression measurement of over 20,000 mouse RefSeq genes in a single assay. Providing the ability to work directly with low input levels of total RNA, the Ion AmpliSeq Transcriptome Mouse Gene Expression Assay is ideal for those interested in obtaining comprehensive and highly sensitive gene expression measurements from a wide range of RNA sources. This particular kit enables manual library preparation with throughput flexibility. For automated production, see the Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit.

The Ion AmpliSeq Transcriptome Mouse Gene Expression Assay offers:
• Flexible, straightforward library preparation—start with as little as 10 ng of total RNA from tissues, cells, or other sources
• Fast gene expression profiling with simple workflow—go from RNA to data in <2 days with ~45 minutes of total hands-on time with the automated workflow of the Ion GeneStudio S5 and Ion Chef systems
• A complementary software plug-in for automated sequencing analysis that provides gene quantitation and reporting as well as quality control metrics
• Compatibility with Ion Xpress Barcode adapters, allowing for multiplexed sequencing

Leveraging the speed and simplicity of Ion AmpliSeq technology, this ultrahigh-multiplex PCR enrichment approach enables rapid gene expression profiling with minimal hands-on time. This research method provides a faster, simpler, and lower-cost sequencing method that is highly correlated to whole-transcriptome RNA sequencing.

Straightforward library preparation and multiplex sequencing with manual kit
Starting with as little as 10 ng of total RNA, libraries can be prepared in approximately seven hours with only one hour of hands-on time. Total RNA is first processed with the SuperScript VILO cDNA Synthesis Kit (not included), and the resulting cDNA is amplified using Ion AmpliSeq technology to accurately maintain expression levels of all genes.

The resulting libraries are ready for downstream template preparation using the Ion OneTouch 2 or Ion Chef System and sequencing on the Ion GeneStudio S5 or Ion Proton System. Libraries can be barcoded for multiplexing, providing flexibility, reduced cost, and increased throughput, with the recommended 16 libraries per Ion 550 Chip and 8 libraries per Ion 540 or Ion PI chip. Other multiplexing options are also possible, depending on the experimental design and desired level of sensitivity.

Collibri™ PS DNA Library Prep Kit for Illumina Systems, with UD indexes(Set D, 73-96) (Invitrogen™)

The Invitrogen Collibri 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 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 consistent, even coverage of variable GC regions from inputs ranging from 1 to 1,000 ng
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PS DNA Library Prep 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 PS DNA Library Prep Kit consistently offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from a wide range of inputs (1 ng to 1 µg) of physically sheared double-stranded DNA (see figure below). Additionally, a PCR-free version is offered for inputs starting at 500 ng DNA. The entire library preparation protocol takes about 3.5 hours with a PCR 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 PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Precision ID Ancestry and Library Kit Bundle (Applied Biosystems™)

The Applied Biosystems™ Precision ID Ancestry Panel and Library Kit Bundle is packaged for easy ordering and preparation of amplicon libraries using the Precision ID Ancestry Panel (Cat. No. A25642) and a Precision ID Library Kit (Cat. No. A26435) for sequencing on Ion Torrent sequencing systems. The Precision ID Ancestry Panel of multiplexed SNPs provides DNA-based investigative leads for forensic casework samples. Specifically, it helps determine the continental bio-geographic ancestry of a sample owner from pristine or degraded samples.

Simple protocol
• 96 well plate–based workflow enables easy sample management
• No library amplification with qPCR quantification

Optimized digestion reagent
• Cleaner digest allows for more efficient downstream sequencing

Scalable multiplex PCR reactions
The Precision ID Ancestry Panel is built on Ion AmpliSeq™ chemistry, which enables scalable multiplex PCR reactions for all 165 markers in the panel using just 1 ng of starting DNA, with superior coverage uniformity and specificity. In addition, the primers contain proprietary modifications that enable removal of primer sequences during library preparation, for efficient target assessment during sequencing. Multiple primer pools can be used to create overlapping amplicons that enable complete coverage of large targets. Learn more about other Precision ID panels >

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

Easy and flexible protocol
The resulting DNA libraries are ready for downstream template preparation for clonal amplification on Ion Sphere™ particles using the automated Ion OneTouch™ 2 System. The intuitive Torrent Suite Software and HID SNP Genotyper plug-in enable you to go from extracted DNA to ancestry-informative genotypes in less than two days*.

*Using the Applied Biosystems Precision ID NGS System for Human Identification

Ion Xpress™ Barcode Adapters 1-16 Kit (Ion Torrent™)

The Ion Xpress™ Barcode Adapters 1-16 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.

