One touch instrument

Manufactured by Thermo Fisher Scientific

Sourced in United States

The One-Touch Instrument is a versatile laboratory equipment designed for efficient and user-friendly operation. It features a simple one-touch interface for seamless control and ease of use. The core function of the instrument is to provide reliable performance in various laboratory settings.

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7 protocols using one touch instrument

Ion Torrent Targeted Sequencing of Tumor Samples

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gDNA from the 11 tumor samples were amplified using the Ion AmpliSeq™ Library Kit 2.0 (ThermoFisher Scientific) starting from 30 ng of gDNA, barcoding each sample following the manufacturer’s instructions. Cycling conditions were performed according to the DNA type and primer pairs per pool: 23 cycles with an extension time of 4 min in the first multiplex PCR, whereas in the second, optional PCR, the gDNA were subjected to five cycles. The library size was checked using the Agilent High Sensitivity DNA Kit by the Bioanalyzer 2100 instrument (Agilent Technologies), and library concentration was evaluated with a Qubit® 2.0 Fluorometer using the Agilent High Sensitivity DNA Kit (Life Technologies). Each diluted library (100 pM) was amplified through emulsion PCR using the OneTouch™ Instrument (ThermoFisher Scientific) and enriched by the OneTouch™ ES Instrument (ThermoFisher Scientific) using the Ion PGM™ Hi-Q™ View OT2 Kit, following the manufacturer’s instructions. Finally, sequencing was performed on the Ion PGM™ (ThermoFisher Scientific) with the Ion PGM™ Hi-Q™ View Sequencing Kit (ThermoFisher Scientific), loading barcoded samples into a 316v.2 chip.

Vanni I., Casula M., Pastorino L., Manca A., Dalmasso B., Andreotti V., Pisano M., Colombino M., Pfeffer U., Tanda E.T., Rozzo C., Paliogiannis P., Cossu A., Ghiorzo P, & Palmieri G. (2020). Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI). Diagnostic Pathology, 15, 143.

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TP53 Mutation Screening in ESCC

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For mutation screening of ESCC samples, five pairs of tumor tissues and corresponding PBMCs were subjected to amplicon sequencing using an Ion AmpliSeq™ TP53 Panel, which covers all coding exons of the TP53 gene with 24 amplicons, according to the manufacturer's protocol (Thermo Fisher Scientific).
Approximately 20 ng DNA per sample was used to prepare barcoded libraries with IonXpress barcoded adapters and the Ion AmpliSeq Library Kit 2.0 (Thermo Fisher Scientific). Ten individual barcoded libraries (100 pM each) were pooled and clonally amplified through emulsion PCR using the One Touch Instrument and the Ion PGM Template OT2 200 kit (Thermo Fisher Scientific). Finally, the sequencing of templates was performed on a PGM 316 chip using the Ion PGM 200 Sequencing Kit v2 according to the manufacturer's instructions (200 bp read length, Thermo Fisher Scientific).

Endo F., Iwaya T., Sasaki Y., Chiba T., Yaegashi M., Kume K., Sato K., Arisue A., Kawagishi R., Matuo T., Akiyama Y., Sasaki A., Suzuki Y., Tokino T., Masuda M., Yamada T., Nakagawa H., & Nishizuka S. (2020). Circulating-tumor DNA from Two Types of Blood Collection Tubes for Monitoring Tumor Burden Validated with Esophageal Squamous Cell Carcinoma Patients.

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Ion Amplicon Sequencing of FFPE Samples

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Overall, up to 10 ng of gDNA was extracted from FFPE samples and amplified using the Ion AmpliSeq Library Kit 2.0 (Life Technologies, Carlsbad, CA) over 20 cycles, with barcoding for each sample. The library concentration was evaluated using QuantStudio Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA). Each diluted library (100 pM) was amplified by emulsion PCR using the One-Touch Instrument (Life Technologies) and was enriched by the OneTouch ES Instrument (Life Technologies) using the Ion PI Hi-Q OT2 200 kit following the manufacturer’s instructions. Finally, sequencing was performed on an Ion Proton instrument (Life Technologies) using an Ion PI Hi-Q Sequencing 200 Kit (Life Technologies). Barcoded samples were loaded onto an Ion PI Chip v3. Sequencing, read mapping, and variant calling were performed with Ion Torrent Suite v5.0.4.0. The ICP genes are shown in S1 Table.

