Mar 05, 2020 to our knowledge, we were the first to adapt sureselect hybridisationbased enrichment protocol for the sequencing on the ion torrent s5 platform, which is intended to work preferably with ampliconbased panels f. This chapter describes some procedures and tools used in ion ampliseq designer. Studies comparing the only two library preparation methods, namely, ampliseq and sureselect for ion proton, are, however, so far missing. Thermo fisher scientific launches ion ampliseq hd technology new library preparation solution for targeted nextgeneration sequencing is first to combine gene panel design customization with ultra. The ion ampliseq transcriptome human gene expression kit ampliseq was recently. Manual inspection of all fns on chr 1, 7, 16, 19, and x.
Thermo fisher will continue to sell ion ampliseq chemistry for both ivd and ruo applications to ion torrent ngs customers, and retains the right to make the technology available on other nextgeneration sequencing platforms. The performance of this panel has previously been evaluated for clinical cancer testing by other groups retrospectively on archival16 and clinical trial specimens. Hear scott dewell, product manager for rna applications with the ion torrent group, describe how easy it is to analyze nextgen sequencing data from the ion ampliseq. Evaluation of a new ngs method based on a custom ampliseq. The aims of our study were 1 to compare the performance of ampliseq and sureselect and 2 to develop an optimized protocol for variant calling for wes on ion proton platform. Andy felton, ion torrents head of product marketing, explains how the new ion ampliseq exome kit works. Configurable to a specific human disease area, and ordered in small reaction packs. When using the ion torrent pairedend protocol, the overlapping reads can be merged into highquality single reads in order to improve sequence accuracy. Ion ampliseq dna custom panels enable affordable targeted sequencing for your genomic region of interest. Thermo fisher will continue to sell ion ampliseq chemistry for both ivd and ruo applications to ion.
The touchtools application starter screen lets the operator select the desired protocol with the touch of a button. Each of these reagents has been functionally validated by preparation of a genomic dna library followed by ion torrent sequencing. Ion ampliseq dna custom panels thermo fisher scientific. Additional dilution points may be required for accurate quantification if alternate protocols are employed. Ion ampliseq dna and rna library preparation user guide pn. One of the advantages of ion ampliseq library preparation is thought to be this high assay success rate. Highly multiplexed ampliseq technology identifies novel variation of. A cohort of previously studied 75 cm patients was screened in order to evaluate this strategy in terms of.
Illumina ilmn ties up with thermo fisher for ion ampliseq. Here, we describe several examples of how these white glove initiatives have resulted in technological advances which will expand the repertoire of targeted rna sequencing applications. Determining genotypic drug resistance by ion semiconductor. Adapting sureselect enrichment protocol to the ion torrent s5. If preparing ion ampliseq exome libraries, see the protocols listed on page 7. The ngs library was constructed using the ion ampliseq library kit 2. Communications protocol and ion modbus register map this document explains the modbus protocol on the ion6200 meter.
Pdf use of the ion ampliseq cancer hotspot panel in. A free design tool that helps you obtain custom assay designs based on pcr target selection ion ampliseq designer. Sample preparation and quantification oncomine dx target test. Manual library preparation using the ion ampliseq library kit plus cat. Analysis of ampliseq rnasequencing enrichment panels. Getting started user guide 7 you can also browse predesigned community panels in the same research areas by clicking the predesigned by our community button in the madetoorder. The ion ampliseq library prep application manages sample data for the ion ampliseq library and ion ampliseq hd library preparation workflows. Portable document format pdf versions of this guide and the documents listed above. For representative results of both library construction using nebnext and ion torrent run results, choose the tabs below. A free design tool that helps you obtain custom assay designs based on pcr target selection. Library preparation was done with the ion ampliseq library kit plus life technologies, usa using 100 ng of dna 100 ngl according to the manufacturers protocol. Ion ampliseq library kit 2 thermo fisher scientific.
