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Ion AmpliSeq™ Cancer Hotspot Panel v2 (Ion Torrent™)

The Ion AmpliSeq™Cancer Hotspot Panel v2 is a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes (download the list of targeted genes and mutations for the Ion AmpliSeq™Cancer Hotspot Panel v2). Building on the mutations included in our original Ion AmpliSeq™Cancer Panel, the latest Ion AmpliSeq™ready-to-use panel provides:
• Maintained compatibility with FFPE samples while expanding mutational content for broader coverage of additional genes and "hot spot" mutations
• Extremely uniform coverage for more efficient sequencing and cost savings
• Enhanced primer design with optimization of new primer sets and even lower strand bias for added confidence in accurate variant calling
• Improved variant detection with Torrent Suite Software v3.0 and Variant Caller Plugin in low allele variant detection along with improved indel sensitivity

Additional Mutational Content for Advancing Cancer Research Studies
The Ion AmpliSeq™Cancer Hotspot Panel v2 is designed to amplify 207 amplicons covering approximately 2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes. This includes the 739 COSMIC mutations from 46 genes in the first Ion AmpliSeq™Cancer Panel along with added hotspot mutations from significant cancer genes. While maintaining our compatibility with FFPE samples and covering the same targets as the first Ion AmpliSeq™Cancer Panel, we have included additional mutations by adding several amplicons for hotspots in EZH2, GNA11, GNAQ, and IDH2, and by adding slightly longer amplicons for other genes to help advance your cancer research. The Ion AmpliSeq™Cancer Hotspot Panel v2 should be used with the Ion AmpliSeq™Library Kit 2.0.

More Efficient and More Cost-effective Sequencing with Extremely Uniform Coverage
The improved primer design in the Ion AmpliSeq™Cancer Hotspot Panel v2 improves upon the coverage uniformity of the Ion AmpliSeq™technology. With coverage that is more uniform, a minimum depth across all amplicons can be achieved using much less sequencing throughput. Consequently, additional samples can be multiplexed using any of the Ion chips. This results in cost savings with more efficient sequencing while maintaining high confidence in variant calling. Additionally, the low strand bias in the primer sets of the Ion AmpliSeq™Cancer Hotspot Panel v2 provides further confidence in accurate variant calling.

Simplicity, Speed, and Scalability of Ion AmpliSeq™Technology
Sustaining the simplicity of the Ion AmpliSeq™technology, the Ion AmpliSeq™Cancer Hotspot Panel v2 enables cancer genetic studies from FFPE tissues with as little as 10 ng of input DNA for targeted library construction. The Ion AmpliSeq™Cancer Hotspot Panel v2 also maintains the revolutionary workflow using standard PCR equipment and a simple PCR reaction for ultra-high multiplex PCR-based target selection, with no need for extensive capital investment. Additionally, the Ion AmpliSeq™Cancer Hotspot Panel v2 continues to enable you to achieve the fastest time to targeted libraries in approximately 3.5 hours. Scalability and flexibility is also preserved with the Ion AmpliSeq™Cancer Hotspot Panel v2, allowing the ability to sequence one sample or multiplex barcoded samples using any of the Ion chips.

Improved Variant Detection with Torrent Suite Software v3.0
The intuitive Torrent Suite Software and Variant Caller Plugin enable you to go from extracted DNA to variant calls in as little as 10 hours. With improvements to algorithms, you will see more sensitive indel detection along with more sensitive SNP detection with lower frequency alleles. Ion Reporter™Software can then be used for annotation of variants in routine DNA assays for the advancement of clinical research.

Ion Ampliseq™ Cancer Hotspot Panel v2 Chef-Ready Kit (Ion Torrent™)

The Ion Ampliseq™ Cancer Hotspot Panel v2 Chef-Ready Kit combines a single pool of primers with the reagents necessary to prepare libraries of frequently mutated regions in human cancer genes on the Ion Chef™ System. This automated workflow utilizes the same chemistry as the manual library construction workflow. It provides equivalent or better performance with exceptional reproducibility, on-target reads, and sample balance. Automated production of libraries using the Ion Chef System reduces hands-on time to less than 15 minutes.

The Ion Ampliseq Cancer Hostpot Panel v2 Chef Ready Kit consists of the following components:
• Ion Ampliseq™ Cancer Hotspot Research Panel Primers
• Ion Ampliseq™ Kit for Chef DL8

The simple sample-to-data workflow can be executed in less than two days and offers the following features and benefits:
• Production of high-quality DNA libraries using the Ion Chef System
• Proven performance of Ion Ampliseq™ technology, FFPE compatibility, uniform coverage for efficient sequencing, accurate variant calling, and improved variant detection via Torrent Suite™ Software
• Ability to scale and multiplex on Ion™ chips based on desired throughput needs, driving cost savings and efficiency
• Simplified workflow and reduced hands-on time when used with the Ion Ampliseq™ Direct FFPE DNA Kit
• Low input amount of only 1 ng per sample

Additional mutational content for advancement of cancer research studies
The Ion AmpliSeq Cancer Hotspot Panel v2 is designed to amplify 207 amplicons covering approximately 2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes. The panel should be used with the Ion AmpliSeq™ Library Kit 2.0.

Minimal hands-on time
Leveraging the automation capabilities of the Ion Chef System, the included Ion AmpliSeq Kit for Chef Kit DL8 enables the reproducible preparation of Ion AmpliSeq amplicon libraries, with less than 15 minutes of hands-on time and only 3 liquid transfer steps. Compatible with 1- and 2-pool Ion AmpliSeq panel designs, the kit automates the preparation of libraries from 8 samples in a single run, delivering a single tube of pooled libraries ready for downstream templating and sequencing. The kit provides sufficient material for the preparation of 32 libraries.

Simplicity and ease-of-use of Ion solutions
Utilizing plug and play, pre-packaged, single-use cartridges and PCR plates for a fully automated workflow, users of all experience levels will find library preparation straightforward with minimal effort. Supplied with barcodes conveniently dried-down in 96-well plates, multiplexing samples is easy and requires no additional pipetting steps.

Ion AmpliSeq™ Comprehensive Cancer Panel (Ion Torrent™)

The Ion AmpliSeq™ Comprehensive Cancer Panel provides highly multiplexed target selection of genes implicated in cancer research. Encompassing over 50% of the Wellcome Trust Sanger Institute Cancer Gene Census, this is the most comprehensive cancer gene panel available. With all-exon coverage of 409 genes, the Ion AmpliSeq™ Comprehensive Cancer Panel delivers fast, FFPE-compatible, target selection for a broad survey of key genes for semiconductor sequencing. View the Ion AmpliSeq™ Comprehensive Cancer Panel list of target genes (PDF).

The Ion AmpliSeq™ technology allows ultra-high multiplex PCR combined with targeted sequencing library construction in just 16 hours for over 400 genes. Utilizing only 10 ng of input DNA per primer pool for a total of 40 ng of input DNA, analysis of restricted samples like FFPE samples is possible. The Ion AmpliSeq™ Comprehensive Cancer Panel is optimized for library construction with the Ion AmpliSeq™ Library Kit 2.0. Libraries are then ready for template preparation on the Ion OneTouch™ System and sequencing on the Ion PGM™ Sequencer. The Ion AmpliSeq™ Comprehensive Cancer Panel is not compatible with Ion Ampliseq™ 2.0 Beta Kits.

Features and Benefits:

• Broad survey of 409 key genes in a simple PCR reaction, no additional capital equipment required
• Unmatched plexy of 16,000 primer pairs in only four pools with Ion AmpliSeq™ technology
• Low DNA input of only 40 ng DNA and short amplicons enable FFPE samples and needle biopsies
• Start comprehensive genomic studies quickly with pre-designed primer pools
• Simplify analysis and annotation of variants with Ion Reporter™ software

Comprehensive Gene Content Including Genes from Hotspot Panel
Ion Torrent has designed the most extensive cancer panel available for sequencing with Ion PGM™ and, soon, Ion Proton™ Sequencers. Working with key cancer researchers and reviewing literature and databases, the Ion AmpliSeq™ Comprehensive Cancer Panel was designed to target all exons of key tumor suppressor genes and oncogenes most frequently cited and most frequently mutated. Strategically designed to interrogate CDS and splice variants across multiple gene families simultaneously, pathway-based gene selection profiles mutational spectrum in cancer driver genes and drug targets, along with signaling cascades, apoptosis, DNA repair, transcription regulators, inflammatory response, and growth factor genes in a single assay. Additionally, all genes from the focused Ion AmpliSeq™ Cancer Panel are included in the Ion AmpliSeq™ Comprehensive Cancer Panel providing corresponding complementary data.

Unmatched Level of Multiplex PCR
The Ion AmpliSeq™ Comprehensive Cancer Panel is comprised of four primer pools totaling almost 16,000 primer pairs covering 409 genes-that's approximately 4,000 primer pairs in each pool! Used in conjunction with the Ion AmpliSeq™ Library Kit 2.0, the Ion AmpliSeq™ Comprehensive Cancer Panel maintains high uniformity and specificity at this high plexy, advancing multiplex PCR to new levels.

Over 400 Genes, Only 40 ng DNA Required
While other target selection methods typically require micrograms of DNA input, the Ion AmpliSeq™ Comprehensive Cancer Panel uses only 40 ng DNA. This breakthrough in low DNA input requirement enables the interrogation of restricted samples like formalin-fixed, paraffin-embedded samples (FFPE) and fine needle aspiration biopsies (FNAB). Additionally, shorter amplicon design (average 155 bp) allows for compatibility with degraded samples.

