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MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes

Xiaoqi Zheng12, Qian Zhao34, Hua-Jun Wu2, Wei Li25, Haiyun Wang3, Clifford A Meyer25, Qian Alvin Qin35, Han Xu25, Chongzhi Zang25, Peng Jiang25, Fuqiang Li6, Yong Hou6, Jianxing He7, Jun Wang1011689, Jun Wang1, Peng Zhang12*, Yong Zhang3* and Xiaole Shirley Liu25*

Author Affiliations

1 Department of Mathematics, Shanghai Normal University, Shanghai, China

2 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA

3 Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China

4 Tongji University Advanced Institute, Translational Medicine, Shanghai, China

5 Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

6 BGI-Shenzhen, Shenzhen, China

7 The First Affiliated Hospital of Guangzhou Medical College, Guangzhou, China

8 Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark

9 Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia

10 Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China

11 Department of Medicine, University of Hong Kong, Pokfulam, Hong Kong

12 Department of Thoracic Surgery, Shanghai Pulmonary Hospital of Tongji University School of Medicine, Shanghai, China

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Genome Biology 2014, 15:419  doi:10.1186/s13059-014-0419-x

Published: 7 August 2014


We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated regions (DMRs) from individual tumor methylome samples, without genomic variation information or prior knowledge from other datasets. In simulations with mixed bisulfite reads from cancer and normal cell lines, MethylPurify correctly inferred tumor purity and identified over 96% of the DMRs. From patient data, MethylPurify gave satisfactory DMR calls from tumor methylome samples alone, and revealed potential missed DMRs by tumor to normal comparison due to tumor heterogeneity.