Amplify target regions from dna or cdna with the ion ampliseq library kit and ion ampliseq readytouse, custom, or community panel. This library kit is compatible with the following instruments. We adapted our ion rna ampliseq primer designer to enable design to multiple. The existence of potentially significant variants was further reassessed through manual inspection of aligned reads in igv 2. Ion ampliseq rna cancer panel was developed as an rna complement to the ion ampliseq cancer hotspot panel v2. Scalable multiplex pcr reactions the ion ampliseq 2. Ion ampliseq dna and rna library preparation user guide. The new ion ampliseq exome kit delivers the best exome sequencing performance in the. Thus, the aim of our study was to evaluate the efficiency of a fast protocol based on custom ampliseq panel and ion pgm sequencer for sequencing most prevalent cmcausing genes myh7, mybpc3, myl2, lmna, scn5a, tnnt2, tnni3 and tpm1. Change product name to hidion ampliseq library kit. Illumina will sell the product directly to its customers under the name ampliseq for illumina. The ion torrent dx cdna synthesis kit and the oncomine dx target test and controls are used to reverse transcribe the quantified rna into cdna. Added support for the ion ampliseq direct ffpe dna kit.
Ampliseq for illumina comprehensive cancer panel, store at 25c to 15c. Designed for individuals preparing ion ampliseq libraries for sequencing on the ion torrent systems. In the select a report format section, select the pdf or text. Ampliseq for illumina is a suite of ampliseq chemistry products that are compatible with illumina nextgeneration sequencing platforms. Get started with ion ampliseq designer welcome to ion ampliseq designer. The accelngs dna library kit designed for the ion torrent platform is the only commerciallyavailable kit capable of producing pcrfree libraries with as little as 5 ng of input dna. Ion reporter ampliseq multiplex pcr ion ampliseq sample id panel simple and accurate sample identification for downstream verification figure 1. Briefly, after amplifying the target region using 12 pools of ion ampliseq primers 24,000 primer pairs totaling to 294,000, we partially digested. Panels can be designed using a number of preloaded reference genomes, or you can upload your own reference sequence for any other organism. This ion ampliseq methylation panel protocol combines a one day bisulfite kit protocol with the one day ion ampliseq library kit plus protocol to create ngs libraries for target dna methylation assessment during sequencing. For ultimate flexibility, the soontobereleased ion ampliseq designer webbased software will enable scientists to upload custom human content for assay designs. Five independent janus protocols are used in the ion ampliseq library preparation workflow.
Pdf in order for nextgeneration sequencing to become widely used as a. The protocol is simple to use and enables high yield and uniformity, reliably and reproducibly. Process extracted dna, rna or ffpe samples through library prep and pooling with the ion torrent ion chef system or manual preparation. The ion ampliseq comprehensive cancer panel provides highly multiplexed target selection of genes implicated in cancer research. Ion ampliseq technology enables scalable, multiplex polymerase chain reactions pcr from 12 to 24,000plex in a single well. One way this can be illustrated is with looking at the reagents each sequencing enrichment kit contains. Comprehensive evaluation of ampliseq transcriptome, a novel. Ion ampliseq library preparation for human identification applications. Easy and robust protocol the ion ampliseq library kit plus uses a platebased format for easier sample handling and tracking, and for compatibility with automation and highthroughput laboratories. Madetoorder ion ampliseq research panels of dna and rna designs for germline or somatic analysis of. Ion ampliseq library prep platform for science marketplace.
Ion ampliseq sample id panel thermo fisher scientific. Apr 07, 2015 one of the advantages of ion ampliseq library preparation is thought to be this high assay success rate. Thermo fisher will continue to sell ion ampliseq chemistry for both ivd and ruo applications to ion torrent. Ampliseq for illumina comprehensive cancer panel contents. The ion ampliseq library kit plus is designed for rapid preparation of amplicon libraries using ion ampliseq panels. Ampliseq for illumina is a targeted resequencing solution that delivers highly accurate data for a wide range of sample types, including ffpe tissue and low sample input. Evaluation of the performance of ampliseq and sureselect. Prepare dna with the ion ampliseq direct ffpe dna kit. On demand ion ampliseq research panels of optimized amplicons for germline analysis. Aug 11, 2015 hear scott dewell, product manager for rna applications with the ion torrent group, describe how easy it is to analyze nextgen sequencing data from the ion ampliseq transcriptome solution. Ion ampliseq library preparation on the ion chef system user.
