Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2 / Journal of the Korean Cancer Association, 대한암학회지
Cancer Research and Treatment
;
: 255-264, 2018.
Article
Dans Anglais
| WPRIM
| ID: wpr-739611
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 ANDMETHODS:
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.
Texte intégral:
Disponible
Indice:
WPRIM (Pacifique occidental)
Sujet Principal:
ADN
/
Statistiques comme sujet
/
Génome
/
Séquençage nucléotidique à haut débit
Type d'étude:
Etude diagnostique
Limites du sujet:
Humains
langue:
Anglais
Texte intégral:
Cancer Research and Treatment
Année:
2018
Type:
Article
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