Comparative Study of NGS Platform Ion Torrent Personal Genome Machine and Therascreen Rotor-Gene Q for the Detection of Somatic Variants in Cancer

Abstract

Molecular profiling of a tumor allows the opportunity to design specific therapies which are able to interact only with cancer cells characterized by the accumulation of several genomic aberrations. This study investigates the usefulness of next-generation sequencing (NGS) and mutation-specific analysis methods for the detection of target genes for current therapies in non-small-cell lung cancer (NSCLC), metastatic colorectal cancer (mCRC), and melanoma patients. We focused our attention on EGFR, BRAF, KRAS, and BRAF genes for NSCLC, melanoma, and mCRC samples, respectively. Our study demonstrated that in about 2% of analyzed cases, the two techniques did not show the same or overlapping results. Two patients affected by mCRC resulted in wild-type (WT) for BRAF and two cases with NSCLC were WT for EGFR according to PGM analysis. In contrast, these samples were mutated for the evaluated genes using the therascreen test on Rotor-Gene Q. In conclusion, our experience suggests that it would be appropriate to confirm the WT status of the genes of interest with a more sensitive analysis method to avoid the presence of a small neoplastic clone and drive the clinician to correct patient monitoring.

To Get the Most out of the Least: BRAF Molecular Evaluation in Melanoma Metastases on Cell Suspension from Fine Needle Aspiration Cytology Needle Rinses

“…Different vials and technical supports can be used to collect biomaterial from CM metastasis FNAC samples for predictive assessment of BRAF mutational status, including direct smears, cytocentrifugated slides, cell-block sections, and cell suspensions [15,16]. This assessment can be performed using a variety of molecular procedures, including direct product sequencing PCR, pyrosequencing, real-time PCR, molecular analysis filter hybridization, and mass spectrometry [17]. Currently, the BRAF molecular assessment on CM metastases FNAC samples implies the loss of one or more diagnostic smears, or the execution of one or more passes to obtain dedicated cytological samples.…”

Predictive Evaluation on Cytological Sample of Metastatic Melanoma: The Role of BRAF Immunocytochemistry in the Molecular Era

“…Therefore, the molecular workflow for CM should start with the identification of BRAF mutation in stage IIIC or IV CM patients [ 9 ]. This evaluation can be carried out using different molecular procedures, including direct sequencing of the PCR product, pyrosequencing, RealTime PCR, molecular hybridization on filter and mass spectrometry [ 10 ]. Recently, a BRAF V600E mutation-specific immunohistochemical antibody was introduced, with sensitivity and specificity comparable to the molecular tests in histological samples [ 11 , 12 , 13 ].…”