Ion AmpliSeq™ Transcriptome Human Gene Expression Panel, Chef-Ready Kit (Ion Torrent™)

The Ion AmpliSeq™ Transcriptome Human Gene Expression Panel, Chef-Ready Kit, enables automated production of Ion Ampliseq transcriptome libraries on the Ion Chef™ System. For manual library production, see the Ion AmpliSeq Transcriptome Human Gene Expression Kit.

The Ion AmpliSeq Transcriptome Human Gene Expression Panel allows simultaneous gene expression measurement of over 20,000 human RefSeq genes in a single assay. The Chef-ready kit utilizes the same chemistry as that designed for a manual workflow, providing equivalent or better performance with exceptional reproducibility, on-target reads, and sample balance. Libraries can be produced from as little as 10 ng of total RNA from FFPE or fresh/frozen samples with only 15 minutes of hands-on time to setup the Ion Chef System.

In addition, the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit, offers:
• Wider dynamic range and improved detection sensitivity compared to conventional microarray analysis
• A complementary software plug-in for automated sequencing analysis that provides gene quantitation and reporting, as well as quality control metrics
• Compatibility with Ion Xpress™ barcode adapters allowing for multiplex sequencing

Wider dynamic range for enhanced performance
With a wider dynamic range and improved gene detection compared to conventional microarray analysis, the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-ready Kit, offers a clear solution to researchers needing enhanced performance for their gene expression needs. A simple workflow allows for sample-to-gene quantitation in less than 2 days, helping to reduce workload and increase throughput.

Straightforward library preparation and multiplex sequencing
The Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit, includes the reagents and materials required for automated preparation of 32 barcoded Ion AmpliSeq transcriptome libraries. The Ion Chef System can automate up to 8 barcoded libraries per run, so the kit provides reagents and materials sufficient for 4 runs. Starting with as little as 10 ng of total RNA from FFPE or fresh/frozen samples, the total RNA is first processed using the SuperScript™ VILO™ cDNA Synthesis Kit (not included), and the resulting cDNA is amplified using Ion AmpliSeq technology to accurately maintain expression levels of all genes. Approximately 7 hours of instrument run time and only 15 minutes of hands-on time are needed to set up the Ion Chef System for library construction from cDNA.

The resulting libraries are ready for downstream template preparation using the Ion Chef System and sequencing on the Ion GeneStudio™ S5™ or Ion Proton™ Sequencing System. With the recommended 16 libraries per Ion 550 Chip and 8 libraries per Ion 540 or Ion PI chip, libraries are multiplexed for flexibility, throughput increase, and cost reduction. Other multiplexing options are also possible, depending on the experimental design and desired level of sensitivity.

Automatic data analysis with Torrent Suite plug-in
Using the complementary analysis plug-in available with Torrent Suite™ software, gene quantitation information is automatically compiled, minimizing the requirement for costly computational resources and bioinformatics expertise to process raw sequencing data into meaningful information. An easy-to-interpret, highly portable table is produced containing all genes interrogated and their respective expression levels—output that may be used with a variety of existing software applications for downstream analysis of microarray or next-generation sequencing data.

Learn more about the Ion AmpliSeq Transcriptome Human Gene Expression Kit ›

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™ Mouse TCR Beta SR Assay, RNA (Ion Torrent™)

The Ion AmpliSeq Mouse TCR Beta SR Assay is a robust, targeted next-generation sequencing (NGS) assay designed to accurately identify and measure the clonal expansion of T lymphocytes by targeting the complementarity-determining region 3 (CDR3) of the T-cell receptor (TCR) gene locus from total RNA input. The assay can be used for basic and translational research to identify T-cell clones since the nucleotide sequence of the CDR3 region is unique to each T cell and codes for the part of the TCR beta chain that is involved in antigen recognition. For DNA samples please see Cat. No. A45488.

Benefits of the Ion AmpliSeq Mouse TCR Beta SR Assay, RNA, include:
Compatibility with a vast array of research sample types, including FFPE tissue, fresh-frozen (FF) tissue, whole blood, PBLs, and PBMCs
High sensitivity and low limit of detection (LoD) for rare clone identification through dual-barcode indexing
Efficient workflow with 48 hour sample-to-results time
Flexible input requirements ranging from 25 ng to 1 µg
Streamlined and user-friendly informatics solution with with multi-sample analysis functionality

The Ion AmpliSeq Mouse TCR Beta SR Kit, RNA, provides a single pool of multiplex PCR primers and library reagents to generate 90-bp amplicons that can be sequenced on all chip types supported by the Ion GeneStudio S5 sequencing systems, allowing you to pick the best multiplexing configuration for your unique sample batching needs and throughput requirements. The entire workflow from library preparation to analysis of samples can be accomplished in two days using the Ion Chef templating system and Ion GeneStudio S5 system.

