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.
authors.forename: Xiaoqi
authors.initials: X
authors.lastname: Zheng
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhao
authors.forename: Hua-Jun
authors.initials: HJ
authors.lastname: Wu
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Haiyun
authors.initials: H
authors.lastname: Wang
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Qian Alvin
authors.initials: QA
authors.lastname: Qin
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.forename: Chongzhi
authors.initials: C
authors.lastname: Zang
authors.forename: Peng
authors.initials: P
authors.lastname: Jiang
authors.forename: Fuqiang
authors.initials: F
authors.lastname: Li
authors.forename: Yong
authors.initials: Y
authors.lastname: Hou
authors.forename: Jianxing
authors.initials: J
authors.lastname: He
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xiaole Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D000465:Algorithms; D001940:Breast / Q000378:metabolism / Q000473:pathology; D001943:Breast Neoplasms / Q000235:genetics*; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D005260:Female; D018740:Genetic Heterogeneity; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D015233:Models, Statistical; D017422:Sequence Analysis, DNA
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