Abstract 6251: Validation and implementation of whole-transcriptome sequencing assay into cancer care: An experience from a cancer center
Authors: Moran Jillian A. , Hughes Edward G. , Green Donald C. , Sukhadia Shrey , Tsongalis Gregory J. , Allen Samantha F. , Tafe Laura , Houde Brianna , Ognjenovic Nevena B. , Barbuto Jennifer N. , Riano Ivy , Shah Parth 
Published: March 2024

Abstract
Introduction Transcriptome sequencing is a well-established diagnostic tool to characterize and quantify gene expression profiles and to detect fusion transcripts. The utilization of whole-transcriptome sequencing (WTS), in clinical workflows can tremendously help improve diagnosis, risk stratification, and therapy selection. However, there are multiple challenges to widespread clinical implementation of WTS including nucleic acid input, defining appropriate quality control (QC) criteria, tumor specific baseline controls and depth of sequencing. Here, we present a validation study to deploy routine whole transcriptome sequencing with automated analysis in a mid-size academic center. Methods Nucleic acid material was obtained through clinical residual samples in the Center for Genomics and Advanced Technology. RNA samples were extracted using the Purigen Ionic® FFPE to Pure RNA Kit. RNA input sample quantities ranged from 34-100ng. WTS libraries were prepared using the Illumina® RNA Prep with Enrichment (L) Tagmentation kit with the Illumina Exome Panel for FFPE tumor samples. The validation was performed on a set of patient samples with known clinically reported variants from the Illumina TruSight® Tumor 170 assay. A total of 84 true positives with reportable fusions, 5 splicing events, 16 negative samples, and 15 limit of detection (LOD) samples were used. Libraries were prepared in a three-plex format. Sequencing was performed on the Novaseq-6000 system using S2 and S4 flow cells with a target read count of 100 million. All data was processed through the AUGMET informatics platform for demultiplexing, quality control, fusion detection, transcript quantification and determination of alternatively spliced transcript. Results The WTS validation assay demonstrated 98% (n=49/50) sensitivity, with only one false negative, and 100% (n=68/68) specificity. A final review of our data was determined to develop stable QC standards for RNA sequenced libraries to be &gt; 60M reads and &gt; 130bp read length. When analyzing (LOD) for WTS, interestingly, read length was inversely proportional to input and as a result detection of the clinically relevant fusion. Based on our LOD experiments, a minimum input threshold of 20ng of RNA was determined to maintain the sensitivity and specificity. An LOD study for tumor purity was not performed due to the known lack of correlation between tumor purity and fusion transcript quantity. Discussion WTS can detect all clinically reported fusions and splicing events with comparable sensitivity to panel assays. Moreover, simultaneously available transcript quantification and variant calling provide the ability to implement several disease classifiers. This work lays the foundation for integration with our clinically available tumor exome sequencing assay to allow joint exome transcriptome analysis in a single informatics platform.
Citation Format: Jillian A. Moran, Edward G. Hughes, Donald C. Green, Shrey Sukhadia, Gregory J. Tsongalis, Samantha F. Allen, Laura Tafe, Brianna Houde, Nevena B. Ognjenovic, Jennifer N. Barbuto, Ivy Riano, Parth Shah. Validation and implementation of whole-transcriptome sequencing assay into cancer care: An experience from a cancer center [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6251.