evotec_Nov23_PanOmicsDriven - 14

The PanHunter Platform
to organ (or multiple organ) toxicity and eventual
adverse health effects in patients. Additionally,
identifying fingerprints of MIEs can be used
for future hazard identification
and risk assessment.
NEXT GENERATION SEQUENCING (NGS)
IN TRANSCRIPTOMICS RESEARCH
Initial toxicogenomics efforts primarily
involved transcriptional profiling (the study of
transcriptional changes in mRNA and other RNA
molecules) of in vivo and in vitro samples from
pre-clinical safety studies using microarray technology.
Microarrays have limited throughput and
dynamic range. At the start of the millennium,
the field of transcriptomics advanced significantly
through the introduction of RNA-Seq, a
method based on NGS. Using this technique, it
is possible to sequence the entire transcriptome
of the cell efficiently and quantitatively with an
unprecedented dynamic range and limited sample
requirements. Molecular profiling, particularly
in the field of transcriptome analysis has become
omnipresent and new technologies such as
high-throughput barcoding and NGS are bringing
down costs. These advances allow for processing
of thousands of samples in parallel and thus
testing of large numbers of compounds, concentrations
and individual time points.
Microarrays
Throughput
Bulk RNA-Seq
(individual samples)
Require species- or
transcript-specific probes
Detected genes defined
by the probes
Semi-quantitative quantification per gene
(no direct cross-gene comparison possible)
Limited dynamic range (103)
Data output size
Commonly available
Straight forward data analysis
$$$
Throughput (individual samples or
max 96 well format)
Whole mRNA body coverage:
detects novel transcripts, gene fusions
& all single nucleotide variants
Deep sequencing
(up to 20k genes detected)
Digital quantification. No UMIs
(PCR bias is not addressed)
Broad dynamic range (>105)
Data output size
Commonly available
Straight forward data analysis
$$
HT-RNA-Seq
Throughput
(multiple 384 well plates)
3' mRNA part-focused library prep:
limited info on transcripts
Shallow sequencing
(up to 16k genes detected)
Digital quantification. UMIs are used
(precise mRNA quantification)
Broad dynamic range (>105)
Data output size
Proprietary
platform
Data analysis for large sample number,
requires specific tools (PanHunter platform)
$
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evotec_Nov23_PanOmicsDriven

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