Ion torrent pgm sequencing

Comparison of error correction algorithms for ion torrent pgm data. As in other kinds of ngs, the input dna or rna is fragmented, this time 200bp. By creating a direct connection between chemical and digital information, ion torrent technology will democratize research, providing a fast, simple, scalable sequencing solution that every lab can afford. Adaptors are added and one molecule is placed onto a bead. Includes torrent suite software with all necessary software components to deliver signal processing, base calling, read alignment, and variant calling. Next generation sequencing ion torrent semiconductor sequencing. The ion pgm hiq view sequencing kit is configured to support all of your sequencing needs for applications requiring 200 bp or 400 bp read lengths. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011. Comparison of illumina miseq and the ion torrent pgm and s5. Here we compare the results obtained with those platforms to the performance of the illumina hiseq, the current market. What is the difference between ion torrent and illumina. Includes torrent suite software with all necessary software components to. Ion torrents pgm data had highly biased coverage while sequencing the extremely atrich p. Whole transcriptome sequencing, or rnaseq, for both discovery and gene ex pression analysis.

Next generation sequencing ion torrent semiconductor. When we left off, the final product of the clonal amplification had been prepared ion sphere particles isps covered in single stranded amplicons hopefully all of the same amplicon. Which one would you recommend illumina miseq or ion torrent pgm. Underlying data for sequencing the mitochondrial genome. Here we compare the results obtained with those platforms to the. We first analyzed the uniformity of each mps run and sample. Ion 318 chip v2 bc ion 316 chip v2 bc ion 314 chip v2 bc the ion pgm hi. The dried blood specimens taken during the newborn screening process meet this requirement, making the ion torrent pgm a good future candidate for largescale use in screening. A30044 includes reagents and materials for sequencing up to 400. However, indels at homopolymer regions impacted the 42 accuracy of consensus genome sequences. Pdf quality control of ion torrent sequencing library. Ion pgm system and accessories 4462921 ion pgm torrent server 4483643 ion chip minifuge. Sequencing data were processed by the torrent suite software v4. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the ion torrent pgm platform on the merchant yacht hanse explorer.

Ion torrent semiconductor sequencing is performed on either the personal genome machine pgm or proton instrument depending on. Jul 30, 2012 ion torrent data was slightly more uneven coverage. Ion pgm comes with three chip options for different data output speeds. Evaluation of next generation mtgenome sequencing using the ion torrent personal genome machine pgm. The fastq files were run in nextgenes overlap merger tool and the resulting fasta files were aligned to a genbank. Life technologie ion torrent 508u001 pgm personal genome machinedna sequencing system this unit was used in an active working environment and in working condition prior to removal. Ion semiconductor sequencing may also be referred to as ion torrent sequencing, phmediated sequencing, silicon sequencing, or semiconductor. Which one would you recommend illumina miseq or ion. The ion pgm dx instrument system is intended for targeted sequencing of human genomic dna gdna derived from peripheral wholeblood and dna and rna extracted from formalinfixed, paraffinembedded ffpe samples.

Underlying data for sequencing the mitochondrial genome with. A tale of three next generation sequencing platforms. The ion torrent personal genome machine pgm is a new sequencing platform that substantially differs from other sequencing technologies by measuring ph rather than light to detect polymerisation events. The uniformity of the read number for each mps run was. Jul 17, 2019 nextgeneration sequencing is a powerful tool for virological surveillance. The distribution of the read numbers produced by each sequence run is shown in figure 1. With the ion torrent personal genome machine pgm system, human disease researchers can detect variants by targeted gene sequencing in cancer and. Fast clinical molecular diagnosis of hyperphenylalaninemia. With as little as 10 ng input dna, the new ion 314, 316, and 318 chips yield 99. Christina strobl, a gabriela huber, a bettina zimmermann, a sibylle m. Next generation sequencing ngs refers to a number of different technologies that all sequence relatively short nucleic acid sequences 25 to 600 nucleotides in a parallel, highthroughput manner via sequence by synthesis sbs technologies.