Easy analysis of ion ampliseq transcriptome data youtube. This can reduce the amount of filtering that is needed and increase the percentage of. How does ampliseq ngs enrichment compare to pillar. Ion torrent semiconductor sequencing is performed on either the personal genome machine pgm or proton instrument depending on desired read length and application. Frontiers evaluation of the performance of ampliseq and. Ampliseq designer and any custom references you have uploaded. The ampliseq for illumina solution offers a highly multiplexed polymerase chain reaction pcrbased workflow for use with targets ranging from a few to hundreds in a single run. The ion ampliseq transcriptome human gene expression kit ampliseq was recently introduced by life. Ion ampliseq rna cancer panel targets 50 oncogenes with detection of key genes kras, braf, and egfr. Ion ampliseq direct ffpe dna kit ion torrent dual barcode kit 196 ioncode barcode adapters 84 kit ion xpress barcode adapters kits ion library equalizer kit ion ampliseq readytouse panels ion ampliseq madetoorder and community panels. See ampliseq for illumina comprehensive cancer panel compatible products for information on compatible products, including index and library prep kits. These amplicons are sequenced on the ion pgm, allowing for rapid turnaround and low cost.
This guide contains everything a firsttime user needs, including an overview of the ampliseq for illumina exome panel protocol, tips and techniques, protocol steps, kit contents, and usersupplied consumables. The ion6200 meter performs modbus rtu communications according to the modicon standard. This panel, with improved primer design, contains 207 primer pairs in a single tube and. Aug 07, 2018 looking through and comparing the steps of the protocol, ion ampliseq has 59 protocol steps, while pillars slimamp has only 34.
The ampliseq for illumina comprehensive cancer panel includes the following reagents. The ion ampliseq library preparation used in this study required only 20 ng dna samples, and the quality of the dna samples did not. Ion ampliseq dna and rna library preparation user guide pub. Ion proton system, ion pgm system, and ion s5 system. Ion ampliseq targeted sequencing technology thermo fisher. The overall illumina ion ampliseq workflow is available as a handy graphic see this reference guide pdf online. Ion ampliseq comprehensive cancer panel facilitates broad oncology surveys using only 40 ng of dna with 16,000 primer pairs multiplexed into just 4 pools. Simply spike any pcr multiplex reaction with 1 l of the panel and continue with the standard ion ampliseq protocol. Ion ampliseq dna and rna library preparation user guide chapter 1 product information procedure overview 1 procedure overview if starting with rna, first reversetranscribe 10 ng to make cdna. Purpose of the guide the ion pi sequencing 200 kit v2 user guide pub.
With emphasis on validation with relevant single molecular pathology tests. Jun 10, 2014 thus, the aim of our study was to evaluate the efficiency of a fast protocol based on custom ampliseq panel and ion pgm sequencer for sequencing most prevalent cmcausing genes myh7, mybpc3, myl2, lmna, scn5a, tnnt2, tnni3 and tpm1. Pdf progress in ion torrent semiconductor chip based. Use of the ion ampliseq cancer hotspot panel in clinical molecular pathology laboratories for analysis of solid tumours. Ion ampliseq ion ampliseq panels how is a protocol started. Man0006735 for detailed instructions, including protocols for 3. Ampliseq panels can accommodate highquality samples such as blood, cell culture, or fresh frozen tissue and also challenging samples such as formalinfixed paraffinembedded ffpe tissue. From predesigned to customizable dna and rna panels for nextgeneration sequencing ngs, all of our content is available within the ion ampliseq designer including indepth descriptions and gene lists for each panel. Nextgeneration sequencing ngs libraries can be prepar. Whole transcriptome sequencing rnaseq represents a powerful approach for whole transcriptome gene expression analysis. Following protocol selection, specific run information including any variable number of.
Clinical application of a custom ampliseq library and ion. These library kits use a platebased protocol for easy sample handling, and for compatibility with automation in high throughput. Ion ampliseq designer home page before you start a panel design or browse predesigned panels, sign in at ampliseq. You can access this calculator either by the navigation bar at the top of the screen, or on individual panel pages.