The Ion AmpliSeq Mouse TCR Beta SR RNA Assay, with its high sensitivity and specificity, supports key applications in the field of immunology, immuno-oncology, hemato-oncology, and vaccine research. The high-sensitivity dual-barcode indexing, flexible input requirements (100 ng–1 µg), high-depth sequencing, and high-throughput capability make this assay ideal for testing a variety of hypotheses for basic or translational biomarker research. A small fragment size requirement from the input materials for library creation and high multiplexing on the Ion 530 Chip of the Ion GeneStudio S5 sequencers enables researchers to focus on testing a variety of use cases in mouse models including the role of T cells in generating immune response to immunotherapies such as checkpoint blockade inhibitors, cancer vaccines, or chimeric antigen receptor (CAR) T-cell therapies.

Learn more about the assay ›

Note: Information about data analysis using Ion Reporter Software v5.12 can be found in the User Guide below.

Oncomine™ Comprehensive Assay v3C (Ion Torrent™)

The Oncomine Comprehensive Assay v3 is a targeted, next-generation sequencing (NGS) assay that enables the detection of relevant SNVs, CNVs, gene fusions, and indels from 161 unique genes to help inform drug discovery research and clinical trial research programs. It provides the reagents for library construction and four pools—two DNA and two RNA—of multiplex PCR primers for preparation of amplicon libraries from formalin-fixed paraffin embedded (FFPE) tumor samples. Designed to help you go from hundreds down to a few relevant cancer drivers, this assay is part of a comprehensive workflow that enables NGS data analysis from as little as 10 ng of nucleic acid per pool. The assay is optimized for sequencing on the Ion GeneStudio S5 Systems with the Ion 540 Chip to enable up to 8 samples (7 samples and one no-template control) per run.

When combined with Oncomine Reporter Software, you can create reports that align labels, guidelines, and clinical trials to your results so you can focus on key drivers of cancer in your research.

Key features of the assay are:
• Enables analysis of variants across 161 genes
• Detection of SNVs, CNVs, gene fusions, and indels
• Robust performance from as little as 10 ng per pool (40 ng total) isolated from FFPE samples including fine needle biopsies
• Characterized with molecular standards and controls
• Content driven by the Oncomine Knowledgebase and experienced scientists helps assure coverage of key targets aligned to published evidence

From sample to answer
The Oncomine Comprehensive Assay is part of an NGS workflow that helps researchers to filter variant results from hundreds to just a few key cancer driver variants. Enabled by Oncomine Informatics, this filtering, as well as the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps you contextualize and interpret findings to move toward the answers you need.

The workflow has been adopted by large-scale national clinical trial research programs including NCI-MATCH (United States) and LC-SCRUM (Japan), and includes:
• Proven Ion AmpliSeq chemistry
• Automated library and template prep on the Ion Chef System
• Scalable sequencing on the Ion GeneStudio S5 Systems
• Optimized Oncomine informatics

Multiple configurations
The Oncomine Comprehensive Assay v3 comes in the following configurations to match your laboratory needs:

Manual library preparation configuration:
Oncomine Comprehensive Library Assay v3M
This configuration contains all the reagents needed to prepare libraries for 24 or 96 samples:
    • Oncomine Comprehensive Panel v3M DNA—contains the DNA primer pools
    • Oncomine Comprehensive Panel v3M RNA—contains the RNA primer pools
    • Ampliseq Library Plus reagents—allow you to manually create your library
Ion Chef automated library preparation configuration:
Oncomine Comprehensive Library Assay v3C
This configuration contains all the reagents needed to prepare libraries for 32 samples:
    • Oncomine Comprehensive Panel v3C DNA—contains the DNA primer pools
    • Oncomine Comprehensive Panel v3C RNA—contains the RNA primer pools
    • Ion AmpliSeq Kit for Chef DL8 reagents—allows you to automate library prep on the Ion Chef System


MuSeek Index Set 1, Illumina compatible (Thermo Scientific™)

Thermo Scientific MuSeek Index Set 1, Illumina™ compatible, is designed for generation of indexed genomic DNA libraries for sequencing on the Illumina MiSeq™ and HiSeq™ instruments. The set provides 4 indexed P5 adapters and 6 MuSeek indexed P7 adapters. This enables pooling of up to 24 dual-indexed libraries and conducting multiplexed sequencing analysis. The MuSeek Index Set 1, in combination with MuSeek Library Preparation kit, Illumina™ compatible, allows fast and simple indexed library construction from 50 ng of sample DNA, eliminating the need for physical shearing, end conversion and adapter ligation steps.

Highlights

• Enables sequencing of up to 24 dual-indexed fragment libraries in a single sequencing run.

Applications

• Indexed DNA fragment library preparation for next generation sequencing.