This post we will discuss the technology and process behind the ion torrent sequencing step. While illumina and ion torrent sequencing platforms are used extensively for generating viral rna genome sequences, there is limited data comparing different platforms. Nextflex dna barcodes for ion pgm and ion proton library. In 2011, life sciences released a new sequencer, the ion torrent personal genome machine pgm. Taking advantage of the recent development of benchtop nextgeneration sequencers ngss and of bigsdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of ion torrent personal genome machine pgm sequencing for genomic typing of meningococci. We evaluated the illumina miseq, ion torrent pgm and ion torrent s5 platforms using a panel of sixteen specimens containing picornaviruses and. Jul 22, 2017 illumina amplifies individual library molecules on a solid surface to form polonies ion torrent uses emulsion pcr on beads they were working on another scheme. The ion personal genome machine pgm sequencer then sequentially floods the chip with one nucleotide after another. Life technologies ion torrent personal genome machine 508. Ion torrent semiconductor sequencing combines the simple, integrated wetlab workflow with torrent suite software and thirdparty solutions for fast identification, characterization, and reporting of the most biologically interesting transcripts. The dna sequencing core offers next generation sequencing on the ion torrent pgm using several validated methods. Because we can produce results so quickly and accurately, sequetech is the ideal choice for sequencing small genomes, sets of genes, and amplicon sequencing. Comparing the performance of three nextgen sequencers. When we left off, the final product of the clonal amplification had been prepared ion sphere particles isps.

Q view sequencing kit is designed for use with the ion pgm. Ion torrent semiconductor sequencing technology is as simple as it is fast. Ion torrent nextgeneration sequencing nextgeneration sequencing ngs utilizes massively parallel sequencing to generate thousands of megabases of sequence information per day, opening doors to new research studies that were once difficult to accomplish in a practical manner. Clinical application of a custom ampliseq library and ion. For whole genome sequencing on the ion proton system, the ion pi chip enables the highest throughput with up to 10 gb. Ion torrent pgm sequencing sequetech dna sequencing service. This kit supports the ion 314 chip v2 bc, ion 316 chip v2 bc, and ion 318 chip v2 bc and is compatible with the ion.

The equipment needed for performing an ampliseq for illumina library prep is the same as the equipment needed for performing an ampliseq library experiment on the ion torrent. Personal genome sequencing technology is now faster and. Illumina benchtop sequencing consumables are single cartridgebased with a separate flow cell. Ion pgm torrent server specifications product configuration a single freestanding tower computer appliance, included with the purchase of the ion pgm system. Use the ion genestudio s5 systems combined with invitrogen rna purification and ion torrent library construction kits for identification and quantitation of both known and novel transcripts, including gene fusions and. We believe ion torrent s technology will represent a profound. While illumina and ion torrent sequencing platforms are used extensively for generating viral rna genome sequences, there is limited data. Compared to the hiseq sequencing technology, the ion torrent pgm has two biggest advantages.

If you are going to use ion pgm for 16s rrna sequencing, i would recommend illumina miseq over ion pgm. The ion torrent pgm harnesses the power of semiconductor technology detecting the protons released as nucleotides are incorporated during. The ion pgm bacterial datasets two paired end sequencing datasets from the ion pgm sequencer were provided by life technologies. To compare pgm chips and sequencing kits, mock m1 and m2 and oklahoma amplicons were sequenced on a 314 v2 chip with the ion pgm 400bp kit first and then sequenced on a 318 v2 chip with both the 400bp kit and the ion pgm hiq kit along with the arlington crop rotation samples. The ion torrent method uses the same idea as the small molecule real time sequencing where they sequence at enzymatic rate using the dna polymerase. Transitioning from ion torrent to illumina ngs platforms. For 200 bp sequencing, here is the number of runs that may be saved for these chip types.

Performance comparison of illumina and ion torrent next. These barcodes are compatible with the nextflex dna sequencing kits ion torrent compatible, the nextflex cell free dnaseq kit ion torrent compatible, and other genomic and chipseq dna library prep protocols compatible with the ion torrent pgm, ion proton, ion s5, and ion s5 xl sequencers. Using re sequencing datasets, we comprehensively characterise the biases and errors introduced by the pgm at both the base and flow level. The developers of ion torrent semiconductor sequencing have marketed it as a rapid, compact and economical sequencer that can be utilized in a large number of laboratories as a bench top machine. We have selected the ion torrent pgm for our next generation sequencing platform because of its excellent balance of throughput and turnaround time.

Three possible scenarios for each dna sequence in each nucleotide flow on the ion torrent pgm. Weve finally made it to the sequencing step of the ngs workflow. Ion torrent personal genome machine sequencing for genomic. Jul 24, 2012 next generation sequencing ngs technology has revolutionized genomic and genetic research. The output of the variant caller was presented in tabular format, as a list of differences to the rcrs without a graphical display of the aligned reads. Processing paired end data from the ion pgm sequencer using. Evaluation of next generation mtgenome sequencing using the.

The molecules are amplified on the bead by emulsion. Nextgeneration ion torrent sequencing of drug resistance. Using the ion torrent pgm platform, we sequenced the extended hbv rt region 0 bp in 19 viral samples. Torrent suite assay development software is for research use only, and not for use in diagnostic procedures. In recent years, technological advances have led to the availability of highthroughput, lowcost dna sequencing machines sequencers. Ion torrent sequencing microarray and sequencing resource.

Instead, they exploit the fact that addition of a dntp to a dna. Ion torrent s pgm, pacific biosciences rs and the illumina miseq. If the next nucleotide that floods the chip is not a match, no voltage change will be recorded and no base will be called. The semiconductor will inevitably transform the life sciences, just as it has transformed every other industry it has touched. Quality scores by base position 0 5 10 15 20 25 30 35 40 0 50 100 150 it 316 dh10b miseq dh10b read 1 miseq dh10b read 2 mean quality score base position predicted quality scores at corresponding base positions for dh10b read 1 and read 2 of a 2. Powered by semiconductor chips, ion torrent nextgeneration sequencing technology helps you implement a fast and simple workflow that. I have done sequencing using ion pgm and i found it very hard when it came to analysis. This video gives an overview on ion torrent sequencing, another type of next generational sequencing. The ion torrent pgm was run according to ion torrent 314 chip specifications, including a 65cycle sequencing protocol, use of 18 megaohms purified water, and standard compressed argon gas to drive fluidics through the pgm system. Comparison of illumina miseq and the ion torrent pgm and.

Life technologies now thermofisher expanded their ngs portfolio with the acquisition of ion torrent and their first system, the ion personal genome machine pgm sequencer, in 2010. The molecules are amplified on the bead by emulsion pcr. For whole genome sequencing on the ion proton system, the ion pi chip enables the highest throughput with up to 10 gb reads in 24 hours. All pgm sequences were analyzed with the ion torrent software suite v 4. Ion torrent semiconductor sequencing has the potential to vastly expand the capabilities of human identification laboratories, enabling simultaneous analysis of a wide range of forensically.

Jan 09, 2016 this dna sequencing lecture explains about the ion torrent sequencing technology in details. Ion torrent has pioneered an entirely new approach to sequencing that enables a direct connection between chemical and digital information. Libraries were sequenced on the ion 314 chip with the ion pgm 200 sequencing kit life technologies following the recommended protocol. Ion pgm system for nextgeneration sequencing thermo fisher. We offer two great options for transcriptome analysis. The ion torrent personal genome machine pgm is a smallscale, bench top instrument capable of processing samples for targeted dna and rna sequencing, small rna sequencing, gene expression profiling, microbial genome sequencing, and bacterial and viral typing applications.

Apr 11, 20 all pgm sequences were analyzed with the ion torrent software suite vs. Transcriptome sequencing by ion torrent nextgeneration. The ion pgm hiq view sequencing kit contains reagents and consumables for robust and highly accurate sequencing of 200 and 400 base pair libraries using the ion onetouch 2 system combined with the ion pgm system. Nextgeneration sequencing ngs utilizes massively parallel sequencing to generate thousands of megabases of sequence information per day, opening doors to new research studies that were once difficult to accomplish in a practical manner. Ion pgm system the ph of the nucleotides may be out of range or there may have been a minor problem during measurement.

