Abstract 3561: Whole transcriptome analysis of testicular germ cell tumors

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Next generation sequencing of the whole transcriptome enables high resolution measurement of gene expression activity in different tissue and cell types. This methodology provides an in depth study of known transcripts and depending on the data analysis, allows identification of additional transcript types such as transcript variants, fusion transcripts, and small and long ncRNAs. In this study we performed RNA-Seq using the Ion Torrent sequencing platform to compare the expression profile of testicular germ cell tumors (seminoma type, n=3) and normal testis (n=3). Using Partek Flow and Star or TopHat aligners, we aligned the reads to the human genome and mapped sequences to the RefSeq database. We identified a large number of genes that were up and down regulated with high degree of significance p 2X FC). These included genes related to testicular tissue type, stem cell pleuripotency (NANOG; POU5F1) and proliferation (KRAS, CCND2). In addition, a number of differentially expressed noncoding RNAs were identified (SNORD12B, XIST). The method was validated on a small set of genes (>20) using qPCR (TaqMan Assays). We used the Open Array platform to quantitatively screen a larger number of differentially expressed genes (224) across a number of different testicular germ cell tumor types (non-seminoma). Citation Format: Lovorka Degoricija, Kathy Y. Lee, Sunali Patel, Shirley Chu, Ad J.M. Gillis, Martin Rijlaarsdam, Lambert C.J. Dorssers, Leendert Looijenga. Whole transcriptome analysis of testicular germ cell tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3561. doi:10.1158/1538-7445.AM2014-3561