Cancer Res Treat.  2018 Jan;50(1):255-264. 10.4143/crt.2017.062.

Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2

• Hwang SM
• Lee KC
• Lee MS
• Park KU

• KMID: 2403494
• DOI: http://doi.org/10.4143/crt.2017.062

Abstract

PURPOSE
Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2.
MATERIALS AND METHODS
The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2. Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite.
RESULTS
Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant.
CONCLUSION
Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.

Keyword

High-throughput nucleotide sequencing; Ion PGM; Ion PGM Dx; Genes; BRCA1; BRCA2

MeSH Terms

DNA
Genome*
High-Throughput Nucleotide Sequencing
Humans
Statistics as Topic
DNA

Figure

• 

  Fig. 1. Alignment of an indel variant (c.922_924delinsT) in a clinical sample viewed by Integrative Genomics Viewer, called as a single nucleotide variant, c.922C>T, by both Ion PGM/OTG-snpcaller and Ion PGM Dx/Torrent Suite.

• 

  Fig. 2. (A) Alignment of a 40-bp deletion in BRCA1 (c.1175_1214del40) in the reference Coriell DNA sample (NA14094) which was called by Ion PGM/OTG-snpcaller but not by Ion PGM Dx/Torrent Suite. (B) A 4-bp deletion in BRCA1 (c.4065_4068delTCAA) not called by Ion PGM Dx/Torrent Suite present in a reference Coriell DNA sample (NA14634). (C) A 1-bp deletion in BRCA2 (c.994delA) not called by Ion PGM Dx/Torrent Suite present in a clinical sample.

Reference

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