Abstract A44: Randomized adapter pools for microRNA sequencing of colorectal cancer cell lines and primary tumors

Single-nucleotide resolution, high throughput and excellent precision make small RNA sequencing ideally suited for addressing a wide array of microRNA (miRNA) research questions. It is however known that adapter ligation introduces bias distorting the relation between sample expression levels and sequencing read counts. To investigate how this issue may affect studies aiming to identify miRNA biomarkers, we utilized the recently published High Definition library preparation protocol to generate miRNA profiles of 35 colorectal cancer cell lines, 55 primary cancer biopsies and 5 adjacent normal mucosa samples. The protocol minimizes ligation bias by means of randomized adapter pools. Comparing the resulting data against publicly available colorectal cancer miRNA datasets, we demonstrate that the High Definition protocol moderates read count distributions, increases accuracy and improves sensitivity while maintaining high reproducibility. Moreover, by taking advantage of the more quantitative read counts, the cancer cell line panel and the normal mucosa samples, we identify a set of miRNAs that are highly expressed in epithelial cancerous cells, deregulated in colorectal cancer as compared to normal mucosa and differentially expressed between established molecular subgroups. As such, these miRNAs present strong candidates for functional validation and biomarker testing. In conclusion, we here present High Definition miRNA sequencing data for a large panel of clinically relevant colorectal cancer samples highlighting the potential of improved small RNA library preparation methods. Citation Format: Peter W. Eide, Lina Cekaite, Ping Xu, Leonardo A. Meza-Zepeda, Tamas Dalmay, Ragnhild A. Lothe. Randomized adapter pools for microRNA sequencing of colorectal cancer cell lines and primary tumors. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A44.