Versatile ion S5XL sequencer for targeted next generation sequencing of solid tumors in a clinical laboratory

• Published in: PloS one Vol. 12; no. 8; p. e0181968
• Main Authors: Mehrotra, Meenakshi, Duose, Dzifa Yawa, Singh, Rajesh R, Barkoh, Bedia A, Manekia, Jawad, Harmon, Michael A, Patel, Keyur P, Routbort, Mark J, Medeiros, L Jeffrey, Wistuba, Ignacio I, Luthra, Rajyalakshmi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02-08-2017; Public Library of Science (PLoS)
• Subjects: Adult; Aged; Biology and Life Sciences; Biopsy; Cancer; Cancer genetics; Clinical Laboratory Services; Data analysis; Data processing; Deoxyribonucleic acid; Dilution; DNA; DNA sequencing; DNA, Neoplasm - analysis; Female; Formaldehyde; Genomics; Genotyping; High-Throughput Nucleotide Sequencing - instrumentation; Humans; Laboratories; Libraries; Male; Middle Aged; Multiplexing; Mutation; Neoplasms - genetics; Onboard; Paraffin; Physical Sciences; Reproducibility; Research and Analysis Methods; Sensitivity; Sensitivity analysis; Sensitivity and Specificity; Sequence Analysis, DNA - instrumentation; Sequences; Software; Solid tumors; Time Factors; Tumors; Workflow; Young Adult; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0181968

Next generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. Semiconductor based next generation platforms varied from low throughput Ion PGM to high throughput Ion Proton and Ion S5XL sequencer. In this study, we compared Ion PGM and Ion Proton, with a new Ion S5XL NGS system for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing performance in a clinical laboratory.
Eighteen solid tumor samples positive for various mutations as detected previously by Ion PGM and Ion Proton were selected for study. Libraries were prepared using DNA (range10-40ng) from micro-dissected formalin-fixed, paraffin-embedded (FFPE) specimens using the Ion Ampliseq Library Kit 2.0 for comprehensive cancer (CCP), oncomine comprehensive cancer (OCP) and cancer hotspot panel v2 (CHPv2) panel as per manufacturer's instructions. The CHPv2 were sequenced using Ion PGM whereas CCP and OCP were sequenced using Ion Proton respectively. All the three libraries were further sequenced individually (S540) or multiplexed (S530) using Ion S5XL. For S5XL, Ion chef was used to automate template preparation, enrichment of ion spheres and chip loading. Data analysis was performed using Torrent Suite 4.6 software on board S5XL and Ion Reporter. A limit of detection and reproducibility studies was performed using serially diluted DLD1 cell line.
A total of 241 variant calls (235 single nucleotide variants and 6 indels) expected in the studied cohort were successfully detected by S5XL with 100% and 97% concordance with Ion PGM and Proton, respectively. Sequencing run time was reduced from 4.5 to 2.5 hours with output range of 3-5 GB (S530) and 8-9.3Gb (S540). Data analysis time for the Ion S5XL is faster 1 h (S520), 2.5 h (S530) and 5 h (S540) chip, respectively as compared to the Ion PGM (3.5-5 h) and Ion Proton (8h). A limit detection of 5% allelic frequency was established along with high inter-run reproducibility.
Ion S5XL system simplified workflow in a clinical laboratory, was feasible for running smaller and larger panels on the same instrument, had a shorter turnaround time, and showed good concordance for variant calls with similar sensitivity and reproducibility as the Ion PGM and Proton.