title: Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants inBRCA1andBRCA2.
abstract: OBJECTIVE
  Transition to next generation sequencing (NGS) forBRCA1/BRCA2analysis 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 ofBRCA1/2.
  
  
  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 forBRCA1/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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.|Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.
authors.forename: Sang Mee
authors.initials: SM
authors.lastname: Hwang
authors.affiliation: Eone-Diagnomics Genome Center, Incheon, Korea.
authors.forename: Ki Chan
authors.initials: KC
authors.lastname: Lee
authors.affiliation: Eone-Diagnomics Genome Center, Incheon, Korea.
authors.forename: Min Seob
authors.initials: MS
authors.lastname: Lee
authors.affiliation: Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.|Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.
authors.forename: Kyoung Un
authors.initials: KU
authors.lastname: Park
mesh_terms: D019313:BRCA1 Protein / Q000235:genetics*; D024682:BRCA2 Protein / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics*; D005260:Female; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans
chemical_list: D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D024682:BRCA2 Protein; C551750:BRCA2 protein, human
keywords: BRCA1; BRCA2; Genes; High-throughput nucleotide sequencing; Ion PGM; Ion PGM Dx