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Related Experiment Video

Updated: Apr 27, 2026

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

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Highly sensitive amplicon-based transcript quantification by semiconductor sequencing.

Jitao David Zhang, Tobias Schindler, Erich Küng

¹Roche Pharmaceutical Research and Early Development, Department of Pharmaceutical Sciences/ Translational Technologies and Bioinformatics, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland. ulrich.certa@roche.com.

|July 7, 2014

Summary

This summary is machine-generated.

This study presents AmpliSeq-RNA, a novel method for accurate gene expression profiling. This high-throughput semiconductor sequencing approach enables robust transcript quantification and detection of genetic variations in multiple samples.

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Area of Science:

Molecular Biology
Genomics
Transcriptomics

Background:

Custom gene panels are crucial for efficient transcript profiling in research.
Existing methods like TaqMan assays have limitations in dynamic range and throughput.
A need exists for technologies measuring large gene sets across multiple samples.

Purpose of the Study:

To adapt and evaluate AmpliSeq-RNA for accurate mRNA quantification.
To assess the performance of AmpliSeq-RNA compared to microarrays and RNA sequencing.
To demonstrate the application of AmpliSeq-RNA in studying stem cell differentiation.

Main Methods:

Adaptation of a commercial mRNA quantification assay (AmpliSeq-RNA) utilizing high-throughput semiconductor sequencing.
Parallel quantification of approximately 1000 transcripts across multiple samples.
Validation using stem cell differentiation models and comparison with DNA-microarrays and quantitative RNA sequencing.

Main Results:

AmpliSeq-RNA demonstrated accurate quantification over a five-log dynamic range.
Good correlation (r = 0.78) was observed between AmpliSeq-RNA and DNA-microarrays.
AmpliSeq-RNA detected low-abundant transcripts missed by microarrays, with high correlation (r = 0.87) to RNA sequencing.
Signaling cascade changes during stem cell differentiation were visualized.

Conclusions:

AmpliSeq-RNA technology enables robust, multiplexed transcript quantification via amplicon frequency analysis.
High-throughput sequencing overcomes artefacts, allowing for at least 900 parallel PCR reactions.
This method facilitates simultaneous RNA quantification and genetic variation detection.