Research Papers:

PIK3CA mutation detection in metastatic biliary cancer using cell-free DNA

Seung Tae Kim, Maruja Lira, Shibing Deng, Sujin Lee, Young Suk Park, Ho Yeong Lim, Won Ki Kang, Mao Mao, Jin Seok Heo, Wooil Kwon, Jeeyun Lee, Kee-Taek Jang and Joon Oh Park _

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Oncotarget. 2015; 6:40026-40035. https://doi.org/10.18632/oncotarget.5432

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Seung Tae Kim1,*, Maruja Lira2,*, Shibing Deng2, Sujin Lee1, Young Suk Park1, Ho Yeong Lim1, Won Ki Kang1, Mao Mao3, Jin Seok Heo4, Wooil Kwon4, Kee‑Taek Jang5, Jeeyun Lee1,6, Joon Oh Park1,6

1Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea

2Precision Medicine, Oncology Research Unit, Pfizer, Inc, San Diego, CA, USA

3WuXi AppTec, Shanghai, China

4Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea

5Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea

6Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea

*These authors have contributed equally to this work

Correspondence to:

Joon Oh Park, e-mail: [email protected]

Jeeyun Lee, e-mail: [email protected]

Keywords: cell free DNA (cfDNA), PIK3CA mutation, droplet digital PCR (ddPCR)

Received: July 13, 2015     Accepted: October 05, 2015     Published: October 16, 2015


PIK3CA mutation is considered a good candidate for targeted therapies in cancers, especially biliary tract cancer (BTC). We evaluated the utility of cell free DNA (cfDNA) from serum by using droplet digital PCR (ddPCR) as an alternative source for PIK3CA mutation analysis. To identify matching archival tumour specimens from serum samples of advanced BTC patients, mutation detection using ddPCR with Bio-Rad’s PrimePCR mutation and wild type assays were performed for PIK3CA p.E542K, p.E545K, and p.H1047R. Thirty-eight patients with metastatic BTC were enrolled. Only one (BTC 29T) sample (n = 38) was positive for PIK3CA p.E542K and another (BTC 27T) for p.H1047R mutation; none was positive for PIK3CA p.E545K. Matched serum sample (BTC 29P) was positive for PIK3CA p.E542K with 28 mutant copies detected, corresponding to 48 copies/ml of serum and an allelic prevalence of 0.3%. Another matched serum sample (BTC 27P) was positive for PIK3CA p.H1047R with 10 mutant copies detected, i.e. 18 copies/ml and an allelic frequency of 0.2%. High correlation was noted in the PIK3CA mutation status between tumour gDNA and serum cfDNA. Low-level PIK3CA mutations were detectable in the serum indicating the utility of cfDNA as a DNA source to detect cancer-derived mutations in metastatic biliary cancers.

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