Choi J.Y., Choi S., Lee M., Park Y.S., Sung J.S., Chang W.J., Kim J.W., Choi Y.J., Kim J., Kim D.S., Lee S.H., Seok J., Park K.H., Kim S.H, & Kim Y.H. (2020). Clinical Implication of Concordant or Discordant Genomic Profiling between Primary and Matched Metastatic Tissues in Patients with Colorectal Cancer. Cancer Research and Treatment : Official Journal of Korean Cancer Association, 52(3), 764-778.

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Comprehensive cfDNA/gDNA Sequencing Protocol

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Overall, up to 10 ng of cfDNA and gDNA was extracted from serum, FFPE, and buffy coat and amplified using the Ion AmpliSeq™ Library Kit 2.0 (Life Technologies, Carlsbad, CA), with barcoding of each sample. Twenty cycles were performed. Library concentration was evaluated with QuantStudio™ Real-Time PCR Systems (Thermo Fisher Scientific). Each diluted library (100 pM) was amplified through emulsion PCR using the OneTouch™ Instrument (Life Technologies) and enriched by the OneTouch™ ES Instrument (Life Technologies) using the Ion PI Hi-Q OT2 200 kit following the manufacturer’s instructions. Finally, sequencing was performed on an Ion Proton instrument (Life Technologies) using an Ion PI Hi-Q Sequencing 200 Kit (Life Technologies). Barcoded samples were loaded onto an Ion PI Chip v3.

Sung J.S., Chong H.Y., Kwon N.J., Kim H.M., Lee J.W., Kim B., Lee S.B., Park C.W., Choi J.Y., Chang W.J., Choi Y.J., Lee S.Y., Kang E.J., Park K.H, & Kim Y.H. (2017). Detection of somatic variants and EGFR mutations in cell-free DNA from non-small cell lung cancer patients by ultra-deep sequencing using the ion ampliseq cancer hotspot panel and droplet digital polymerase chain reaction. Oncotarget, 8(63), 106901-106912.

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Ion AmpliSeq Cancer Hotspot Panel Library Preparation

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The template that contained 10 ng of DNA was used to generate an amplicon library for sequencing. Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Cancer Hotspot Panel v2 (Life Technologies) were used to prepare the libraries. Genomic DNA targets were amplified by PCR, and primer sequences were then partially digested. DNA ligase was used to ligate adapters to amplicons. Agencourt AMPure XP Reagent (Beckman Coulter) was used to purify the unamplified library; quantitative PCR (qPCR) with the Ion Library Quantitation Kit was used to dilute the concentration of each Ion AmpliSeq library to 100 pM. And each diluted library (100 pM) was amplified through emulsion PCR by OneTouch Instrument (Life Technologies) according to the manufacturer’s instructions.

Tian Y., Zhao X., Li P., Lu M, & Tian H. (2021). Correlation of EGFR G873R mutation with prognosis of docetaxel in non-small cell lung cancer. Journal of Thoracic Disease, 13(10), 5964-5972.

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Ion Torrent Library Preparation and Sequencing

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Prior to Ion torrent library construction, concentration and fragment length of samples was determined with a Bioanalyzer 2100 and the High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA). The libraries were diluted to a final concentration of 26 pM. According to manufacturer’s protocol the library fragments were attached to Ion Sphere particles using the One Touch instrument and Ion PGM Template OT2 400 kit (Life Technologies, Carlsbad, CA, USA). Subsequently, Ion Sphere particles were loaded on an Ion 318 v2 Chip for the first run and an Ion 314 v2 chip for the second run, after which the amplicon libraries were sequenced according to manufacturer’s protocol using the ION PGM Sequencing 400 Kit, using 850 nucleotide flows. Run 1 (318 chip) resulted in 35,790 reads with an average read length of 132 base pairs. Run 2 resulted in 180,870 reads with an average read length of 275 base pairs.

Kox M.A., Aalto S.L., Penttilä T., Ettwig K.F., Jetten M.S, & van Kessel M.A. (2018). The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses. AMB Express, 8, 76.

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Ion Torrent PGM Sequencing Protocol

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Emulsion PCR was performed on the One Touch Instrument (Life Technologies, Carlsbad, CA, USA) using the Ion PGM Template OT2 400 Kit (Life Technologies) according to the manufacturer’s protocol. Sequencing was performed on the Personal Genome Machine (PGM) using the Ion PGM Sequencing 400 Kit with a 314 V2 chip according to the manufacturer’s protocol.

Imabayashi Y., Moriyama M., Takeshita T., Ieda S., Hayashida J.N., Tanaka A., Maehara T., Furukawa S., Ohta M., Kubota K., Yamauchi M., Ishiguro N., Yamashita Y, & Nakamura S. (2016). Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing. Scientific Reports, 6, 28110.

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