Transcriptomic and spliceosomic landscapes of pancreatic neuroendocrine tumors generated through Oxford Nanopore Technology sequencing

#4209

Introduction: Pancreatic Neuroendocrine tumors (PanNETs) are rare neoplasms with heterogenous nature, still poorly understood. Their low mutational burden has prompted to explore other molecular aspects, from epigenomics to transcriptomics. Increasing evidence indicates that transcriptomic changes, often derived from alterations in alternative splicing, can generate isoforms with oncogenic potential. In this context, long-read Oxford Nanopore Technology (ONT) has emerged as an ideal suited sequencing tool to deeply study transcriptomics and splicing variants.

Aim(s): To achieve a detailed characterization of PanNETs transcriptomic and spliceosomic landscapes using new sequencing tools to gain further understanding of their molecular architecture and identify new biomarkers and actionable targets.

Materials and methods: We used ONT to sequence cDNA from a set of 8 PanNETs and 3 reference tissues. After a quality check (pycoQC), we used the software EPI2ME to preprocess, identify full-length reads, trimming and correct the orientation. Then, we mapped the sequences to the human reference genome (minimap2); assembled the sequences (stringtie); compared to the reference annotation (gffcompare) and detected fusion genes (JAFFAL).

Conference:

Presenting Author: Moreno Montilla M

Authors: Moreno Montilla M, Jones G, Jeffries A, Blazquez Encinas Rey R, Bamford R,

Keywords: Pancreatic Neuroendocrine Tumor, Oxford Nanopore Technology Sequencing, Transcriptomics, Splicing, Fusion Genes,