Includes
• MuSeek Indices M501-4
• MuSeek Indices M701-6

IonCode Barcode Adapters, 0701-0796 (Ion Torrent™)

IonCode Barcode Adapters 0701-0796 are 96 unique barcode adapters designed for optimal performance with Ion Torrent semiconductor sequencers. When used in combination with other IonCode barcode adapters and the AgriSeq HTS Library Kit, users can pool up to 768 amplicon libraries and then conduct multiplexed sequencing analysis, which helps increase lab efficiency and reduce sequencing costs per sample.

Key product features:
• Robust barcodes ligate efficiently and uniformly to generate balanced representation of libraries
• Unbiased performance enables identical genotypes independent of barcode used
• Robust error correction built in by design for added confidence in sample identification
Increase sample multiplexing without impacting data quality
Multiplexing with barcoded libraries enables more cost effective runs by permitting up to 768 samples per run, and helps significantly decrease the cost and handling requirements of sequencing. Each barcode was individually evaluated to verify no bias of sequence context representation. The barcodes were also screened for equivalent efficiency to verify balanced read depth between libraries. Regardless of the specific barcode used, AgriSeq targeted genotyping-by-sequencing (GBS) generates highly uniform libraries and concordant genotype calls (see figures below).

Collibri™ PCR-free ES DNA Library Prep Kit for Illumina Systems, with UD indexes (Set D, 73-96) (Invitrogen™)

The Invitrogen Collibri PCR-Free ES DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems.

The Collibri PCR-Free ES 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 preparation success
• Includes all necessary components in a single kit
• Supports PCR-free protocols starting with as little as 100 ng of DNA
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PCR-Free ES DNA Library Prep Kit contains inert dyes that provide visual feedback of preparation progress: the reaction mixes change color in response to the addition of critical components at each step (see figure below for visual tracking). The inert dyes do not interfere with the enzymatic reactions and do not compromise the sequencing results.The Collibri PCR-Free ES DNA Library Prep Kit is designed for fast and convenient library preparation from inputs as low as 100 ng intact DNA. 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 ES DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Ion Xpress™ Barcode Adapters 81-96 Kit (Ion Torrent™)

The Ion Xpress™ Barcode Adapters 81-96 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.

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.

MuSeek Library Preparation Kit, Illumina compatible (Thermo Scientific™)

Thermo Scientific™ MuSeek™ Library Preparation Kit, Illumina™ compatible is designed for generation of high‐quality genomic DNA libraries for sequencing with the Illumina™ MiSeq™ and HiSeq™ systems. The fast protocol utilizes the 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 adapters are added using a robust and accurate Thermo Scientific Phusion™ High-Fidelity DNA polymerase. Starting with only 50 ng or 100 ng of sample the protocol can be used to generate 100 bp - 1,000 bp insert libraries. The kit contains components sufficient for 12 fragmentation reactions and the subsequent adapter-addition polymerase chain reactions. Sequencing primers required for sequencing libraries prepared by this method are provided as well.

Highlights

Convenient—no physical shearing, end-repair and ligation steps
Fast—generates NGS fragment libraries in less than 90 minutes
Low sample input—DNA fragment libraries from 50 ng DNA input
Indexing compatible—MuSeek Index Set 1 enables preparation of up to 24 dual-indexed DNA libraries for sequencing in one run.

Applications

• DNA fragment library preparation for downstream use in next generation sequencing workflow.
• Library preparation from gDNA, ds DNA, bacterial DNA, DNA amplicons.

Includes
• MuSeek Enzyme Mix, IL
• MuSeek Fragmentation Reaction Buffer
• MuSeek Stop Solution
• Water, nuclease-free
• Control DNA
• MuSeek Adapter Addition Primer Mix, IL
• MuSeek Adapter Addition Reaction Buffer, IL
• Phusion™ Hot Start II High-Fidelity DNA Polymerase, IL
• MuSeek Sequencing Primer, Read 1
• MuSeek Sequencing Primer, Read 2
• MuSeek Sequencing Primer, Index Read

Notes
The kit is shipped on dry ice. Upon arrival store at -20°C, avoid repeated freeze-thaw cycles. The Stop Solution can be stored at room temperature.

Collibri™ PS DNA Library Prep Kit for Illumina Systems, with UD indexes (Set B, 25-48) (Invitrogen™)

The Invitrogen Collibri 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 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 consistent, even coverage of variable GC regions from inputs ranging from 1 to 1,000 ng
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PS DNA Library Prep 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 PS DNA Library Prep Kit consistently offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from a wide range of inputs (1 ng to 1 µg) of physically sheared double-stranded DNA (see figure below). Additionally, a PCR-free version is offered for inputs starting at 500 ng DNA. The entire library preparation protocol takes about 3.5 hours with a PCR 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 PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Ion Library Equalizer™ Kit (Ion Torrent™)

The Ion Library Equalizer™ Kit is a simple and seamless bead-based solution replacing the need for library quantification and library dilutions for library normalization as required for any next generation sequencing workflow. The Ion Library Equalizer™ Kit helps reduce labor, reagent costs, and further simplifies the Ion semiconductor sequencing workflow for high sample-throughput or barcoded projects, as well as single or low sample number projects.

