Multiplexed molecular profiling of lung cancer with malignant pleural effusion using next generation sequencing in Chinese patients

Abstract

Lung cancer is the most common type of cancer and the leading cause of cancer-associated death worldwide. Malignant pleural effusion (MPE), which is observed in ~50% of advanced non-small cell lung cancer (NSCLC) cases, and most frequently in lung adenocarcinoma, is a common complication of stage III-IV NSCLC, and it can be used to predict a poor prognosis. In the present study, multiple oncogene mutations were detected, including 17 genes closely associated with initiation of advanced lung cancer, in 108 MPE samples using next generation sequencing (NGS). The NGS data of the present study had broader coverage, deeper sequencing depth and higher capture efficiency compared with NGS findings of previous studies on MPE. In the present study, using NGS, it was demonstrated that 93 patients (86%) harbored EGFR mutations and 62 patients possessed mutations in EGFR exons 18-21, which are targets of available treatment agents. EGFR L858R and exon 19 indel mutations were the most frequently observed alterations, with frequencies of 31 and 25%, respectively. In 1 patient, an EGFR amplification was identified and 6 patients possessed a T790M mutation. ALK + EML4 gene fusions were identified in 6 patients, a ROS1 + CD74 gene fusion was detected in 1 patient and 10 patients possessed a BIM (also known as BCL2L11) 2,903-bp intron deletion. In 4 patients, significant KRAS mutations (G12D, G12S, G13C and A146T) were observed, which are associated with resistance to afatinib, icotinib, erlotinib and gefitinib. There were 83 patients with ERBB2 mutations, but only two of these mutations were targets of available treatments. The results of the present study indicate that MPE is a reliable specimen for NGS based detection of somatic mutations.

Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review

“…Other smaller DNA-targeted panels have been evaluated on FFPE clinical samples: a good concordance with gold standard methods and a good sensitivity and specificity was observed, the overall amount of DNA input required is usually equal to 50–250 ng [ 47 , 48 , 49 , 50 , 51 , 52 ]. Moreover, this approach has also been specifically tested on critical clinical samples like Endobronchial Ultrasound Guided Transbronchial Needle Aspiration (EBUS).…”

“…Particularly, Xie and collaborators evaluated 85 FFPE EBUS specimens using the Lung Core 56 gene panel (Burning Rock Biotech; Asia-Pacific) and found that 77 samples also resulted as adequate when the percentage of tumor cells was as low as 5% [ 47 ]. Recently, Ruan et al evaluated 108 malignant effusions from lung cancer patients; they used a panel including 17 lung cancer-associated genes and they successfully identified both gene mutations and rearrangements [ 48 ].…”

Detection ofMETexon 14 skipping mutations in non-small cell lung cancer: overview and community perspective

“…Given the diversity of METex14 events and the potential for these alterations to occur in regions flanking exon 14, the ability to probe larger regions of interest makes the hybrid capture approach more amenable to detecting the alterations leading to METex14 [36,47]. Additionally, because of the favorable properties of hybrid capture-based assays, this methodology has been used to capture other alterations leading to oncogenic gene fusion events [51,52]. However, it should be noted that hybrid capture-based platforms may not be suitable for small tissue samples, because they require relatively large amounts of DNA, ranging from 50 to 250 ng, whereas amplicon-based platforms require about 10 ng of DNA input [53][54][55].…”

“…Additionally, an in silico study comparing 7 different DNA amplicon-based assays revealed that the detection of known METex14 ranged from 3% to 63% [27]. The hybrid capture approach is a preferred method for detecting alterations leading to METex14 and other oncogenic gene fusions because the assay is able to isolate large fragments of DNA -including regions surrounding the target of interestdue to the probes being significantly longer than PCR primers, which avoids allele dropout [45,47,51,52]. However, this method also requires bioinformatic tools optimized to detect these events, which could be an additional obstacle for oncologists and laboratories looking to switch testing panels [47].…”

Construction of a reference material panel for detectingKRAS/NRAS/EGFR/BRAF/METmutations in plasma ctDNA

“…Based on targeted sequencing using PCR amplicons or hybrid capture, next-generation sequencing (NGS) is used to detect more loci. NGS can also detect amplifications, deletions and fusion in a single test, 25 and promises to improve diagnostic yield.…”