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Introduction: Gene fusions are frequently associated with tumorigenesismalignant tumors. Highly sensitive and reproducible detection of gene fusions in clinical samples, especially formalin-fixed paraffin-embedded (FFPE) specimens, is important for diagnosis, prognosis, and treatment guidance. Although many clinical tests utilize next-generation-sequencing (NGS) for detection of genetic alterations, reliable detection of gene fusions by NGS in FFPE samples remains a challenge. Methods: Five FFPE non-small cell lung cancer samples confirmed by FISH to contain EML4-ALK or KIF5B-RET fusions were selected for testing along with the Seraseq™ FFPE Tumor Fusion RNA Reference Material, v1, which evaluates forcontains 12 known fusions. Four operators prepared NGS libraries for each sample (89-250ng input) using the commercially available QIAseq RNAscan Oncology Panel, which targets 223 fusion gene pairs or 576 unique breakpoints. The resulting libraries were sequenced on an Illumina® NextSeq 500 sequencer. Demultiplexed FASTQ files were analyzed using cloud-based QIAseq RNAscan Analysis pipeline v1.7.20.2. Detected fusions that are on the panel's target list were reported as curated gene fusions and assigned a score based on unique molecules supporting the transcript. Results: For the Seraseq™ FFPE Tumor Fusion RNA Reference v1 sample, all 12 expectedknown fusions were detected in each of the libraries generated by four different operators. The analysis pipeline correctly called the expected fusion in all four replicates of the five clinical FFPE samples tested, which varied in both input quantityamount and quality. Reproducibility was evaluated by comparing the score values across replicate libraries for each sample; expected fusion detection was 100% consistent between users, and the average correlation coefficient for the fusion score was 0.995. Conclusions: The commercially available QIAseq RNAscan Oncology panel is a highly sensitive and robust product for detection of gene fusions in FFPE samples. QIAseq RNAscan methodology provides a useful tool for studying gene fusions in tumor samples and with optimization, customization, and validation can further fit the specific needs for of clinical laboratories. Citation Format: Jeffrey Falk, Parth Sitlani, Claire Orosco, Maya Panjikaran, Dana Weiner, Song Tian, Raed Samara, John DiCarlo, Yexun Wang, Eric Lader, Frank Reinecke. Robust gene fusion detection in formalin-fixed tissue sample with QIAseq RNAscan Oncology Panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5356.

e24178Background: MET exon 14 skipping is detected in 2%-4% of NSCLC and is known to confer increased sensitivity to MET inhibitors. Over 100 distinct DNA sequence variants have been identified tha...

e24177Background: There are significant prognostic and therapeutic benefits in monitoring minimal/measurable residual disease (MRD) in hematologic malignancies. However, monitoring of MRD requires ...

Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5’ to 3’ exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs., Author Summary Cells undergoing changes in gene expression programs such as nutritional deprivation and other stresses exhibit formation of ribonucleoprotein (RNP) complexes. In Saccharomyces cerevisiae, the majority of investigations to date involve analysis of P-body (PB) and stress-granule RNP formation following nutritional stress. Few studies have investigated RNP formation induced by the mating-MAP-kinase pathway. In this study, we examined how this process influences genome stability via control of retrotransposon activation. During the mating response, expression of the retrotransposon Ty3 is induced and Ty3 virus-like particles form in RNP clusters called retrosomes. We show that mating retrosomes contain PB components that are essential for Ty3 expression, re-localization of Ty3 RNA and protein from polysomes into foci, and retrotransposition. In animal germ cell lineages, PB components are found in perinuclear complexes with RNA interference suppressors of retrotransposition. We speculate that when RNA interference is relaxed and retrotransposition is observed, some members of these complexes play positive roles as we observe in budding yeast.