The kit workflow consists of three simple steps:

1) Library amplification with Equalizer™ Primers
2) Library capture onto Equalizer™ Beads
3) Heat elution of the normalized library using a specially formulated Equalizer™ Elution Buffer

Simple Workflow
• Seamlessly integrates into your existing library preparation workflow
• Reduced pipetting compared to the Agilent 2100 Bioanalyzer®-based workflow
• Faster workflow in high-throughput applications-no need for DNA quantification, calculations, and dilution of DNA libraries
• Minimizes library-to-library variability

Cost Effective
• No additional capital equipment required
• Less expensive than Agilent 2100 Bioanalyzer®-based workflow (up to 10 samples)
• Reduced AMPure® XP reagent usage compared to Agilent 2100 Bioanalyzer®-based workflow
• Long shelf life: up to 18 months
• Convenient 96-reaction kit helps reduce ordering frequency

Flexible
• Compatible with all Ion DNA library kits including Ion AmpliSeq™ DNA panels, Ion fragment library kits, and Ion Xpress™ Barcode adaptors
• Use with a single sample or in a 96-well plate format
• Compatible with 3rd party automated liquid handling systems for integrated library preparation and normalization

Includes:
The Ion Library Equalizer Kit includes the necessary reagents to complete 96 normalization reactions.

Required for Workflow:
Ion AmpliSeq™ Library Kit 2.0
Ion AmpliSeq™ Ready-to-Use Panel or Custom Panel designed via the Ion AmpliSeq™ Designer (www.ampliseq.com)
--OR--
Ion Plus Fragment Library Kit
--OR--
Ion Xpress™ Plus Fragment Library Kit

Optional:
Ion Xpress™ Barcode Adapters Kits

Oncomine™ BCR IGH LR Assay, RNA (Ion Torrent™)

The Oncomine BCR IGH LR Assay is a robust, targeted next-generation sequencing (NGS) assay designed for use in immuno-oncology, infectious disease, and basic immunology research. Unlike other technologies, the Oncomine BCR IGH-LR Assay offers more than 400 base amplicons of library sequencing through long-read sequencing chemistry, enabling comprehensive coverage of the B cell receptor (BCR) immunoglobin heavy (IGH) chain. The assay kit includes a single pool of multiplex PCR primers, cDNA synthesis kit, and AmpliSeq library reagents.

The Oncomine BCR IGH LR Assay is designed to accurately measure clonal expansion, quantify somatic hypermutation, and isotype B lymphocytes using total RNA extracted from bone marrow, whole blood, peripheral blood leukocytes (PBLs), peripheral blood mononuclear cells (PBMCs), or sorted cells in fresh frozen (FF) research specimens. The assay utilizes Ion AmpliSeq multiplex PCR technology. It amplifies framework 1 (FR1) and constant gene region of BCR IGH gene to interrogate highly diverse complementarity-determining regions CDR1, CDR2, and CDR3, as well as the CH1 domain of the constant gene to enable distinction of all nine isotypes. IGH CDR-region amino acid motifs may reveal signatures of B cell responses to defined antigens for use as future markers of autoimmune or infectious disease. Automated clonal lineage analysis and multi-sample analysis capability facilitates tracking of B cell clonal evolution arising from somatic hypermutation and class switch recombination in research samples.

Oncomine BCR IGH LR Assay benefits include:
• Extended amplicon allows for quantification of variable gene somatic hypermutation and isotype identification to enable immuno-oncology, and infectious disease translational and clinical research
• Assay primers are designed to amplify all variable and joining gene alleles in the gold-standard IMGT database
• RNA input improves detection of changes in plasmablast and plasma cell populations in research samples following immune challenge or administration of immunomodulatory agents
• Superior multiplex PCR design through AmpliSeq technology assures high accuracy and sensitivity through a superior multiplex PCR design
• Ultra-low substitution error rate minimizes artifacts arising from sequencing errors to enable highly accurate assessment of somatic hypermutation and clonal heterogeneity in malignant B cell research samples of interest
• The entire workflow from isolation of RNA to analysis of samples can be accomplished within two days using the Ion Chef templating system and the Ion Genestudio S5 sequencing systems
• Flexible input requirements ensures successful library construction with as low as 25 ng and up to 2 µg total RNA input
• Streamlined and user-friendly informatics solution offers automated clonotyping, somatic hypermutation quantification, clonal lineage analysis, reporting of key repertoire features, and multi-sample analysis capability to track oB cell clones across research samples

Learn more about the assay ›

Note: Information about data analysis using Ion Reporter Software v5.12 can be found in the User Guide below.

