#Clc rna seq driver
#Clc rna seq software

Twenty ALK fusion partners have been described to date, including kinesin family member 5B ( KIF5B), trafficking from ER to golgi regulator ( TFG) and kinesin light chain 1 ( KLC1). ĪLK rearrangements occur in 3–8% of NSCLC cases, are generally mutually exclusive with EGFR or KRAS mutations and commonly found in adenocarcinomas of younger patients with light or no smoking history. Indeed, despite numerous resistance mechanisms associated with targeted therapies, treatment with EGFR (epidermal growth factor receptor) or ALK (ALK receptor tyrosine kinase) tyrosine kinase inhibitors has been shown to significantly improve progression-free and overall survival compared to standard chemotherapy in patients with advanced lung cancer harboring activating EGFR mutations or ALK rearrangements.

#Clc rna seq driver

A characteristic feature of NSCLCs is the addiction to single oncogenic driver events, which render these cancer types vulnerable to drugs targeting corresponding kinases. Unfortunately, around 75% of patients with lung cancer present with non-resectable, advanced stages of disease and thus most patients are not eligible for curative therapy. Lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) are the two most commonly occurring NSCLC subgroups. Non-small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancers. Subsequently, many fusion genes were identified in a variety of cancer types since, including lung cancer and many other solid tumors. The first fusion gene, BCR- ABL was discovered in chronic myeloid leukemia patients. In summary, especially RNA-based parallel sequencing approaches are potent tools for reliable detection of targetable gene fusions in clinical diagnostics.Ĭhromosomal rearrangements leading to the fusion of coding regions of two genes can result in expression of oncogenic hybrid proteins driving tumor progression. Additionally, many false positive fusions were observed.

#Clc rna seq software

The DNA-based SureSelect XT HS Custom Panel (Agilent) missed three fusions and nine fusions were only called by one software version. The Oncomine Focus Assay (Thermo Fisher Scientific) was the least adequate assay for our purposes, seven fusions were not covered by the assay and two fusions were classified as uncertain. Among the RNA-based assays, the Qiagen panel had the highest number of false positive events. Both, the ArcherDX and Qiagen panels missed only one fusion event. The Illumina assay detected all tested fusions and showed the smallest number of false positive results. Four RNA-based assays and one DNA-based assay were compared two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific). Reliable detection of multiple gene fusions is therefore essential.įive commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Gene fusions represent promising targets for cancer therapy in lung cancer.