Next-Generation Sequencing Approach to Non–Small Cell Lung Carcinoma Yields More Actionable Alterations

Abstract

Context.— Different testing algorithms and platforms for EGFR mutations and ALK rearrangements in advanced-stage lung adenocarcinoma exist. The multistep approach with single-gene assays has been challenged by more efficient next-generation sequencing (NGS) of a large number of gene alterations. The main criticism of the NGS approach is the detection of genomic alterations of uncertain significance. Objective.— To determine the best testing algorithm for patients with lung cancer in our clinical practice. Design.— Two testing approaches for metastatic lung adenocarcinoma were offered between 2012–2015. One approach was reflex testing for an 8-gene panel composed of DNA Sanger sequencing for EGFR, KRAS, PIK3CA, and BRAF and fluorescence in situ hybridization for ALK, ROS1, MET, and RET. At the oncologist's request, a subset of tumors tested by the 8-gene panel was subjected to a 50-gene Ion AmpliSeq Cancer Panel. Results.— Of 1200 non–small cell lung carcinomas (NSCLCs), 57 including 46 adenocarcinomas and NSCLCs, not otherwise specified; 7 squamous cell carcinomas (SCCs); and 4 large cell neuroendocrine carcinomas (LCNECs) were subjected to Ion AmpliSeq Cancer Panel. Ion AmpliSeq Cancer Panel detected 9 potentially actionable variants in 29 adenocarcinomas that were wild type by the 8-gene panel testing (9 of 29, 31.0%) in the following genes: ERBB2 (3 of 29, 10.3%), STK11 (2 of 29, 6.8%), PTEN (2 of 29, 6.8%), FBXW7 (1 of 29, 3.4%), and BRAF G469A (1 of 29, 3.4%). Four SCCs and 2 LCNECs showed investigational genomic alterations. Conclusions.— The NGS approach would result in the identification of a significant number of actionable gene alterations, increasing the therapeutic options for patients with advanced NSCLCs.

Molecular Pathology of Lung Cancer

“…Akciğer adenokarsinomlarının yaklaşık %1-2'sinde görülür ve yine aynı ALK gibi ROS1 rearranjmanı saptanan hastalar bir tirozin kinaz inhibitörü olan krizotinibe yanıt verir (12,19). ROS1 rearranjmanı gösterebilmek için FİSH, PCR, yeni nesil sekanslama gibi pek çok yöntem kullanılabilir (20,21). ROS1'de uygulanan FİSH yöntemi ALK rearranjmanı için uygulanan yöntemle aynı olup, pozitiflik sınır değeri de %15 ve üstü olarak belirlenmiştir.…”

Genetic Markers in Lung Cancer Diagnosis: A Review

“…The National Comprehensive Cancer Network Guidelines recommends testing a panel of genes for NSCLC, which consists of epidermal growth factor ( EGFR ) mutations, anapestic lymphoma kinase ( ALK ) rearrangements, and c-ros oncogene 1 ( ROS1 ) rearrangements. These biomarkers are considered the “must-tests” biomarkers in lung cancer patient diagnosis and are analyzed by single-gene assays such as PCR, immunohistochemistry (IHC), and FISH [ 20 , 55 , 56 , 57 , 58 , 59 , 60 ]. Sanger sequencing, qPCR, ddPCR, IHC, and FISH are regarded as the gold standard techniques of molecular analysis in clinical practice, while tumor-only sequencing, matched-tumor, and normal-tissue sequencing are the gold standards in somatic mutation detection [ 18 , 61 ].…”

Needle Biopsy Adequacy in the Era of Precision Medicine and Value-Based Health Care

“…Genomic Marker Assessment.-The assessment of genomic markers, particularly for mutations and gene rearrangements in tumors, 20,21,39 is evolving quickly, with preparations ranging from DNA isolation 40 and RNA probes 41,42 to next-generation sequencing. 43,44 The amount of sample required varies with the genomic technology. For DNA extraction from CNB histologic preparations, 1 lg of DNA is required.…”