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
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Jae Sook Sung1, Hyon Yong Chong2, Nak-Jung Kwon2, Hae Mi Kim2, Jong Won Lee1, Boyeon Kim1, Saet Byeol Lee1, Chang Won Park2, Jung Yoon Choi3, Won Jin Chang3, Yoon Ji Choi3, Sung Yong Lee4, Eun Joo Kang4, Kyong Hwa Park1,3 and Yeul Hong Kim1,3
1Cancer Research Institute, Korea University, Seoul, Republic of Korea
2Macrogen, Seoul, Republic of Korea
3Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
4Department of Internal Medicine, Guro Hospital, Korea University, Seoul, Republic of Korea
Yeul Hong Kim, email: firstname.lastname@example.org
Keywords: non-small-cell lung carcinoma; multiplex polymerase chain reaction; missense mutation; cell-free DNA; molecular targeted therapy
Received: June 01, 2017 Accepted: October 17, 2017 Published: November 15, 2017
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. Ultra-deep 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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