Bile-based detection of extrahepatic cholangiocarcinoma with quantitative DNA methylation markers and its high sensitivity

So Hyun Shin, Kyoungbun Lee, Baek Hui Kim, Nam Yun Cho, Jin Young Jang, Yong Tae Kim, Donguk Kim, Ja June Jang, Gyeong Hoon Kang

Research output: Contribution to journalArticlepeer-review

35 Citations (Scopus)


Extrahepatic cholangiocarcinoma (EHC) is usually difficult to diagnose by bile cytology because of cellular disintegration. However, DNA samples from bile fluid can provide sufficient materials to screen for the presence of EHC. We developed DNA methylation marker panels that can be used for MethyLight assay-based detection of EHC in bile fluid specimens. The methylation status of 59 DNA methylation markers was investigated in 20 EHC and 20 non-neoplastic gallbladder tissue samples with MethyLight assay to determine cancer-specific DNA methylation markers. Through assaying cancer-specific DNA methylation markers in a training set (n = 40) and validation set (n = 45) of bile fluid specimens from patients with EHC or those without cancer, we selected suitable marker panels that were assessed for their performance in a third set (test set; n = 40). Four marker panels showed a sensitivity of 60% or more and a specificity of 100% in both the training and validation sets, whereas bile cytology displayed a sensitivity of 40% to 46% and a specificity of 100%. In an independent test set of bile fluid samples, a five-gene panel (CCND2, CDH13, GRIN2B, RUNX3, and TWIST1) detected EHC at a sensitivity of 83%, which was far higher than that of bile cytology (46%, P = 0.004). Using bile fluids, a methylation assay consisting of a five-gene panel may be useful for detecting EHC and in helping to increase the sensitivity of preoperative diagnoses.

Original languageEnglish
Pages (from-to)256-263
Number of pages8
JournalJournal of Molecular Diagnostics
Issue number3
Publication statusPublished - 2012 May
Externally publishedYes

Bibliographical note

Funding Information:
Supported by a grant from the Seoul National University Hospital Research Fund ( 30-2009-001-0 ), a grant from the Korea Research Foundation Grant (MOEHRD; KRF-2008-041-E00099 ), a grant from the National R&D Program for Cancer Control, Ministry of Health & Welfare , Republic of Korea ( 0720540 ), and a grant from Priority Research Centers Program, National Research Foundation of Korea (NRF), funded by the Ministry of Education, Science and Technology ( 200-0093820 ).

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine


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