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

被引：72

作者：

Zheng, Xiaoqi ^{[1
,2
,3
]}

Zhao, Qian ^{[4
,5
]}

Wu, Hua-Jun ^{[2
,3
]}

Li, Wei ^{[2
,3
,6
]}

Wang, Haiyun ^{[4
]}

Meyer, Clifford A. ^{[2
,3
,6
]}

Qin, Qian Alvin ^{[4
,6
]}

Xu, Han ^{[2
,3
,6
]}

Zang, Chongzhi ^{[2
,3
,6
]}

Jiang, Peng ^{[2
,3
,6
]}

Li, Fuqiang ^{[7
]}

Hou, Yong ^{[7
]}

He, Jianxing ^{[8
]}

Wang, Jun ^{[1
,7
,9
,10
,11
,12
]}

Zhang, Peng ^{[13
]}

Zhang, Yong ^{[4
]}

Liu, Xiaole Shirley ^{[2
,3
,6
]}

机构：

[1] Shanghai Normal Univ, Dept Math, Shanghai, Peoples R China

[2] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[3] Harvard Univ, Sch Publ Hlth, Boston, MA 02115 USA

[4] Tongji Univ, Sch Life Sci & Technol, Dept Bioinformat, Shanghai 200092, Peoples R China

[5] Tongji Univ, Adv Inst, Shanghai 200092, Peoples R China

[6] Dana Farber Canc Inst, Ctr Funct Canc Epigenet, Boston, MA 02115 USA

[7] BGI Shenzhen, Shenzhen, Peoples R China

[8] Guangzhou Med Univ, Affiliated Hosp 1, Guangzhou, Guangdong, Peoples R China

[9] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

[10] King Abdulaziz Univ, Princess Al Jawhara Ctr Excellence Res Hereditary, Jeddah 21589, Saudi Arabia

[11] Macau Univ Sci & Technol, Macau 999078, Peoples R China

[12] Univ Hong Kong, Dept Med, Hong Kong, Hong Kong, Peoples R China

[13] Tongji Univ, Shanghai Pulm Hosp, Sch Med, Dept Thorac Surg, Shanghai 200092, Peoples R China

来源：

GENOME BIOLOGY | 2014年 / 15卷 / 08期

基金：

美国国家卫生研究院;

关键词：

COPY-NUMBER ALTERATION; EPIGENETIC INACTIVATION; CANCER; GENE; HYPOMETHYLATION; IDENTIFICATION; HETEROGENEITY; VARIABILITY; LANDSCAPE; MARKERS;

D O I：

10.1186/s13059-014-0419-x

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：13

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