Jun 19, 2016

Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow

Nucleic Acids Research
Dominik BuschmannMichael W Pfaffl

Abstract

Small RNA-Seq has emerged as a powerful tool in transcriptomics, gene expression profiling and biomarker discovery. Sequencing cell-free nucleic acids, particularly microRNA (miRNA), from liquid biopsies additionally provides exciting possibilities for molecular diagnostics, and might help establish disease-specific biomarker signatures. The complexity of the small RNA-Seq workflow, however, bears challenges and biases that researchers need to be aware of in order to generate high-quality data. Rigorous standardization and extensive validation are required to guarantee reliability, reproducibility and comparability of research findings. Hypotheses based on flawed experimental conditions can be inconsistent and even misleading. Comparable to the well-established MIQE guidelines for qPCR experiments, this work aims at establishing guidelines for experimental design and pre-analytical sample processing, standardization of library preparation and sequencing reactions, as well as facilitating data analysis. We highlight bottlenecks in small RNA-Seq experiments, point out the importance of stringent quality control and validation, and provide a primer for differential expression analysis and biomarker discovery. Following our recomme...Continue Reading

  • References224
  • Citations11

References

  • References224
  • Citations11

Citations

Mentioned in this Paper

Biological Markers
Real-Time Polymerase Chain Reaction
Microarray Analysis
Small Nuclear RNA
Research
Molecular Diagnostics; Reverse Transcription
Research Personnel
RNA, Small Temporal
Nucleic Acid Sequencing
Gene Expression

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