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

Xiaoqi Zheng; Qian Zhao; Hua Jun Wu; Wei Li; Haiyun Wang; Clifford A. Meyer; Qian A.lvin Qin; Han Xu; Chongzhi Zang; Peng Jiang; Fuqiang Li; Yong Hou; Jianxing He; Jun Wang; Peng Zhang; Yong Zhang; Xiaole S.hirley Liu

doi:10.1186/s13059-014-0419-x

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

Xiaoqi Zheng, Qian Zhao, Hua Jun Wu, Wei Li, Haiyun Wang, Clifford A. Meyer, Qian A.lvin Qin, Han Xu, Chongzhi Zang, Peng Jiang, Fuqiang Li, Yong Hou, Jianxing He, Jun Wang, Peng Zhang, Yong Zhang, Xiaole S.hirley Liu

Research output: Contribution to journal › Article › peer-review

69 Scopus citations

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.

Original language	English (US)
Pages (from-to)	419
Number of pages	1
Journal	Genome biology
Volume	15
Issue number	8
DOIs	https://doi.org/10.1186/s13059-014-0419-x
State	Published - 2014
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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Zheng, X., Zhao, Q., Wu, H. J., Li, W., Wang, H., Meyer, C. A., Qin, Q. A. L., Xu, H., Zang, C., Jiang, P., Li, F., Hou, Y., He, J., Wang, J., Zhang, P., Zhang, Y., & Liu, X. S. H. (2014). MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome biology, 15(8), 419. https://doi.org/10.1186/s13059-014-0419-x

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title = "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. ",

author = "Xiaoqi Zheng and Qian Zhao and Wu, {Hua Jun} and Wei Li and Haiyun Wang and Meyer, {Clifford A.} and Qin, {Qian A.lvin} and Han Xu and Chongzhi Zang and Peng Jiang and Fuqiang Li and Yong Hou and Jianxing He and Jun Wang and Peng Zhang and Yong Zhang and Liu, {Xiaole S.hirley}",

year = "2014",

doi = "10.1186/s13059-014-0419-x",

language = "English (US)",

volume = "15",

pages = "419",

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TY - JOUR

T1 - MethylPurify

T2 - tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes

AU - Zheng, Xiaoqi

AU - Zhao, Qian

AU - Wu, Hua Jun

AU - Li, Wei

AU - Wang, Haiyun

AU - Meyer, Clifford A.

AU - Qin, Qian A.lvin

AU - Xu, Han

AU - Zang, Chongzhi

AU - Jiang, Peng

AU - Li, Fuqiang

AU - Hou, Yong

AU - He, Jianxing

AU - Wang, Jun

AU - Zhang, Peng

AU - Zhang, Yong

AU - Liu, Xiaole S.hirley

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

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AN - SCOPUS:84924551236

SN - 1474-7596

VL - 15

SP - 419

JO - Genome biology

JF - Genome biology

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ER -

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

Abstract

ASJC Scopus subject areas

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