The panel is a single pool of primers targeting 50 oncogenes and tumor suppressor genes including the kras, braf, and egfr genes. The ion ampliseq cancer hotspot panel v2 is now expanded to allow translational and disease researchers to fasttrack oncology research by surveying hotspot regions of 50 oncogenes and tumor suppressor genes, with wide coverage of the kras, braf, and egfr genes. The ion ampliseq transcriptome human gene expression kit ampliseq was recently introduced by life technologies as a wholetranscriptome, targeted gene quantification kit to overcome these limitations of rnaseq. With low dna input, the panel provides high accuracy, ease of use, and short time to answer. Comprehensive evaluation of ampliseq transcriptome, a. Ion ampliseq library kit plus thermo fisher scientific. Ion ampliseq ngs panels transform genetic research with ultrahighmultiplex pcr primer pools designed for fast and simple production of thousands of targeted amplicons from samples containing as little as 1 ng of input dna, such as formalinfixed, paraffinembedded ffpe and fine needle biopsy fnb research samples. Ion torrent sequencing microarray and sequencing resource. Ion ampliseq hd library kit thermo fisher scientific. Working with key cancer researchers and incorporating information from literature. Ion ampliseq dna and rna library preparation user guide for use with. For rnaseq libraries, the quality of input rna, purification. Looking through and comparing the steps of the protocol, ion ampliseq has 59 protocol steps, while pillars slimamp has only 34.
Processing ion ampliseq cancer panel data using nextgene software introduction the ion ampliseq cancer panel uses highly multiplexed pcr in order to generate amplicons from 46 different cancer genes. Ion ampliseq rna cancer panel thermo fisher scientific. Ion pi sequencing 200 kit v2 kansas state university. Ampliseq for illumina works with dna and rna samples and requires as little as 1 ng of input. The aims of our study were 1 to compare the performance of ampliseq and sureselect and 2 to develop an optimized protocol for variant calling for wes on ion. The detailed protocol was described elsewhere usami et al. Evaluation of the performance of ampliseq and sureselect exome. Progress in ion torrent semiconductor chip based sequencing. Lowdna input protocol and a singleday ion ampliseq workflow. Automation protocol for information about preparing ion ampliseq libraries on the tecan freedom. Jan 15, 2018 illumina ilmn ties up with thermo fisher for ion ampliseq.
Novel cutting edge applications of ion ampliseq rna. Application guide ion ampliseq library preparation on the ngs express perkinelmer 4 introduction the janus ngs express ion ampliseq application is designed for automated preparation of amplicon libraries using ion ampliseq panels and custom primer pools and then sequencing on the ion personal genome machine pgm system. Access codes are used to integrate between all ion torrent software. Get the benefit of a comprehensive, growing menu of content, scalable sequencing platforms and local or cloudbased analysis solutions. Thermo fisher scientific and illumina sign agreement to. Processing ion ampliseq cancer panel data using nextgene.
To assess the performance of this new methodology, we. Ion torrent is a trademark owned bythermo fischer scientific. Ion ampliseq dna and rna library preparation user guide 7. Processing ion ampliseq data using nextgene software v2. Clinical application of a custom ampliseq library and ion torrent pgm sequencing to comprehensive mutation screening for deafness genes. Attendees will benefit by having training in a class environment, handson lab practicals, and interaction with fellow attendees and ion torrent application scientists during lecture, discussion, and lab sessions. Encompassing over 50% of the wellcome trust sanger institute cancer gene census, this is the most comprehensive cancer gene panel available. The ion ampliseq library preparation used in this study required only 20 ng dna samples, and the quality of the dna samples did not affect the sequence results. Application guide ion ampliseq library preparation on the ngs express perkinelmer 5 because there are several points at which the samples can be stored in the process, the overall library preparation was broken down into multiple smaller steps. Lets find out what this new technology can do for you. Library preparation was done with the ion ampliseq library kit plus life. From predesigned to customizable dna and rna panels for nextgeneration sequencing ngs, all of our content is available within the ion ampliseq designer including indepth descriptions and gene lists for. Thermo fisher scientific launches ion ampliseq hd technology. Sample preparation and quantification oncomine dx target.
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