Can massive parallel sequencing replace fluorescent in situ hybridization for detection of fusion genes in patients with non-small cell lung cancer?

Abstract: Abstract Today the golden standard method to find fusion genes is with fluorescent in situ hybridization. Massive parallel sequencing is a method that can analyze several genes and samples at the same time at a lower cost. The aim of this study was to compare massive parallel sequencing with fluorescent in situ hybridization for detection of fusion genes in patients with non-small cell lung cancer. Additionally, an evaluation of RNA extraction was performed to obtain RNA samples with quality. Four different purification methods were evaluated and method C, a semi-automatic method showed the highest quantity and a good quality. Method C was used to extract 23 samples from non-small cell lung cancer patients and analyzed with massive parallel sequencing and panel Oncomine Solid Tumour Fusion Transcript Kit (Thermo Fisher Scientific). A total of 11/14 samples showed concordant results with fluorescent in situ hybridization. Three samples either had too low quality or there was too little tissue left on the FFPE block to determine the tumor cell content. Unfortunately, there is a shortage of positive fusion genes samples since the qualities of the samples were uncertain and especially the proportion of tumor cells. No conclusion can be drawn if massive parallel sequencing can replace fluorescent in situ hybridization in the future for patients with non-small cell lung cancer. Further studies are required.