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Detection of somatic variants and EGFR mutations in cell-free DNA from non-small cell lung cancer patients by ultra-deep sequencing using the ion ampliseq cancer hotspot panel and droplet digital polymerase chain reaction

Authors
Sung, Jae SookChong, Hyon YongKwon, Nak-JungKim, Hae MiLee, Jong WonKim, BoyeonLee, Saet ByeolPark, Chang WonChoi, Jung YoonChang, Won JinChoi, Yoon JiLee, Sung YongKang, Eun JooPark, Kyong HwaKim, Yeul Hong
Issue Date
5-12월-2017
Publisher
IMPACT JOURNALS LLC
Keywords
non-small-cell lung carcinoma; multiplex polymerase chain reaction; missense mutation; cell-free DNA; molecular targeted therapy
Citation
ONCOTARGET, v.8, no.63, pp.106901 - 106912
Indexed
SCIE
SCOPUS
Journal Title
ONCOTARGET
Volume
8
Number
63
Start Page
106901
End Page
106912
URI
https://scholar.korea.ac.kr/handle/2021.sw.korea/81213
DOI
10.18632/oncotarget.22456
ISSN
1949-2553
Abstract
Highly sensitive genotyping assays can detect mutations in cell-free DNA (cfDNA) from cancer patients, reflecting the biology of each patient's cancer. Because circulating tumor DNA comprises a small, variable fraction of DNA circulating in the blood, sensitive parallel multiplexing tests are required to determine mutation profiles. We prospectively examined the clinical utility of ultra-deep sequencing analysis of cfDNA from 126 non-small cell lung cancer (NSCLC) patients using the Ion AmpliSeq Cancer Hotspot Panel v2 (ICP) and validated these findings with droplet digital polymerase chain reaction (ddPCR). ICP results were compared with tumor tissue genotyping (TTG) results and clinical outcomes. A total of 853 variants were detected, with a median of four variants per patient. Overall concordance of ICP and TTG analyses was 90% for EGFR exon 19 deletion and 88% for the L858R mutation. Of 34 patients with a well-defined EGFR activating mutation defined based on the results of ICP and TTG, 31 (81.6%) showed long-term disease control with EGFR TKI treatment. Of 56 patients treated with an EGFR tyrosine kinase inhibitor (TKI), the presence of the de novo T790M mutation was confirmed in 28 (50%). Presence of this de novo mutation did not have a negative effect on EGFR TKI treatment. Ultradeep sequencing analysis of cfDNA using ICP combined with confirmatory ddPCR was effective at defining driver genetic changes in NSCLC patients. Comprehensive analysis of tumor DNA and cfDNA can increase the specificity of molecular diagnosis, which could translate into tailored treatment.
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