Simplified Target Selection Without Primer Design
With pre-designed primers in the Ion AmpliSeq™ Comprehensive Cancer Panel, researchers can bypass gene selection, primer design, and optimization, and advance straight to generating results for a broad survey of hundreds of genes in key research samples. To further focus your cancer research, you may choose to conduct in-depth somatic variant analysis on a subset of genes or specific cancer subtype. Using Ion AmpliSeq™ Designer, researchers can simply add or subtract genes from this panel to create your own custom panel. The flexibility and scalability of Ion AmpliSeq™ Solutions spans across the Ion AmpliSeq™ Ready-to-use Panels and Ion AmpliSeq™ Custom Panels.

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

Ion AmpliSeq™ Kit for Chef DL8 (Ion Torrent™)

The Ion AmpliSeq™ Kit for Chef DL8 is designed for use with the Ion Chef™ System for automation of Ion AmpliSeq library construction. The kit offers:

• Simplest workflow for targeted sequencing library preparation using 1 or 2 pool Ion AmpliSeq panel designs*
• Low input
• Easy-to-use cartridge format with reagent barcoding for full reagent tracking
• Proven performance of Ion AmpliSeq technology, compatible with DNA extracted from formalin-fixed, paraffin-embedded tissue and other challenging sources

*See www.AmpliSeq.com for custom 1-2 pool panels. Note that some panels (e.g., Transcriptome, Cancer Hotspot, Oncomine BRCA, Pharmacogenomics) have been prepared in an Ion Chef-ready kit by incorporating the respective ready-made primer pool with the DL8 kit.

Leveraging the automation capabilities of the Ion Chef System, the Ion AmpliSeq Kit for Chef DL8 enables the reproducible preparation of Ion AmpliSeq amplicon libraries, with less than 15 minutes of hands-on time and only 3 liquid transfer steps. Compatible with 1- and 2-pool Ion AmpliSeq panel designs, the kit automates the preparation of libraries from 8 samples in a single run, delivering a single tube of pooled libraries ready for downstream templating and sequencing. The kit provides sufficient material for the preparation of 32 libraries (4 Ion Chef runs).

Utilizing plug and play, pre-packaged, single-use cartridges and PCR plates for a fully automated workflow, users of all experience levels will find library preparation straightforward with minimal effort. Supplied with barcodes conveniently dried-down in 96-well plates, multiplexing samples is easy and requires no additional pipetting steps.

More information on Ion AmpliSeq technology >

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.

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 >

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 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 AmpliSeq™ Direct FFPE DNA Kit (Ion Torrent™)

The Ion AmpliSeq™ Direct FFPE DNA Kit enables the preparation of DNA from formalin-fixed, paraffin-embedded (FFPE) tissues for library construction using the Ion AmpliSeq protocol, without the need for deparaffinization or DNA purification. This kit is suitable for FFPE tissue sections up to 10 µm thick.

Features of the Ion AmpliSeq Direct FFPE DNA Kit include:
• Simple one-tube 2-step protocol that minimizes sample loss
• Efficient 30-minute workflow with only 10 minutes of hands-on time
• Ideal for FFPE DNA samples with limited DNA amount
• No deparaffinization of FFPE sections required
• No column or bead-based DNA purification required
• Ion AmpliSeq library preparation with as little as 1 ng input DNA
• Uracil-D-glycosylase treatment to remove deaminated cytosines is an optional step

Extraction of DNA from samples with limited DNA amount
Archived tissue samples can provide clinically relevant information, but it can be difficult to isolate the small amount of nucleic acid they contain. Deparaffinization of FFPE tissue sections and purification of the DNA in these samples can be a complicated, multi-step procedure requiring considerable hands-on time, and the associated sample-loss makes it an unsuitable approach for processing FFPE DNA samples with limited DNA amounts.

A simpler and faster method
The Ion AmpliSeq Direct FFPE DNA Kit provides a user-friendly protocol that eliminates the need for deparaffinization of FFPE tissue sections and purification of the DNA. From an FFPE section mounted on a glass slide, the area of interest is removed using Transfer Solution and pipetted into a PCR tube or 96-well plate. After the addition of Direct Reagent, the sample is incubated at 65°C for 15 minutes. The FFPE DNA is now ready for the Ion AmpliSeq™ Library Preparation protocol. The prepared FFPE DNA can be quantified using the Qubit™ HS DNA Quantitation Kit, if necessary. The simplicity of this protocol eliminates the need for complicated deparaffinization and DNA extraction procedures, and libraries can be prepared either manually or with the automated Ion Chef™ System.

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 eight libraries per Ion 540 or Ion PI Chip. Other multiplexing options are also possible, depending on the experimental design and desired level of sensitivity.

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.