Ion proton sequencer pdf

Optimized data analysis workflows have been developed for genome sequencing, targeted rna and dna. Dec 19, 2012 a launch video for ion torrents ion proton sequencer. It is equipped with ion reporter software, providing integrated tools for tertiary data analysis for dna variation analysis across single, paired, or trio research samples. Ion proton sequencer decodes dna fast and on the cheap. This hydrogen ion carries a charge that the proton systems ion sensoressentially the worlds smallest solidstate ph metercan detect. Ion semiconductor sequencing is a method of dna sequencing based on the detection of. Given its output capability currently up to 1gb and speed of runs 2 hours, it is being targeted towards.

Ion torrent has developed a benchtop research semiconductor sequencer, the ion proton, that uses a novel cmos chip with 165 million 1. Spin creative shot on location in san francisco with the arri alexa to. It enables researchers access to proven, high quality target enrichment technology. Evaluation of exome variants using the ion proton platform. Ion torrent has pioneered an entirely new approach to sequencing that enables a direct connection between chemical and digital information. The htsfs ion proton sequencer provide excellent sequencing by synthesis capabilities, yielding data quickly and affordably. Ion torrent proton sequencing nevada genomics center. Life technologies introduces the benchtop ion proton. The ion proton sequencer from thermo fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. Ion semiconductor sequencing is a method of dna sequencing based on the detection of hydrogen ions that are released during the polymerization of dna. The molecules are amplified on the bead by emulsion pcr. We evaluated the illumina miseq, ion torrent pgm and ion torrent s5 platforms using a panel of sixteen specimens containing picornaviruses and.

Here, we developed a protocol and adapters for double. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. Introducing the ion proton sequencer the benchtop genome center 21 the content provided herein may relate to products that have not been officially released and is subject to change without notice. Sureselect target enrichment system kit for sequencing on ion proton 5. Since that dramatic announcement in the summer of 2011, life technologies and ion. Technically speaking, this phbased method is called ion semiconductor sequencing. Agilents sureselect ion proton is a target enrichment solution for the ion proton ngs system. What are possible reasons of low quality reads on ion. Ion torrent sequencing microarray and sequencing resource. Sequence reads are processed in the torrent server and a simple file is exported to common genomics data analysis. Nextgeneration sequencing is a powerful tool for virological surveillance. This is a method of sequencing by synthesis, during which a complementary strand is built based on the sequence of a template strand.

Rapid, accurate, and inexpensive sequencing of exomes is critical to understand dna variation in human disease. Frontiers evaluation of the performance of ampliseq and. Ion pgm sequencer, the ion proton sequencer will put wholegenome sequencing within the reach of. In this study, we compared ion pgm and ion proton, with a new ion s5xl ngs system for workflow scalability, analytical.

If a nucleotide joins up with the sample, a hydrogen ion is released, so these sensors monitor the acidity of the solution for changes. Ten barcoded libraries were pooled together on an equimolar basis and run using three piv3 chips on an ion torrent proton using hiq chemistry. Ion proton system for nextgeneration sequencing thermo. The ion pi sequencing 200 kit v2 includes reagents and materials for sequencing up to 200. New highthroughput chips will enable a human genome to be sequenced in a singleday workflow. We also extend previous findings on the validity of ion proton sequencing using ampliseq by evaluating different target regions, coverage ranges 44x to 270x using wet lab sequencing and by manually inspecting all false negative fn and fp variants on chromosome chr. Use the following workflow to perform sequencing runs with the ion proton system. Chapter 2, create a planned run q chapter 3, clean and initialize the ion proton sequencer clean the ion proton sequencer on page 21 q initialize the ion proton sequencer on page 24 q. Unlike illumina and 454, ion torrent and ion proton sequencing do not make use of optical signals.

Software updates through the networkinternet are free. A26433 or for use with ion chef system sequencing reagents are provided as part of the ion pi hiq chef kit ion pi chip kit v3 bc, 8pack cat. The ion s5 sequencer or the torrent server should be connected to a network with internet access. Joe boland discusses 12 gb runs on the ion proton sequencer and moving toward 15 gb duration. To our knowledge, this is the first study systematically comparing the performances of ampliseq and sureselect on ion proton. Previous studies compared running cost, time and other performance measures of popular sequencing platforms. And sequencer, well, thats just what the machine is a sequencer. See the fc1 cycler appendix in this manual for more detailed instructions. Ion proton reads prepared by all the 2ug libraries is further summarized in table 2. Comparison of illumina miseq and the ion torrent pgm and. Ion proton next generation sequencing, sureselect ion proton. As the sequencer floods the chip with one nucleotide after another, any nucleotide added to a dna template will be detected as a voltage change, and the ion proton system will call the base. The system combines semiconductor sequencing technology with biochemistry to directly translate chemical information into digital data. Unlike the sanger 3730 sequencing data that we back up and store on the server, the data from a proton sequencing run cannot be backed up here at ngc.

