Simon Cawley, PhD, Senior Director, Software and Informatics presented a workshop on the last day of AGBT 2016. Simon’s talk focused on leading innovations in targeted sequencing, discussing developments with the Ion S5™ system, cancer research tools, RNA research tools and advances in read length and speed.
The Ion S5™ and Ion S5™ XL systems
- The simplest NGS workflow for targeted sequencing with less than 15 mins to set up a sequencing run and less than 45 mins total hands-on time from DNA to data with the Ion Chef system with run time as little as 3.5 hours.
- The Ion S5 systems are scalable for all your targeted applications, where you can scale from 5 million to 80 million reads with just a change in chips.
- 1-10 ng of DNA/RNA input using the Ion AmpliSeq™ technology
- Easy setup and training, single day installation, and plug and play cartridge-based reagents.
Cancer Research Tools
- The Ion AmpliSeq technology for pre-NGS sample prep with customizable or pre-designed panels with hundreds of gene variants per sample in a single run, requiring low input amounts.
- Ion Torrent™ systems for next-generation sequencing providing fast turnaround times with minimal sample inputs.
- Oncomine™ Knowledgebase, a curated cancer genomic database for all your bioinformatics needs.
- Oncomine™ Focus Assay includes hotspot SNVs and indels, CNVs, and gene fusions.
- LiquidBiopsy Platform and workflow allowing isolation and analysis of CTCs, cfDNA and germline cells.
Cancer Research Tools under development
- Demonstration of Oncomine Focus Assay using Ion Chef System and Ion S5 Systems.
- Workflow simplification: Library Prep Direct from FFPE samples without nucleic acid isolation
- Ion AmpliSeq Direct FFPE DNA kit allows highly efficient library prep from very small quantities of FFPE tumor tissue, eliminating the need for tissue deparaffinization, protease digestion and DNA purification.
- qPCR/digital PCR for expression levels of single gene targets
- Targeted Ion Ampliseq RNA Panels for gene-level expression and fusion detection
- Ion Ampliseq Transcriptome for differential gene expression/profiling and sensitivity for low-abundance RefSeq genes
- RNA sequencing on the Ion S5 systems for differential gene expression and discovery of novel transcripts/fusions and sensitivity for low-abundance RefSeq genes.
- The Ion AmpliSeq technology is a single workflow solution for many research applications, requiring 1ng of input and has high sensitivity (FFPE compatible).
- Ion AmpliSeq Custom RNA Fusion Panel allows for detection of fusion genes by targeting RNA fusion transcripts. Panels can be customized here
Improvement in Read length and Speed Underway
- Ion S5 XL system – DNA to Data in 6.5 hours (4 Million, 100bp, reads sequenced in 1 hour).
- 5 hours for Library Prep (Ion Ampliseq 16S & Bacterial ID Research Panel)
- 2 hours Template Prep (Isothermal Amplification)
- 40 mins Sequencing (Ion S5 systems)
- 9 mins Data Analysis
- Isothermal amplification gave >99% accuracy with 600bp reads on the Ion S5 system with the Ion 530 Chip.
- >97% concordance was observed with the IonS5 system 600bp and NXType HLA typing.
Together by extending the Ion S5 System capabilities for Oncology research, Ion AmpliSeq technology for RNA and improving read length and speed, a complete sample to answer solution is available for your research needs.
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*For Research Use Only. Not for use in diagnostic procedures