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 ›

Collibri™ PCR-free ES DNA Library Prep Kit for Illumina Systems, with UD indexes (Set B, 25-48) (Invitrogen™)

The Invitrogen Collibri PCR-Free ES DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems.

The Collibri PCR-Free ES 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 preparation success
• Includes all necessary components in a single kit
• Supports PCR-free protocols starting with as little as 100 ng of DNA
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PCR-Free ES DNA Library Prep Kit contains inert dyes that provide visual feedback of preparation progress: the reaction mixes change color in response to the addition of critical components at each step (see figure below for visual tracking). The inert dyes do not interfere with the enzymatic reactions and do not compromise the sequencing results.The Collibri PCR-Free ES DNA Library Prep Kit is designed for fast and convenient library preparation from inputs as low as 100 ng intact DNA. 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 ES DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Oncomine™ Focus Assay, AmpliSeq™ Library (Ion Torrent™)

The Oncomine Focus Assay is a targeted next-generation sequencing (NGS), multi-biomarker assay that enables the detection of variants across 52 cancer-relevant genes from DNA and RNA in a single workflow. The assay provides reagents for library construction and two pools—one DNA and one RNA—of multiplex PCR primers for preparation of amplicon libraries from formalin-fixed paraffin embedded (FFPE) tumor samples. Using as little as 10 ng of nucleic acid per primer pool, the assay enables analysis of hotpots, SNVs, indels, CNVs, and gene fusions in a single sequencing run.

The Oncomine Focus Assay, AmpliSeq Library, is for use as part of the Ion Chef and Ion GeneStudio S5 Systems workflow. Scalability and flexibility are achieved using Ion Xpress or IonCode barcode adapters for multiplexing barcoded samples on Ion S5 chips. For a kit that also includes reagents and consumables for automated library preparation on the Ion Chef System, please see the Oncomine Focus Assay, Chef-Ready Library.

From sample to answer
The Oncomine Focus Library Assay is part of an NGS workflow that helps researchers filter variant results from hundreds to just a few key cancer driver variants. Enabled by Oncomine informatics, this filtering, as well as the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps you contextualize and interpret findings to move toward the answers you need.

Learn more about Oncomine Focus Assay and Oncomine oncology.

Genexus™ Barcodes 1-32 HD (Ion Torrent™)

The Ion Torrent Genexus Barcodes 1-32 HD kit provides one plate filled with 32 dried-down, single-use barcodes and covered with a pierceable foil seal, eliminating the risk of cross contamination between wells. The barcodes can be flexibly utilized in increments of 1 to 32, until all barcodes are exhausted.When used in conjunction with Ion Torrent Genexus Library Strips 1 and 2-HD, this kit supports flexible, fully automated preparation and normalization of up to 32 Ion AmpliSeq HD libraries. For Ion AmpliSeq-based assays, choose from other available barcode kits: Ion Torrent Genexus Barcodes 1-32 AS, 33-64 AS, 65-96 AS, or 1-96 AS.

As part of the Genexus Integrated Sequencer workflow, the Genexus Barcodes 1-32 HD kit:
• Automates library preparation for 200–400 base-read Ion AmpliSeq HD libraries
• Supports intake variability of clinical research samples in a cost-effective manner
• Maximizes flexibility with the ability prepare 1 to 32 single-pool libraries per run
• Enables parallel processing of up to four compatible assays in a single run
• Delivers fast and simple instrument setup, with less than five minutes of hands-on time

The Ion Torrent Genexus Integrated Sequencer automates library preparation, sequencing, analysis, and reporting in a hands-off, walkaway workflow to deliver results in a single day. The innovative, multilane sequencing chip is designed to enable cost-effective processing of 1 to 32 single pool libraries.

Collibri™ PCR-free PS DNA Library Prep Kit for Illumina Systems, with UD indexes (Set C, 49-72) (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™ TCR Beta-LR Assay (Ion Torrent™)

The Oncomine TCR Beta-LR Assay is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor beta chain rearrangements. This assay utilizes a newly developed long-read sequencing technology on the Ion GeneStudio S5 next-generation sequencing systems. The assay kit provides a single pool of multiplex PCR primers, library reagents, and sample barcodes. Ion AmpliSeq libraries can be generated from research samples such as RNA extracted from whole blood, fresh-frozen tissue, or FACS-sorted cells.

Learn more about the assay ›

The assay is designed to efficiently capture all three complementarity determining regions of the TCR beta chain (CDR1, CDR2, CDR3) with high accuracy. It enables key applications such as predictive or prognostic biomarker discovery, T cell characterization, and identification of variable gene polymorphisms. The identification of rare and abundant clones can be achieved with a flexible RNA input amount of 10 ng (minimum) and up to 1 µg. The use of RNA template allows sequencing of productive and relevant variable (V), diversity (D), and joining (J) rearrangements—improving the identification of rare clones.

