Identification of Novel MET Exon 14 Skipping Variants in Non-Small Cell Lung Cancer Patients: A Prototype Workflow Involving in Silico Prediction and RT-PCR.

Background and aims: The MET exon 14 skipping (METex14) is an oncogenic driver mutation that provides a therapeutic opportunity in non-small cell lung cancer (NSCLCs) patients. This event often results from sequence changes at the MET canonical splicing sites. We characterize two novel non-canonical splicing site variants of MET that produce METex14.

Gene Fusion Identification Using Anchor-Based Multiplex PCR and Next-Generation Sequencing.

Background: Methods for identifying gene fusion events, such as fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and transcriptome analysis, are either single gene approaches or require bioinformatics expertise not generally available in clinical laboratories. We analytically validated a customized next-generation sequencing (NGS) panel targeting fusion events in 34 genes involving soft-tissue sarcomas.

Methods: Specimens included 87 formalin-fixed paraffin-embedded (FFPE) tissues with known gene fusion status.

Real-time PCR and targeted next-generation sequencing in the detection of low level mutations: Instructive case analyses.

Background: Allele specific real-time PCR and next-generation sequencing (NGS) are widely used to detect somatic mutation in non-small cell lung cancer (NSCLC). Both methods commonly use formalin-fixed paraffin-embedded (FFPE) tissues as diagnostic materials. Real-time PCR has the advantage of being easy to use and more tolerant of variable DNA quality, but has limited multiplex capability.

Next-generation sequencing of liquid-based cytology non-small cell lung cancer samples.

Background: The detection of mutated epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) with residual cell pellets derived from liquid-based cytology (LBC) samples (eg, endoscopic ultrasound-guided fine-needle aspiration) has been validated with allele-specific polymerase chain reaction. The aim of this study was to validate next-generation sequencing (NGS) technology for detecting gene mutations with residual cell pellets from LBC.

Methods: Archived DNA extracted from LBC samples of adenocarcinoma stored in PreservCyt with a known EGFR mutation status was retrieved.

Colorectal carcinomas with submucosal invasion (pT1): analysis of histopathological and molecular factors predicting lymph node metastasis.

Submucosally invasive colorectal carcinoma (pT1) has the potential to be cured by local excision. In US surgical intervention is reserved for tumors with high-grade morphology, lymphvascular invasion, and close/positive margin. In other countries, particularly Japan, surgical therapy is also recommended for mucinous tumors, tumors with >1000 μm of submucosal invasion, and those with high tumor budding.

Does neoadjuvant therapy alter KRAS and/or MSI results in rectal adenocarcinoma testing?

To our knowledge, the genotoxic effects of neoadjuvant chemoradiation therapy on molecular diagnostic testing results are unknown. However, if neoadjuvant treatments were to alter molecular test results, clinical decision-making could be misled. This raises questions about the appropriateness of using posttreatment tumor for testing.