Torrentsuite 4

Manufactured by Thermo Fisher Scientific

Sourced in United States

TorrentSuite 4.2 is a software suite for the analysis of sequencing data. It provides tools for data processing, alignment, and variant calling.

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Lab products found in correlation

4 protocols using torrentsuite 4

Targeted Sequencing of Key ccRCC Genes

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A custom Ampliseq panel (Thermo Fisher Scientific, Paisley, UK) was designed to assess 48 key ccRCC genes in 63 samples across 13 patients for which DNA samples remained following the methylome analysis. Eleven patients had all five associated samples (normal, biopsy (Bx), and three post-treatment nephrectomy (Nx)), one patient (SU16) had all but the normal sample, and one patient (SU54) had only two nephrectomy samples. Multiplex PCRs were performed according to the manufacturer's instructions across two primer pools. The samples were sequenced on an Ion Proton sequencer to a mean on-target depth of 4000X with 97-98% of bases over 15X. Samples were aligned to the hg19 human genome reference assembly and variants identified with TorrentSuite 4.2 (Thermo Fisher Scientific). Sequencing data is available via NCBI SRA (Accession number SRP056914).

Stewart G.D., Powles T., Van Neste C., Meynert A., O'Mahony F., Laird A., Deforce D., Van Nieuwerburgh F., Trooskens G., Van Criekinge W., De Meyer T, & Harrison D.J. (2016). Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer. Oncotarget, 7(18), 25241-25250.

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Targeted Exome Sequencing Across Platforms

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ES/targeted exome NGS was carried out by a diagnostic genomics laboratory. Our cohort was sequenced under different protocols and sequencing platforms due to technological advances and changes in the diagnostic service through time. The TargetSeq Exome V2 kit was used for exome enrichment for sequencing on the SOLiD system. SOLiD ES data were analysed under LifeScope 2.5, with default parameters for exome analysis. The Ion AmpliSeq Exome RDY kit was used for exome enrichment for sequencing on the Ion Proton System. Ion Torrent ES data were analysed under Torrent Suite 4.2, using Thermo Fisher’s default exome-customized analysis parameters. Illumina ES analysis was carried out using TruSight™ One (~4800 genes) or TruSight™ One Expanded (~6700 genes) panels (Illumina Inc., Victoria, Australia) sequenced on the MiSeq or NextSeq 550 systems and analysed using MiSeq Reporter. Human genome version 19 (hg19) was used as the reference genome in all cases.

Lassmann T., Francis R.W., Weeks A., Tang D., Jamieson S.E., Broley S., Dawkins H.J., Dreyer L., Goldblatt J., Groza T., Kamien B., Kiraly-Borri C., McKenzie F., Murphy L., Pachter N., Pathak G., Poulton C., Samanek A., Skoss R., Slee J., Townshend S., Ward M., Baynam G.S, & Blackwell J.M. (2020). A flexible computational pipeline for research analyses of unsolved clinical exome cases. NPJ Genomic Medicine, 5, 54.

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NGS Panel for Hypothyroidism Genes

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Genomic DNA was extracted from peripheral leukocytes using PureLink® Genomic DNA Mini Kits (Thermo Scientific, USA). A custom Ion Ampliseq™ panel (Ion Torrent, Thermo Scientific, USA) targeting 12 genes associated with hypothyroidism (TPO, PAX8, NKX2-5, IYD, SLC26A4, TG, FOXE1, NKX2-1, DUOX2, DOUXA2, TSHR, SLC5A5) was used for DNA library preparation. Sequencing was performed using Personal Genome Machine (PGM) semiconductor sequencer (Ion Torrent, Thermo Scientific, USA). Bioinformatics analysis was carried out using Torrent Suite 4.2.1 (Thermo Scientific, USA) and ANNOVAR ver. 2014Nov12 software packages [30 (link)]. The results of the NGS were confirmed by Sanger sequencing using Genetic Analyzer 3130 sequencer (Life Technologies, USA). Interpretation of the sequencing results and assessment of the pathogenicity of sequence variants were performed according to the ACMG guidelines [29 (link)]. Sequence variants rated as ‘benign’ or ‘likely benign’ were excluded from the analysis. A description of the sequence variants was carried out in accordance with the recommendations of den Dunnen and Antonarakis [31 (link)].

Makretskaya N., Bezlepkina O., Kolodkina A., Kiyaev A., Vasilyev E.V., Petrov V., Kalinenkova S., Malievsky O., Dedov I.I, & Tiulpakov A. (2018). High frequency of mutations in 'dyshormonogenesis genes' in severe congenital hypothyroidism. PLoS ONE, 13(9), e0204323.

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Ion Torrent-based Transcriptome and Genotyping

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Emulsion PCR (emPCR) was performed with the Ion PGM Template IA 500 Kit (Thermo Fisher Scientific) and GeneAmp PCR system 9700 (Thermo Fisher Scientific) for transcription analysis of FLA-I genes and with the Ion 520 and 530 Kit-OT2 and OneTouch 2 instrument (Thermo Fisher Scientific) for genotyping of FLA-I and FLA-DRB genes and confirmation of genotyping data in FLA-E/H/K genes. After the emulsion PCR, the beads carrying the single-stranded DNA templates were enriched with the Ion OneTouch Enrichment System (Thermo Fisher Scientific) according to the manufacture’s recommendation. Sequencing was performed using the Ion PGM Hi-Q View Sequencing Kit and Ion 316 Chip Kit (Thermo Fisher Scientific) for transcription analysis and using the Ion S5 Sequencing Kit and Ion 520/530 Chip Kit (Thermo Fisher Scientific) for genotyping of FLA-I and FLA-DRB genes and confirmation of genotyping data in FLA-E/H/K genes.
The raw data processing and base-calling, trimming and output of quality-filter sequence reads that were binned on the basis of the Ion Xpress Barcodes into separate sequence fastq files, were all performed by the Torrent Suite 4.2.1 (Thermo Fisher Scientific) for the transcription analysis and by the Torrent Suite 5.6.0 (Thermo Fisher Scientific) for the genotyping with full processing for shotgun analysis.

Okano M., Miyamae J., Suzuki S., Nishiya K., Katakura F., Kulski J.K., Moritomo T, & Shiina T. (2020). Identification of Novel Alleles and Structural Haplotypes of Major Histocompatibility Complex Class I and DRB Genes in Domestic Cat (Felis catus) by a Newly Developed NGS-Based Genotyping Method. Frontiers in Genetics, 11, 750.

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