Note: Information about data analysis using Ion Reporter Software v5.6 can be found in the User Guide below.

Benefits of the Oncomine TCR Beta-LR Assay include:
• Long-read RNA sequencing (up to 400 bp amplicon length) comprehensively covering TCR beta chain
• Detection of clones over a wide dynamic range
• Unbiased output generated from Ion AmpliSeq technology
• Efficient workflow with 48 hr sample-to-results time
• Flexible input requirements ranging from 10 ng to 1 µg
• Compatibility with a variety of research sample types including fresh-frozen tissue, whole blood, and sorted cells
• Streamlined and user-friendly informatics solution with multi-sample analysis functionality

Why are immunologists and immuno-oncologists interested in T cell repertoire sequencing research?
• To characterize diversity and monitor features of T lymphocytes in blood and infiltrated tumors
• To identify variable gene polymorphisms implicated in autoimmune disease or immune-mediated adverse events
• To optimize the manufacture and function of therapeutic or engineered T cells

Unlike other technologies, the Oncomine TCR Beta-LR Assay offers:
• Long-read sequencing, enabling comprehensive coverage of TCR beta chain
• High accuracy and sensitivity through a superior multiplex PCR design
• Use of very low input RNA as a starting material (10 ng)
• High multiplexing and low cost per sample, enabling large-scale studies
• Accelerated discovery cycles through fast turnaround time

The entire workflow (figure below) from isolation of RNA to analysis of samples can be accomplished in two days using the Ion Chef templating system and the Ion S5 or Ion S5 XL sequencing system.

Ion Chef™ Food Protection Instrument (Thermo Scientific™)

Simplify the NGS Food Authenticity Workflow by automating the template preparation and chip loading steps with the Ion Chef™ Food Protection Instrument.

Ion 520™ Food Protection Chip Kit

Simplify sample tracking and sequencing using this Chip Kit as part of a complete Thermo Scientific™ NGS Workflow for Food Authenticity. 

Ion AmpliSeq™ Sample ID Panel (Ion Torrent™)

The Ion AmpliSeq™ Sample ID Panel is a versatile, cost effective, and easy-to-use human SNP genotyping panel comprising 9 specially designed primer pairs that can be added to the multiplex PCR reaction to generate a unique ID during post-sequencing analysis of research samples.

Designed to advance clinical research, the Ion AmpliSeq™ Sample ID Panel helps reveal sample misidentification for increased confidence during data analysis and reporting. The Ion AmpliSeq™ Sample ID Panel can be used in conjunction with any Ion AmpliSeq™ ready-to-use panel or custom panel designed via the Ion AmpliSeq™ Designer (www.ampliseq.com).

Verify Various Sample Combinations:

• Tumor/normal paired samples
• Samples from the same individual in longitudinal studies
• Multi-tissue or multi-tumor samples from the same individual

Sample Identification Through SNP Genetyping

• 8 primer pairs target 8 validated SNPs1
• Selected SNPs are unlinked, non-exonic markers that exhibit exceptional robustness and represent high minor-allele frequency in all human populations
• An additional primer pair targets the amelogenin gene, allowing quick gender determination
• The first letter of the Sample ID code provides instant gender determination for the sample
• Optimal discrimination power (~1:5,000*) with minimal sequencing needed

Simple Workflow—Just One Pipetting Step

• Spike 1 µL of the 20X Sample ID primer pool directly into any Ion AmpliSeq™ primer pool for co-amplification and downstream sequencing and data analysis
• Enabled for use with any Ion Xpress™ barcode
• Compatible with the Ion Reporter™ Software, a cloud-hosted software tool for automated variant analysis

Includes:
20X Ion AmpliSeq™ Sample ID Primer Pool

Required:
Torrent Suite Software (v3.0 or greater) that includes the Ion AmpliSeq™ Sample ID Panel plug-in
Ion AmpliSeq™ Library Kit 2.0 User Guide
Ion AmpliSeq™ ready-to-use panel or custom panel designed via the Ion AmpliSeq™ Designer (www.ampliseq.com)

1Pakstis AJ et al. SNPs for a Universal Individual Identification Panel. Hum Genet. 2010 Mar; 127(3):315-24.
*4641 discrimination power calculations assumes no missing genotyping data

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

The Invitrogen Collibri 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 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 consistent, even coverage of variable GC regions from inputs ranging from 1 to 1,000 ng
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PS DNA Library Prep 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 PS DNA Library Prep Kit consistently offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from a wide range of inputs (1 ng to 1 µg) of physically sheared double-stranded DNA (see figure below). Additionally, a PCR-free version is offered for inputs starting at 500 ng DNA. The entire library preparation protocol takes about 3.5 hours with a PCR 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 PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Oncomine™ BRCA Research Assay, Chef-Ready Library Preparation (Ion Torrent™)

