Copy number variation has little impact on bead-array-based measures of DNA methylation.
BACKGROUND
Integration of various genome-scale measures of molecular alterations is of great interest to researchers aiming to better define disease processes or identify novel targets with clinical utility. Particularly important in cancer are measures of gene copy number DNA methylation. However, copy number variation may bias the measurement of DNA methylation. To investigate possible bias, we analyzed integrated data obtained from 19 head and neck squamous cell carcinoma (HNSCC) tumors and 23 mesothelioma tumors.


RESULTS
Statistical analysis of observational data produced results consistent with those anticipated from theoretical mathematical properties. Average beta value reported by Illumina GoldenGate (a bead-array platform) was significantly smaller than a similar measure constructed from the ratio of average dye intensities. Among CpGs that had only small variations in measured methylation across tumors (filtering out clearly biological methylation signatures), there were no systematic copy number effects on methylation for three and more than four copies; however, one copy led to small systematic negative effects, and no copies led to substantial significant negative effects.


CONCLUSIONS
Since mathematical considerations suggest little bias in methylation assayed using bead-arrays, the consistency of observational data with anticipated properties suggests little bias. However, further analysis of systematic copy number effects across CpGs suggest that though there may be little bias when there are copy number gains, small biases may result when one allele is lost, and substantial biases when both alleles are lost. These results suggest that further integration of these measures can be useful for characterizing the biological relationships between these somatic events.
Houseman
E Andrés
EA
Department of Community Health Center for Environmental Health and Technology, Brown University, Providence, RI 02912, USA. E_Andres_Houseman@brown.edu
Christensen
Brock C
BC
Karagas
Margaret R
MR
Wrensch
Margaret R
MR
Nelson
Heather H
HH
Wiemels
Joseph L
JL
Zheng
Shichun
S
Wiencke
John K
JK
Kelsey
Karl T
KT
Marsit
Carmen J
CJ
D002294:Carcinoma, Squamous Cell / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D018628:Gene Dosage; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human; D006258:Head and Neck Neoplasms / Q000235:genetics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA