In case you missed going to AGBT or missed our workshops, posters or talks, don’t worry we’ve got you covered. Here in the wrap-up you can find everything you need.
S is for Serving Science
This year we gave you updates from talks given on all days. Be sure to check out the wrap ups below for each day were we covered research talks from:
Day 1 wrap-up – Viruses, data sharing, to long non-coding RNAs
Day 2 wrap-up – Single cell sequencing, completing genomes, to microbial dark matter
Day 3 wrap-up – Astronauts, sea slugs, to rare mendelian diseases
Day 4 wrap-up – Tracking Viruses to Gorilla genomes
S is for Suite Talks
LiquidBiopsy: A Molecular research Platform that supports Analysis of Circulating Tumor Cells and Circulating Tumor DNA.
– Presented by Paul W. Dempsey, PhD, Cynvenio
High throughput comprehensive sequencing using Ion AmpliSeq Custom Mendelian Research and Oncomine Panels on the Ion S5 XL System.
– Presented by Robert P. Sebra, PhD, Icahn School of Medicine at Mount Sinai
A core lab’s perspective: experiences of human and microbial sequencing on the Ion S5 XL System.
– Presented by Adam Ameur, PhD, Uppsala Genome Centre, Sweden
Time matters: the role of whole genome sequencing in high-resolution bacterial strain typing for foodborne disease research analysis.
– Presented by Lucy E. DesJardin, PhD, State Hygienic Laboratory, University of Iowa
S is for Sponsor Workshop
Simon Cawley closed with our Bronze sponsor workshop talk, talking about all our leading innovations in targeted sequencing. For more information on Simon’s talk – click here.
S is for Scientific Posters
We will also be featuring our scientists presenting posters on the latest R&D innovations directly from our labs (click on the image if you would like to download the poster).
1] Preparing libraries directly from blood, saliva, buccal swabs and FFPE sections on the Ion Chef
We developed a research method to directly use biological samples and low input samples for generating libraries to reduce the time from sample to analysis on an NGS platform. Extremely small samples were successfully processed with this method, which reduces the total time from sample to sequence to 24 hours. Sequencing metrics were comparable or improved for the samples used directly without purification as compared to purified DNA controls. Additionally, as shown for buccal swab samples, there was no detrimental effect on variant calling results.
2] 600 base reads on the Ion S5™ Next-Generation Sequencing System enables accurate HLA typing of 96 research samples on one 530 chip.
Longer read lengths simplify genome assembly, haplotyping, metagenomics, and the design of library primers for targeted resequencing. Several new technologies were developed to enable the sequencing of templates with inserts over 600 bases: a fast isothermal templating technology, an ISP™ that is optimized for maximum template density, a new long-read sequencing polymerase, and instrument scripts that consume less reagents. We demonstrate the combination of these technologies to sequence 600 base long DNAs on an Ion 530 Chip™ with an average AQ20 mean read length over 500 bp. The protocol was used to type human leukocyte antigen (HLA) alleles, a haplotyping application that is greatly simplified by long read length sequence data. 96 HLA samples were typed with 99.7% concordance to truth on one Ion 530 chip.
3] Speeding up the S5 XL sequencing system: Sequencing in an hour enables sample-to-answer workflows in as low as 6.5 hr
With the Ion S5™ XL Sequencer and modifications to the on-instrument flow times and total number of flows, we can reduce the time for sequencing and accurate data analysis for research applications requiring rapid turn around time. For Ion AmpliSeq assays, sequencing and Torrent Suite analysis could be completed in 55-75 minutes. Paired with fast library and template preparation, the total turn around time was at or below a standard workday.
4] Localized gene expression changes by AmpliSeq transcriptome sequencing from Arcturus™ laser capture microdissected formalin-fixed, paraffin-embedded (FFPE) Alzheimers and normal brain sections
Arcturus™ XT™ LCM system enables investigators to isolate and analyze unique groups of cells in brain tissue.
– Arcturus LCM coupled with Ion Torrent NGS can be used to analyze molecular differences at subcellular resolution.
– Arcturus LCM facilitates the enrichment of diseased tissue away from unaffected cellular background, revealing gene expression differences that would be missed from macro- dissected tissue.
– Ion Ampliseq™ Transcriptome Human Gene Expression Research Panel enables scientists to identify gene expression changes from extremely limited amounts of difficult tissue preparations.
5] Detection of somatic mutations at 0.5% frequency from cfDNA and CTC DNA using a multiplex next-generation sequencing assay
The LiquidBiopsy™ Workflow with the Ion Torrent™ platform is a comprehensive 2 days sample-to-variant solution that facilitates researchers to study biomarkers in DNA from germline, CTCs, and cfDNA all available from a single blood sample.
– The “AmpliSeq CHPv2 peripheral/CTC/CF DNA single sample” workflow in Ion Reporter™ 4.4 Software provides a fully automated analysis solution for accurate detection of variants at frequency >0.5%.
– High CTC purity enables detection of 1:1M cells and >99% sensitivity and specificity in variant calling from the blood sample without the need for whole-genome amplification.
– Low-input DNA capability is provided by Ion AmpliSeq™ technology. The CHPv2 panel can survey ~2800 hotspots and ~22K de novo regions of oncogenes and tumor suppressor genes.
6] Simple, rapid, low input library preparation using MuA transposons
We made further improvements to an already simple and rapid library preparation method based on MuA transposons. These improvements are expected to increase library complexity, which is especially critical for low input applications. As a demonstration, we explored two workflows that start with direct from cell lysates:
– We were able to sequence directly from a bacterial colony. Not only was the library protocol simple, with relatively few steps, and rapid, but it was not necessary to inoculate and grow a liquid culture and purify genomic DNA up front.
– We also were able to lyse single human cells and generate libraries sufficient to detect a copy number variant with only 200,000 reads each for the experimental and control samples. Traditionally, Whole Genome Amplification is employed prior to library preparation. Our method further simplifies this technique. Dozens of libraries are often prepared for single sequencing runs. A simple and rapid preparation method is especially beneficial as the number of samples increases. In addition, these methods are more amenable to automation. As we explore more streamlined workflows using MuSeek technology, we hope to enable researchers to increase the scope and power of their experiments. At the same time, reducing input requirements should enable a wider variety of sample types and applications to be utilized.
For a re-cap of AGBT content be sure to check out my blogs and do let me know what you think!
For Research Use Only. Not for use in diagnostic procedures.