DNA was extracted using the QIAamp DNA Mini Kit (#51304, Qiagen). Libraries were prepared with the Ion AmpliSeq Cancer Hotspot Panel v2 (#4475346, Thermo Fisher Scientific) and the Ion AmpliSeq Library Kit 2.0 (#4475345, Thermo Fisher Scientific). Libraries were templated and enriched with the Ion OneTouch 2 and the Ion OneTouch ES automated systems (Thermo Fisher Scientific). Sequencing was performed using semiconductor-sequencing technology (Ion PGM). Data were analysed using the Torrent Server VariantCaller version 5.6 and the Ion Reporter version 5.6 (Thermo Fisher Scientific). Results of the panel sequencing are listed in Supplementary Table 9 .
Torrent server variantcaller version 5
Manufactured by Thermo Fisher Scientific
The Torrent Server VariantCaller version 5.6 is a software tool designed for the analysis and identification of genetic variants from sequencing data. It is capable of processing and interpreting sequencing data to detect single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) within a given genomic sample.
Automatically generated - may contain errors
Lab products found in correlation
Ion onetouch 2, by Thermo Fisher Scientific (2 mentions)
Ion ampliseq library kit 2, by Thermo Fisher Scientific (2 mentions)
Qiaamp dna mini kit, by Qiagen (2 mentions)
Ion ampliseq cancer hotspot panel v2, by Thermo Fisher Scientific (2 mentions)
Ion reporter version 5, by Thermo Fisher Scientific (2 mentions)
Ion onetouch es, by Thermo Fisher Scientific (2 mentions)
Ion reporter software version 5, by Thermo Fisher Scientific (1 mentions)
3 protocols using torrent server variantcaller version 5
1
Ion AmpliSeq Cancer Hotspot Sequencing
2
Ion AmpliSeq Cancer Hotspot Sequencing
3
Comprehensive Cancer Variant Analysis
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Libraries were prepared with the Ion AmpliSeq Cancer Hotspot Panel v2 and the Ion AmpliSeq Library Kit 2.0, strictly according to the manufacturer's recommendations. Subsequently, libraries were templated and enriched with the Ion OneTouch 2 and the Ion OneTouch ES automated systems. Sequencing was performed using semiconductor sequencing technology (Ion PGM). Data analysis was done by the Torrent Server VariantCaller, version 5.6 and the Ion Reporter Software, version 5.6 (Thermo Fisher Scientific). We filtered for somatic, nonsynonymous, exonic variants, and splice site variants in the flanking regions, showing an allele frequency of more than 5%. Variants in the general reported population with a minor allele frequency of more than 0.5% in 1,000 Genomes and dbSNP were excluded. Read statistics are represented in Supplementary Table S4.
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