A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data

Bioinformatics

Volumn 28, Issue 8, 2012, Pages 1109-1113

  Chen, Zhongxue ^a   Liu, Qingzhong ^b   Nadarajah, Saralees ^c  

^a UNIVERSITY OF TEXAS   (United States)

^b SAM HOUSTON STATE UNIVERSITY   (United States)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AGED; ARTICLE; CASE CONTROL STUDY; COMPUTER SIMULATION; DNA METHYLATION; DNA MICROARRAY; FEMALE; GENETICS; HUMAN; MIDDLE AGED; OVARY TUMOR; STATISTICAL MODEL;

AGED; AGED, 80 AND OVER; CASE-CONTROL STUDIES; COMPUTER SIMULATION; DNA METHYLATION; FEMALE; HUMANS; MIDDLE AGED; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS;

EID: 84859750030     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts093     Document Type: Article

References (21)

1. Baylin, S.B. and Ohm, J.E. (2006) Epigenetic gene silencing in cancer-a mechanism for early oncogenic pathway addiction? Nat.Rev.Cancer, 6, 107-116.
2. Chen, Z. (2011) Is the weighted z-test the best method for combining probabilities from independent tests? J. Evolution. Biol., 24, 926-930.
3. Chen, Z. (2011) A new association test based on chi-square partition for case-control GWA studies. Genet. Epidemiol., 35,658-663.
4. Chen, Z. and Nadarajah, S. (2011) Comments on 'Choosing an optimal method to combine p-values' by SunghoWon, Nathan Morris, Qing Lu and Robert C. Elston, Statistics in Medicine 2009; 28: 1537-1553. Stat. Med., 30, 2959-2961.
5. Chen, Z. and Ng, H.K.T. (2012)Arobust method for testing association in genome-wide association studies. Hum. Hered., 73, 26-34.
6. Christensen, B.C. et al. (2009) Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet., 5, e1000602.
7. Cousins, R.D. (2008) Annotated bibliography of some papers on combining significances or p-values. arXiv:0705.2209v2.
8. Esary, J.D. et al. (1967) Association of random variables, with applications. Ann. Math. Stat., 38, 1466-1474.
9. Feinberg, A.P. and Tycko, B. (2004) The history of cancer epigenetics. Nat. Rev. Cancer, 4, 143-153.
10. Fisher, R.A. (1932) Statistical Methods for Research Workers. Oliver and Boyd, Edinburgh.
11. Jabbari, K. and Bernardi, G. (2004) Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene, 333, 143-149.
12. Jones, P.A. and Baylin, S.B. (2002) The fundamental role of epigenetic events in cancer. Nat. Rev. Genet., 3, 415-428.
13. Kuan, P.F. et al. (2010) A statistical framework for Illumina DNA methylation arrays. Bioinformatics, 26, 2849.
14. Kulis, M. and Esteller, M. (2010) DNA methylation and cancer. Adv. Gene., 70, 27-56.
15. Laird, P.W. (2010) Principles and challenges of genome-wideDNAmethylation analysis. Nat. Rev. Genet., 11, 191-203.
16. Owen, A.B. (2009) Karl Pearson's meta-analysis revisited. Ann. Stat., 37, 3867-3892.
17. Rakyan, V.K. et al. (2008) An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res., 18, 1518-1529.
18. Teschendorff, A.E. et al. (2010) Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res., 20, 440-446.
19. Wang, S. (2011) Method to detect differentially methylated loci with case-control designs using Illumina arrays. Genet. Epidemiol., 35, 686-694.
20. Whitlock, M.C. (2005) Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J. Evol. Biol., 18, 1368-1373.
21. Xu, G.L. et al. (1999) Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature, 402, 187-191.