Penalized logistic regression for high-dimensional DNA methylation data with case-control studies

被引：75

作者：

Sun, Hokeun ^{[1
]}

Wang, Shuang ^{[1
]}

机构：

[1] Columbia Univ, Mailman Sch Publ Hlth, Dept Biostat, New York, NY 10032 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 10期

关键词：

VARIABLE SELECTION; REGULARIZATION; LASSO;

D O I：

10.1093/bioinformatics/bts145

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Results: Using simulation studies we demonstrated that the proposed procedure outperforms existing main-stream regularization methods such as lasso and elastic-net when data is correlated within a group. We also applied our method to identify important CpG sites and corresponding genes for ovarian cancer from over 20 000 CpGs generated from Illumina Infinium HumanMethylation27K Beadchip. Some genes identified are potentially associated with cancers.

引用

页码：1368 / 1375

页数：8

共 23 条

[1] Stability Selection for Genome-Wide Association [J].

Alexander, David H. ;

Lange, Kenneth .

GENETIC EPIDEMIOLOGY, 2011, 35 (07) :722-728

[2] High-throughput DNA methylation profiling using universal bead arrays [J].

Bibikova, M ;

Lin, ZW ;

Zhou, LX ;

Chudin, E ;

Garcia, EW ;

Wu, B ;

Doucet, D ;

Thomas, NJ ;

Wang, YH ;

Vollmer, E ;

Goldmann, T ;

Seifart, C ;

Jiang, W ;

Barker, DL ;

Chee, MS ;

Floros, J ;

Fan, JB .

GENOME RESEARCH, 2006, 16 (03) :383-393

[3]

Breheny P, 2009, STAT INTERFACE, V2, P369

[4] PATHWISE COORDINATE OPTIMIZATION [J].

Friedman, Jerome ;

Hastie, Trevor ;

Hoefling, Holger ;

Tibshirani, Robert .

ANNALS OF APPLIED STATISTICS, 2007, 1 (02) :302-332

[5] Regularization Paths for Generalized Linear Models via Coordinate Descent [J].

Friedman, Jerome ;

Hastie, Trevor ;

Tibshirani, Rob .

JOURNAL OF STATISTICAL SOFTWARE, 2010, 33 (01) :1-22

[6] Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions [J].

Houseman, E. Andres ;

Christensen, Brock C. ;

Yeh, Ru-Fang ;

Marsit, Carmen J. ;

Karagas, Margaret R. ;

Wrensch, Margaret ;

Nelson, Heather H. ;

Wiemels, Joseph ;

Zheng, Shichun ;

Wiencke, John K. ;

Kelsey, Karl T. .

BMC BIOINFORMATICS, 2008, 9 (1)

[7] A statistical framework for Illumina DNA methylation arrays [J].

Kuan, Pei Fen ;

Wang, Sijian ;

Zhou, Xin ;

Chu, Haitao .

BIOINFORMATICS, 2010, 26 (22) :2849-2855

[8] Network-constrained regularization and variable selection for analysis of genomic data [J].

Li, Caiyan ;

Li, Hongzhe .

BIOINFORMATICS, 2008, 24 (09) :1175-1182

[9] VARIABLE SELECTION AND REGRESSION ANALYSIS FOR GRAPH-STRUCTURED COVARIATES WITH AN APPLICATION TO GENOMICS [J].

Li, Caiyan ;

Li, Hongzhe .

ANNALS OF APPLIED STATISTICS, 2010, 4 (03) :1498-1516

[10]

London SJ, 1997, CANCER RES, V57, P5001

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