The Oncomine™ BRCA Research Assay consists of two pools of AmpliSeq™ oligonucleotide primers and associated reagents to generate amplicon libraries for next-generation sequencing (NGS) on Ion Torrent™ platforms. The assay is designed to provide sensitive and comprehensive sample amplification of all coding regions of the human BRCA1 and BRCA2 genes. This version of the assay is for automated library preparation using the Ion Chef™ System. For manual library preparation, please see Cat. No. A32840.

Features include:

• Validated for use on Ion 318 and Ion 530 chips
• Detects SNVs, InDels, and large exon/gene deletions/duplications
• Compatible with as little as 10 ng input DNA from formalin-fixed, paraffin-embedded (FFPE) tissue or blood samples
• Highly uniform coverage across all coding exons & splice sites for efficient sequencing and accurate analysis
• Optimized primer design and amplification chemistry enable highly specific target enrichment
• Validated detection of somatic variants to 5% and lower
• Simple and fast workflow produces targeted libraries in 3.5 hours typically

The Oncomine BRCA Research Assay is a complete kit facilitating the amplification of the entire exonic region of both BRCA genes from FFPE tissue or blood samples with as little as 10 ng of input DNA. Leveraging the power of Ion AmpliSeq technology, this highly multiplexed NGS assay enables the generation of results from multiple samples in a single run. Designed for use on either the Ion PGM™ or Ion S5™ sequencing systems, results are delivered in days rather than weeks. The assay is aligned with bioinformatic workflows within Torrent Suite™ and Ion Reporter™ analysis software that utilize optimized variant calling parameters for SNV, InDel, and large exon/gene deletion/duplication detection. Samples can be processed quickly and easily, and variants detected and identified confidently in either germline or somatic DNA analysis pipelines.

BRCA1 and BRCA2 genes are tumor suppressor genes that code for proteins that are vital components of the homologous recombination pathway of DNA damage repair. BRCA mutations resulting in the deficiency of either gene have been shown to result in inefficient activation of this function and are linked to hereditary predisposition to cancer. Errors in the coding sequence of BRCA genes have been detected in germline and somatic mutations and also occur in tumor samples.

Ion AmpliSeq™ CarrierSeq™ ECS Panel (Ion Torrent™)

The Ion AmpliSeq CarrierSeq ECS Panel enables detection of single nucleotide variants (SNVs), insertion/deletions (indels), and copy number variants (CNVs) associated with 418 inherited disorders in a single assay. It is included in the Ion Torrent CarrierSeq ECS kits, which provide all of the reagents and materials necessary for a comprehensive, seamless, and flexible next-generation sequencing (NGS) workflow for expanded carrier screening (ECS). When used with an Ion GeneStudio S5 System, the kits enable a simple, end-to-end workflow for the detection of carrier-positive samples by research labs interested in maximizing the identification of carrier status using genomic DNA isolated from blood or saliva samples.

Benefits of the Ion AmpliSeq CarrierSeq ECS Panel include:
• Targeting of all coding regions and intron/exon boundaries of 420 genes implicated in 418 inherited disorders
• Increased carrier status detection rate through genotyping of SNV, indel, and CNV carrier status by NGS
• Incorporation into a single NGS assay difficult-to-characterize genes due to homology as a result of paralogues (spinal muscular atrophy (SMN1 and SMN2)), pseudogenes (Gaucher disease (GBA and GBAP1)), 21-hydroxylase deficient congenital adrenal hyperplasia (CYP21A2 and CYP21A1P), and loci (alpha-thalassemia (HBA1 and HBA2))

Comprehensive content and consolidated assays
The Ion AmpliSeq CarrierSeq ECS Panel provides comprehensive coverage of common and rare variants to help achieve higher per-disorder detection rate. The panel targets >14,000 amplicons that cover all coding regions of 420 target genes, including intron/exon boundaries, to genotype more than 28,000 SNVs and indels from the ClinVar archive of human variation. The panel also provides robust targeting for CNV analysis to maximize carrier status detection.
vGenetic variants for a number of most prevalent yet serious disorders can be difficult to resolve by NGS assays, and so separate additional stand-alone tests are often required. The Ion AmpliSeq CarrierSeq ECS Panel consolidates such stand-alone assays into a single assay, including difficult-to-sequence genes, such as SMN1 for spinal muscular atrophy, GBA for Gaucher disease, CYP21A2 for 21-hydroxylase deficient congenital adrenal hyperplasia, and HBA1 and HBA2 for alpha thalassemia.