Ion torrent delivers fast run times and economical sequencing for many applications, including whole genome sequencing of bacteria, viruses and microbial. The pgm us ideal for smaller regions such as gene sequencing, mitochondrial sequencing, bacterial genomes, and gene panels. Press the start button and restart the measurement. 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. While this technology uses a sequencing bysynthesis method and emulsion pcr empcr similar to other platforms, it differs in that it doesnt use fluorescence or. Ion 314 chip v2 ion 316 chip v2 ion 318 chip v2 catalog number 4482006 publication number man0007273 revision 3.

The ion pgm dx instrument system is composed of a sequencing instrument that measures the hydrogen ions generated during the incorporation of nucleotides in the dna sequencing reaction and the ancillary instrumentation necessary for sample processing. Finally, in our study, each ion torrent pgm sequencing specimen required only 20 ng of dna 1. The ion torrent s5 outperformed the older ion torrent pgm 40 platform in data quality and cost, and generated the highest proportion of reads for 41 enterovirus d68 samples. Ion pgm system for nextgeneration sequencing thermo. During the 20 southern line islands research expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. Ion pgm sequencing 200 kit v2 user guide 5 about this guide important. Ion torrent is done with an ion personal genome machine pgm, which was released near the end of 2010. Ngs sequencing supporttroubleshooting thermo fisher. Services microarray and sequencing resource boston university. Small rna library construction for exosomal rna sequencing on the ion torrent pgm and ion s5 system january 4, 2017 leave a comment 5,140 views nextgeneration deep sequencing ngs technology represents a powerful and innovative approach to profile small rna. This is the first sequencer to measure changes in ph rather that emitted light to register sequencing reactions.

Comparison of illumina miseq, ion torrent pgm, 454 gs. Ion semiconductor sequencing is a method of dna sequencing based on the detection of. Jul 05, 2018 this post we will discuss the technology and process behind the ion torrent sequencing step. It adopts ion torrent semiconductor sequencing technology for next it adopts ion torrent semiconductor sequencing technology for nextgeneration sequencing, which does not depend on any optical imaging system at all. The ion pgm system is a reliable sequencing platform that combines simple sample preparation and data analysis. This is type of next generation sequencing technology using ion torrent semiconductor sequencing of dna. Ion pgm sequencing 200 kit v2 for use with the ion personal genome machine pgm system and the following ion pgm chips. Ion torrents first instrument, the ion personal genome machine pgm, is the least expensive next generation sequencer on the market, with a.

Nextgeneration sequencing is a powerful tool for virological surveillance. Ion pgm has accessory equipment that might no longer be needed. We evaluated the illumina miseq, ion torrent pgm and ion torrent s5 platforms using a panel of sixteen specimens. Next generation sequencing ngs technology has revolutionized genomic and genetic research. Evaluation of the ion torrent personal genome machine for.

Furthermore, we employed a bidirectional sequencing strategy on both platforms, using selfassembled pairedend sequencing for the illumina miseq platform and fulllength sequencing of the target from both orientations on the ion torrent pgm platform albeit combining those reads without selfassembly. In reality, the sequencing rate is limited by the cycling of substrate nucleotides through the system. Ion torrents pgm, pacific biosciences rs and the illumina miseq. Dec 17, 2014 this video gives an overview on ion torrent sequencing, another type of next generational sequencing. Unlike illumina and 454, ion torrent and ion proton sequencing do not make use of optical signals. The combination of ion torrent ampliseq target technology, an ion pgm system, and fully automated template preparation from the upcoming ion chef system, offers the simplest and fastest workflow for gene panel sequencing. With the ion torrent personal genome machine pgm system, human disease researchers can detect variants by targeted gene sequencing in cancer and genetic disorders, and microbiologists can easily type a bacteria or virus, or characterize novel microbes. Evaluation of next generation mtgenome sequencing using. Like other next generation sequencing techniques, ion torrent also requires sequence amplification, but it is the first technique that uses electrochemical detection, not camera scanning and fluorescence detection. If there is a reason you cannot reboot the system, you can run the ion pgm system without connection to the server. This dna sequencing lecture explains about the ion torrent sequencing technology in details.