On February 12-16 Lexogen team was at Advances in Genome Biology and Technology (AGBT) General Meeting in Orlando, Florida. AGBT is one of the main Next Generation Sequencing events of the year which brings together the latest advances in technology, software, applications, data resources, and public policy.
As a bronze sponsor at AGBT 2018, Lexogen hosted a suite and a talk in the plenary session of the conference.
Stefan L. Ameres from the Institute of Molecular Biotechnology (IMBA) in Austria gave a talk “SLAMseq: Thiol-linked alkylation for the metabolic sequencing of RNA” in the plenary session of the conference.
SLAMseq is a novel high-sensitivity method for time-resolved measurement of newly synthesized and existing RNA which enables the transcriptome-wide resolution of RNA synthesis and degradation kinetics. SLAMseq Metabolic RNA Labeling Kits for RNA-Seq are available at Lexogen.
For details on the method and applications check the recording of the SLAMseq talk at AGBT 2018.
The workshop „SLAMseq and QuantSeq: Efficient Gene Expression Profiling, Now Also Time-Resolved!” took place in the Lexogen suite and brought together four excellent speakers relating their stories about SLAMseq technology, SLAMdunk data analysis pipeline, and application of QuantSeq 3’ mRNA-Seq for highly degraded FFPE samples:
- Time-resolved gene expression profiling with Lexogen’s QuantSeq and SLAMseq kits.
Lukas Paul, Senior Manager of Scientific Affairs, Lexogen, Austria
- SLAMseq, a new method to detect RNA synthesis and decay rates transcriptome-wide.
Stefan L. Ameres, Group Leader, Institute of Molecular Biotechnology (IMBA), Austria
- SLAMdunk – a pipeline for analyzing SLAMseq data in established and emerging applications.
Tobias Neumann, Bioinformatician, Research Institute of Molecular Pathology (IMP), Austria
- QuantSeq gene expression profiling for tumor/immune analysis in mice and man.
Anne-M. Krogsdam, Assistant Professor, Innsbruck Medical University, Austria
Learn more about SLAMdunk data analysis for SLAMseq and QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina.
Lexogen’s Head of Bioinformatics, Andreas Tuerk, presented a poster about estimating pre-PCR fragment numbers from post-PCR frequencies of unique molecular identifiers.
As a transcriptomics company, Lexogen is excited to see developments presented at the AGBT meeting on direct RNA-Seq on the Oxford Nanopore’s MinION device. Matthew Keller, postdoctoral fellow at the US Centers for Disease Control and Prevention, has been testing direct RNA sequencing on the MinIon to obtain the genome of influenza viruses. He stated that “long-read direct RNA sequencing is a unique and transformative technology” with improvements needed to reduce the amount of starting material (the currently needed 500 ng input is not feasible in clinical settings) and to increase accuracy.
Rachael Workman, a researcher in Winston Timp’s laboratory at Johns Hopkins University, presented work of the Nanopore RNA Consortium, a group of six laboratories working on RNA sequencing on the MinIon. The consortium members have generated a dataset of about 13 million direct RNA sequences from 30 flow cells and more than 24 million cDNA sequences from 12 flow cells, which is available at github. Median RNA read identity is around 86%, correlation between dRNA and cDNA datasets is high (R=0.875), 73% of annotated human reference transcripts were captured, and aligned read lengths reach up to 22 kb. Lexogen’s Spike-In RNA Variants (SIRVs) were used in these evaluations to assess gene expression quantification (which correlated well with the spike-in input) and isoform identification (which in some cases suffered from read error, multi-mapping and 5’ degradation). Interestingly, ionic current dwell time can be used to estimate poly(A) tail length in direct RNA-Seq, with human mRNAs determined to carry poly(A) tail of an expected 30 to 150+ nt length, and this approach was validated on data from the SIRV transcripts that uniformly end with 30 adenosines. Slides from this talk can be accessed at the Timp lab homepage.
Further highlights and trends at AGBT 2018 are well covered in blog entries from Omics! Omics! and DeciBio to Dale Yuzuki and include oligo-tagged antibodies, single cell genomics developments, long read human genome assemblies, and the rise of spatial ‘omics.
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Authors: Lukas Paul & Jekaterina Aleksejeva