Clustering of Cancer Cell Lines Using A Promoter- Targeted Liquid Hybridization Capture-Based Bisulfite Sequencing Approach

Fei Gao; Junwen Wang; Guanyu Ji; Siyang Liu; Yu Yao; Tong Wang; Honglong Wu; Yudong Xia; Desheng Gong; Hui Jiang; Huanming Yang; Xiuqing Zhang

doi:10.1177/1533034614500416

Clustering of Cancer Cell Lines Using A Promoter- Targeted Liquid Hybridization Capture-Based Bisulfite Sequencing Approach

Technol Cancer Res Treat. 2015 Aug;14(4):383-94. doi: 10.1177/1533034614500416.

Authors

Fei Gao¹, Junwen Wang², Guanyu Ji², Siyang Liu³, Yu Yao³, Tong Wang³, Honglong Wu³, Yudong Xia³, Desheng Gong³, Hui Jiang³, Huanming Yang⁴, Xiuqing Zhang⁵

Affiliations

¹ Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China These authors contributed equally to this work. [email protected].
² Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China These authors contributed equally to this work.
³ Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China.
⁴ Science & Technology Department, BGI-Shenzhen, Shenzhen 518083, China King Abdulaziz University, Jeddah, Saudi Arabia James D. Watson Institute of Genome Science, Hangzhou, China.
⁵ The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, China.

PMID: 26269607
DOI: 10.1177/1533034614500416

Abstract

DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect to tissue-origins or clinically and etiologically distinct subtypes. In this study, we optimized our liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach on the gene promoter regions of 11 cell lines. Our results indicated that promoter methylomes could not only cluster cancer cell lines with respect to tissue origins but also differentiate cancer subtypes based on CpG island methylator phenotype (CIMP). Promoter-targeted LHC-BS as means for comprehensive screening and classifying cancer cells with promoter methylomes provided a powerful strategy for further complex clinical studies.

Keywords: CIMP; Cancer classification; DNA methylation; Promoter; Targeted bisulfite sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Line, Tumor
Cluster Analysis*
DNA Methylation
Gene Expression Regulation, Neoplastic*
Humans
Neoplasms / genetics*
Nucleic Acid Hybridization*
Promoter Regions, Genetic*
Sequence Analysis, DNA