title: Application of next generation qPCR and sequencing platforms to mRNA biomarker analysis.
abstract: Recent years have seen the emergence of new high-throughput PCR and sequencing platforms with the potential to bring analysis of transcriptional biomarkers to a broader range of clinical applications and to provide increasing depth to our understanding of the transcriptome. We present an overview of how to process clinical samples for RNA biomarker analysis in terms of RNA extraction and mRNA enrichment, and guidelines for sample analysis by RT-qPCR and digital PCR using nanofluidic real-time PCR platforms. The options for quantitative gene expression profiling and whole transcriptome sequencing by next generation sequencing are reviewed alongside the bioinformatic considerations for these approaches. Considering the diverse technologies now available for transcriptome analysis, methods for standardising measurements between platforms will be paramount if their diagnostic impact is to be maximised. Therefore, the use of RNA standards and other reference materials is also discussed.
authors: Molecular and Cell Biology, LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, UK.
authors: Alison S
authors: AS
authors: Devonshire
authors: Rebecca
authors: R
authors: Sanders
authors: Timothy M
authors: TM
authors: Wilkes
authors: Martin S
authors: MS
authors: Taylor
authors: Carole A
authors: CA
authors: Foy
authors: Jim F
authors: JF
authors: Huggett
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D053837:DNA Cleavage; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D006801:Humans; D046210:Microfluidic Analytical Techniques; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction / Q000592:standards*; D012015:Reference Standards; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000592:standards*
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger