Ion pi ot2 200 kit

Manufactured by Thermo Fisher Scientific

The Ion PI OT2 200 Kit is a laboratory equipment product designed for use in scientific and research applications. It provides the core functionality for Ion Torrent sequencing workflows. The kit includes essential components required for sample preparation and Ion PI Chip loading. Detailed product specifications and intended use cases are not provided in this response.

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Lab products found in correlation

Ion onetouch 2 system, by Thermo Fisher Scientific (2 mentions) Ion ampliseq cancer hotspot panel v2, by Thermo Fisher Scientific (1 mentions) Ion proton, by Thermo Fisher Scientific (1 mentions) Ion 318 chip, by Thermo Fisher Scientific (1 mentions) Ion ampliseq cancer panel, by Thermo Fisher Scientific (1 mentions) Ion p1 chip, by Thermo Fisher Scientific (1 mentions) Ion pgm template ot2 200 kit, by Thermo Fisher Scientific (1 mentions)

3 protocols using ion pi ot2 200 kit

Targeted Cancer Hotspot Sequencing

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Sequencing libraries were prepared with the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies) using the Ion AmpliSeq Library Preparation protocol with 3-5ng of DNA, according to manufacturer’s instructions. Following barcoding, libraries were quantified using qPCR and diluted to 100 pM. Libraries were templated with the Ion OneTouch2 system (Life Technologies) and sequenced on a PI chip using the Ion PI OT2 200 Kit (Life Technologies), 520 flows and an average amplicon length of 112 bases to a mean depth of x2721307. The sequencing resulted in 45272–11767856 reads per sample.
Ion torrent Variant caller v4.0-r73742 with no Hotspot region and configuration “Germ Line Low Stringency” was used for calling variants. Read counts for all positions were computed using pileup (SAMtools v1.1 [12 (link)]) and this data was analysed for possible variants using custom Perl and R scripts. Variants at > 3% reported by both analysis methods and not reported in 1000 Genomes Project database (www.1000genomes.org) were identified as possible somatic mutations. The data was cross referenced against the Cosmic database v70 (cancer.sanger.ac.uk) to identify possible hotspot mutations.

Pender A., Garcia-Murillas I., Rana S., Cutts R.J., Kelly G., Fenwick K., Kozarewa I., Gonzalez de Castro D., Bhosle J., O’Brien M., Turner N.C., Popat S, & Downward J. (2015). Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach. PLoS ONE, 10(9), e0139074.

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Targeted Sequencing of Circulating Breast Cancer Mutations

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Sequencing libraries were prepared with a custom Ion AmpliSeq Breast Cancer Panel targeting 14 known breast cancer driver and focal mutations (table S3) using the Ion AmpliSeq Library Preparation protocol with 3 ng of cfDNA, according to manufacturer's instructions. After barcoding, libraries were quantified using qPCR, diluted to 100 pM, and pooled. Libraries were templated with the Ion OneTouch2 system (Life Technologies), and sequenced on a PI chip using the Ion PI OT2 200 Kit (Life Technologies), 520 flows, and an average amplicon length of 97 bases to a mean depth of x9183. The sequencing resulted in 1042543-5763164 reads per sample.
Ion torrent Variant caller v4.0-r73742 with no Hotspot region and configuration “Germ Line Low Stringency” was used for calling variants. Read counts for all positions were computed using pileup (samtools v1.1(21 (link))) and this data was analysed for possible variants using custom perl and R scripts. Variants at > 3% reported by both analysis methods and not reported in 1000 Genomes Project database (www.1000genomes.org) were identified as possible somatic mutations. The data was cross referenced against the Cosmic database v70 (cancer.sanger.ac.uk) to identify possible hotspot mutations Variants not appearing in the 1000 genomes database were taken forward for development of digital PCR assays.

Schiavon G., Hrebien S., Garcia-Murillas I., Cutts R.J., Pearson A., Tarazona N., Fenwick K., Kozarewa I., Lopez-Knowles E., Ribas R., Nerurkar A., Osin P., Chandarlapaty S., Martin L.A., Dowsett M., Smith I.E, & Turner N.C. (2015). Analysis of ESR1 mutation in circulating tumor DNA demonstrates evolution during therapy for metastatic breast cancer. Science translational medicine, 7(313), 313ra182.

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Comprehensive Variant Detection in Oncology

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DNA sequencing was performed using the Ion AmpliSeq™ Cancer Panel (Ion Torrent, Life Technologies, Fisher Scientific) according to the manufacturer's instructions. Briefly, 10 ng of DNA was amplified by PCR using the AmpliSeq™ Cancer Panel Primers pool and Ion AmpliSeq™ Master Mix v2.0. Multiplexed barcoded libraries were enriched by clonal amplification using emulsion PCR on Ion Sphere™ particles (ISPs) (Ion PGM™ Template OT2 200 Kit or Ion PI OT2 200 kit v3) and loaded on an Ion 318™ Chip or Ion P1 Chip (Life Technologies). Massively parallel sequencing was carried out on a Personal Genome Machine™ Sequencer or Ion Proton (Life Technologies, Fisher Scientific). The raw signal data were analyzed using Torrent Suite (version 4.0.1) to generate BAM files after signal processing, base calling adapter trimming and alignment to the reference human genome (hg19). Variants were called with Torrent Suite Variant Caller, and were further analyzed using an internally created software suite. Analysis of copy number variations (CNVs) was performed as previously reported [37 (link)].
Sequencing for mutations and CNVs was performed on all cases with discordant results between ALK FISH and NGS gene fusion.

Dacic S., Villaruz L.C., Abberbock S., Mahaffey A., Incharoen P, & Nikiforova M.N. (2016). ALK FISH patterns and the detection of ALK fusions by next generation sequencing in lung adenocarcinoma. Oncotarget, 7(50), 82943-82952.

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