Semiconductor based next generation platforms varied from low throughput ion pgm to high throughput ion proton and ion s5xl sequencer. While illumina and ion torrent sequencing platforms are used extensively for generating viral rna genome sequences, there is limited data comparing different platforms. The system combines semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. An optimized protocol for generation and analysis of ion. Q sequencing 200 kit must be used with the ion pi hi. Spearheading life technologies new holistic visual design language is ion proton, powered by innovative semiconductor chip technology, it is the first benchtop nextgeneration sequencer to offer fast and affordable human genome and human exome decoding. Ion torrents ion 314 semiconductor sequencing chip will ini tially generate at least 100,000 reads per run with an average length of 100 base pairs. Ion proton sequencer used for an asthma biomarker project duration. I prepare samples for rnaseq using ion proton semiconductor sequencer. Be sure to update your system software before using. When sequencing, a continuous flow of nucleotides go through the chip micro pores. Pdf progress in ion torrent semiconductor chip based. Background next generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. With chip densities up to 1,000fold greater than the ion pgm sequencer, the ion proton sequencer will put wholegenome sequencing within the reach of any lab.

Biz model for ion proton dna sequencer linkedin slideshare. Ion pi sequencing 200 kit v2 kansas state university. The ion proton sequencer is a next generation sequencer based on semiconductor sequencing technology. With chip densities up to 1,000fold greater than the. Semiconductor sequencing of human exomes on the ion proton system. A comparison of illumina and ion torrent sequencing.

Nextgeneration sequencing technologies and their application to. Arctic charr salvelinus alpinus, european whitefish coregonus. Page 2 the information in this guide is subject to change without notice. Versatile ion s5xl sequencer for targeted next generation.

The ion proton system combined with ion targetseq technology delivers fast, flexible, and highquality exome. Ion proton system includes ion proton sequencer and ion proton torrent server 4476610 additional equipment ion chef instrument 4484177 ion onetouch 2 system 4474779 ion reporter server system 4487118 ion torrent storage 20t 7 x 4 tb drives, 20 tb usable storage 4488124 ion torrent storage 40t 12 x 4 tb drives, 40 tb usable. The proportion of proton reads that could be mapped to the reference human transcriptome was small by bwa 49. This speeds up the process considerably and removes the. Connecting to the internet allows you to easily update your software and access remote system support. Jun 16, 2016 when a base is stretched by a dna chain, a proton is released, resulting in a local ph change. Ion semiconductor sequencing may also be referred to as ion torrent sequencing, phmediated sequencing. The surface of each micro hole in the ion torrent semiconductor sequencing chip contains about 1 million dna molecules. Page 1 user guide ion torrent s5 and ion torrent s5 sequencer catalog numbers a27211, a272 publication number man0010811 revision a. Library preparation 1 day emulsion pcr 1 day sequencing 0. The diffusion of next generation sequencing ngs technologies induces an important. The company that builds the ion proton chip that goes into the ion proton sequencer pictured down south is due at the earliest in mid2012 is called ion torrent.

However, misleading variantcalling errors can occur. The device can sequence an entire human genome in less than a day. Discover how you can benefit from superior targeting performance and faster time to results. A launch video for ion torrents ion proton sequencer. Ion proton system ion pi chip v3 catalog number a26433 and a26772 publication number man0010947. Built for speed, the ion proton system provides fast sequencing run times, taking you from dna to variants in a single day.

The optimal ion proton sequencing options and analysis software have been evaluated. However, comprehensive assessment of library construction and analysis protocols for proton sequencing platform remains unexplored. I can generally assess cdna libraries construction and chip loading, but i know little about bioinformatics, and all the. The ion proton system is the first benchtop sequencing system capable of humanscale genome, exome, or transcriptome sequencing in a few hourswith dnatovariants called in a single day. Access array system for the ion torrent pgm sequencing. The ion proton sequencer and ion reporter analysis software are designed to analyze a single genome in one day on a standalone server eliminating the informatics bottleneck and high. This guide uses an optimized protocol for ion xpress plus fragment library preparation. Technology comparison detection of ion release is simpler and faster than optical method from 454 sequencing and illumina ion proton uses semiconductor, thus is able to improve at a high rate in the future 314 chip 316 chip 318 chip proton 1 proton 2 1. We performed a systematic evaluation and manual curation of readlevel alignments for the 675 ultrarare variants reported by the ion proton.

