Gene Expression Detection Assay for Cancer Clinical Use

Narrandes, Shavira; Xu, Wayne

Cell lysates, fresh frozen (FF) tissue, and FFPE samples are widely used in cancer genomics studies by the qRT-PCR, DNA microarray, NanoString nCounter, and Illumina MiSeq RNA-Seq assays to provide data for patient diagnosis and prognosis. FISH and TMAs also employ FFPE specimens. FF samples allow for better preserved RNA but are limited in availability and use as tissue banks and research groups mainly collect and study them; they also have the disadvantage of sample size, transport, and clinical annotation. 79 , 80 The RNA isolation and purification steps are generally the same for the qRT-PCR, DNA microarray, NanoString nCounter, and Illumina MiSeq RNA-Seq methods as commercial kits may be purchased for RNA extraction from cell lysate, FFPE, and FF samples. The TMA has a longer process for sample preparation using FFPE samples.