Research Papers:

Clinical mutational profiling of 1006 lung cancers by next generation sequencing

Peter B. Illei _, Deborah Belchis, Li-Hui Tseng, Doreen Nguyen, Federico De Marchi, Lisa Haley, Stacy Riel, Katie Beierl, Gang Zheng, Julie R. Brahmer, Frederic B. Askin, Christopher D. Gocke, James R. Eshleman, Patrick M. Forde and Ming-Tseh Lin

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Oncotarget. 2017; 8:96684-96696. https://doi.org/10.18632/oncotarget.18042

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Peter B. Illei1,*, Deborah Belchis1,*, Li-Hui Tseng1,2, Doreen Nguyen1, Federico De Marchi1,3, Lisa Haley1, Stacy Riel1, Katie Beierl1, Gang Zheng1, Julie R. Brahmer4, Frederic B. Askin1, Christopher D. Gocke1,4, James R. Eshleman1,4, Patrick M. Forde4 and Ming-Tseh Lin1

1Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA

2Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan

3Division of Hematology and Bone Marrow Transplantation, University of Udine Hospital, Udine, Italy

4Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA

*These authors contributed equally to this work

Correspondence to:

Peter B. Illei, email: [email protected]

Ming-Tseh Lin, email: [email protected]

Keywords: lung, mutation, sequencing, cancer, profiling

Received: February 21, 2017     Accepted: May 10, 2017     Published: May 20, 2017


Analysis of lung adenocarcinomas for actionable mutations has become standard of care. Here, we report our experience using next generation sequencing (NGS) to examine AKT1, BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA genes in 1006 non-small cell lung cancers in a clinical diagnostic setting. NGS demonstrated high sensitivity. Among 760 mutations detected, the variant allele frequency (VAF) was 2–5% in 33 (4.3%) mutations and 2–10% in 101 (13%) mutations. A single bioinformatics pipeline using Torrent Variant Caller, however, missed a variety of EGFR mutations. Mutations were detected in KRAS (36% of tumors), EGFR (19%) including 8 (0.8%) within the extracellular domain (4 at codons 108 and 4 at codon 289), BRAF (6.3%), and PIK3CA (3.7%). With a broader reportable range, exon 19 deletion and p.L858R accounted for only 36% and 26% of EGFR mutations and p.V600E accounted for only 24% of BRAF mutations. NGS provided accurate sequencing of complex mutations seen in 19% of EGFR exon 19 deletion mutations. Doublet (compound) EGFR mutations were observed in 29 (16%) of 187 EGFR-mutated tumors, including 69% with two non-p.L858R missense mutations and 24% with p.L858 and non-p.L858R missense mutations. Concordant VAFs suggests doublet EGFR mutations were present in a dominant clone and cooperated in oncogenesis. Mutants with predicted impaired kinase, observed in 25% of BRAF-mutated tumors, were associated with a higher incidence of concomitant activating KRAS mutations. NGS demonstrates high analytic sensitivity, broad reportable range, quantitative VAF measurement, single molecule sequencing to resolve complex deletion mutations, and simultaneous detection of concomitant mutations.

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