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

ABSTRACT: 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.

SUBMITTER: Zheng X

PROVIDER: S-EPMC4165374 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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

Zheng Xiaoqi X Zhao Qian Q Wu Hua-Jun HJ Li Wei W Wang Haiyun H Meyer Clifford A CA Qin Qian Alvin QA Xu Han H Zang Chongzhi C Jiang Peng P Li Fuqiang F Hou Yong Y He Jianxing J Wang Jun J Wang Jun J Zhang Peng P Zhang Yong Y Liu Xiaole Shirley XS

Genome biology 20140807 8

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 ...[more]

PMID: 25103624

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

Project description:We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. With purity estimate, MethylPurify can identify differentially methylated regions (DMRs) from individual tumor 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. On real patient data where tumor to normal comparison were used as golden standard, MethylPurify called DMR from tumor samples alone at over 57% sensitivity and 91% specificity. Lung adenocarcinoma cancer and normal tissues from 5 patients were captured by Agilent SureSelect Methyl-Seq system, followed by bisulfite sequencing.

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