Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples.

ABSTRACT:

Background

Our objective was to assess whether modifications to a customized targeted RNA sequencing (RNAseq) assay to include unique molecular identifiers (UMIs) that collapse read counts to their source mRNA counts would improve quantification of transcripts from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples. The assay (SET4) includes signatures that measure hormone receptor and PI3-kinase related transcriptional activity (SET_ER/PR and PI3Kges), and measures expression of selected activating point mutations and key breast cancer genes.

Methods

Modifications included steps to introduce eight nucleotides-long UMIs during reverse transcription (RT) in bulk solution, followed by polymerase chain reaction (PCR) of labeled cDNA in droplets, with optimiz

SUBMITTER: Fu C 

PROVIDER: S-EPMC7860187 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature