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Next‐generation sequencing of liquid‐based cytology non–small cell lung cancer samples
Author(s) -
Reynolds Jordan P.,
Zhou Yaolin,
Jakubowski Maureen A.,
Wang Zhen,
Brainard Jennifer A.,
Klein Roger D.,
Farver Carol F.,
Almeida Francisco A.,
Cheng YuWei
Publication year - 2017
Publication title -
cancer cytopathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.29
H-Index - 57
eISSN - 1934-6638
pISSN - 1934-662X
DOI - 10.1002/cncy.21812
Subject(s) - kras , ion semiconductor sequencing , lung cancer , t790m , dna sequencing , medicine , neuroblastoma ras viral oncogene homolog , epidermal growth factor receptor , exon , cancer research , mutation , cancer , microbiology and biotechnology , gene , biology , oncology , genetics
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. Genomic DNA was multiplex‐amplified and enriched with Ion AmpliSeq Cancer Hotspot Panel v2 chemistry and the OneTouch 2 instrument; this was followed by semiconductor sequencing on the Ion Personal Genome Machine platform. The mutation hotspots of 6 NSCLC‐related genes ( BRAF, EGFR, ERBB2, KRAS, MET , and phosphatidylinositol‐4,5‐bisphosphate 3‐kinase catalytic subunit α [ PIK3CA ]) were analyzed with NextGENe and Torrent Suite bioinformatics tools. RESULTS The commonly identified EGFR sequence changes, including 4 L858R mutations, 3 exon 19 deletions, and 1 exon 20 insertion, were in 100% concordance between the assay platforms. Less common NSCLC variants were also found in the mutation hotspots of ERBB2, KRAS, MET , and PIK3CA genes. CONCLUSIONS NSCLC mutation analysis using NGS can be successfully performed on residual cell pellets derived from LBC samples. This approach allows the simultaneous examination of multiple mutation hotspots in a timely manner to improve patient care. Cancer Cytopathol 2017;125:178–187. © 2016 American Cancer Society.