Ion proton sequencer delivers an entire human genome in 24. Ion pgm ion proton 520 530 540 8 mln 1520 mln 90 mln 400 bp 400 bp 200 bp 1 gb 5 gb 10 gb 90 mln 200 bp. The data files generated in proton sequencing are large and thus not accessible through the dnatools server. As in other kinds of ngs, the input dna or rna is fragmented, this time 200bp. Gpuaccelerated primary analysis pipeline in ion proton dna. Conclusions the ion proton system removes the high cost and complexity of genomescale sequenc ing and enables exome sequencing using the ion pi chip and higher exome multiplexing or human genomescale sequencing with the ion pii chip. Validation and optimization of the ion torrent s5 xl sequencer and. However, the most important factor in reducing the sequencing speed so dramatically is the introduction of the next generation.

Pdf in order for nextgeneration sequencing to become widely used as a diagnostic in the healthcare industry, sequencing instrumentation will need to. The chip is where the power of the proton machine really resides. Ion torrent main applications microbial and metagenomic sequencing targeted re sequencing gene panels clinical sequencing chip yield run time read length 314, 316, 318 pgm 0. Putting the proton to work how the ion proton sequencer. Illumina miseq, ion torrent pgm puis ion proton life. This speeds up the process considerably and removes the itrelated bottlenecks. The ion torrent proton sequencer is a largerscale instrument than the personal genome machine, and is capable of processing samples for all applications supported by the pgm in addition to whole transcriptome and exome sequencing.

Access array barcode library for ion torrent pgm sequencer96 fluidigm, pn 100. Aug 10, 2017 though illumina has largely dominated the rnaseq field, the simultaneous availability of ion torrent has left scientists wondering which platform is most effective for differential gene expression dge analysis. Ion proton system includes ion proton sequencer and ion proton torrent server 4476610 additional equipment ion chef instrument 4484177 ion onetouch 2 system 4474779 ion reporter server system 4487118 ion torrent storage 20t 7 x 4 tb drives, 20 tb usable storage 4488124. Adaptors are added and one molecule is placed onto a bead. The htsfs ion proton sequencer provide excellent sequencing by synthesis capabilities, yielding data quickly and affordably the 2. Ion pi sequencing 200 kit v3 thermo fisher scientific.

Gpuaccelerated primary analysis pipeline in ion proton. The hidion pgm system combines semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. The proton ii chip is slated to have 660 million sensors. Emulsion pcr was performed using the one touch system life technologies. A comparison of illumina and ion torrent sequencing platforms. Figure 2 ion s5 sequencer configuration 1 ion s5 sequencer 2 ion template preparation instrument ion chef instrument shown or ion onetouch 2 system 3 local area network 4 internet 5 client computer internet connectivity the ion s5 sequencer or the torrent server should be connected to a network with internet access. Ion proton onetouch system ion kits ion proton sequencer proton torrent server the content provided herein may relate to products that have not been. Data analysis, which has long been a bottleneck for wholegenome sequencing, can also be completed in the same day on a single standalone server.

It was designed to introduce a gamechanger through a. Rnaseq data alignment and normalization we aligned fastq files from both platforms using star v2. Ion pgm sequencer, the ion proton sequencer will put wholegenome. This eliminates the need for expensive optics and complex sequencing chemistries, resulting in a sequencing system that is highlyaffordable. Ion proton in september 2012 ion torrent launched their follow on system, the ion proton, which allows for larger chips with higher densities needed for exome and whole genome sequencing. Sureselect target enrichment system for sequencing on ion proton. We sequenced thirteen genomic libraries of three different nonmodel vertebrate species on ion proton with pi chips. Semiconductor sequencing of human exomes on the ion proton. Ion proton next generation sequencing, sureselect ion. If you choose not to connect your instrument or server to a. Ion proton sequencer delivers an entire human genome. Sureselect target enrichment system for sequencing on ion. Ion comes from ion torrent, the name of the brand owned by life technologies that makes this device.