Copy number variation has little impact on bead-array-based measures of DNA methylation

@article{Houseman2009CopyNV,
  title={Copy number variation has little impact on bead-array-based measures of DNA methylation},
  author={E. Andres Houseman and Brock C. Christensen and Margaret R. Karagas and Margaret R. Wrensch and Heather H. Nelson and Joseph L. Wiemels and Shichun Zheng and John K. Wiencke and Karl T. Kelsey and Carmen J. Marsit},
  journal={Bioinformatics},
  year={2009},
  volume={25 16},
  pages={
          1999-2005
        }
}
MOTIVATION 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. [] Key Method To investigate possible bias, we analyzed integrated data obtained from 19 head and neck squamous cell carcinoma (HNSCC) tumors and 23 mesothelioma tumors.

Figures and Tables from this paper

Learning from multiple genomic information in cancer for diagnosis and prognosis

The role of DNA methylation as a surrogate biomarker of clonality between cells would allow for a powerful clinical tool for to elaborate appropriate treatments for specific patients with breast cancer relapses and the existence of the universal biological phenomenon related to the hypermethylator phenotype is tackled.

Using high-density DNA methylation arrays to profile copy number alterations

It is demonstrated that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms, and high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment.

Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

The method significantly reduces the risk of false discoveries when using the HM450K bead array, while maximising the power of the array to detect methylation status genome-wide, and demonstrates the utility of the method through extraction of biologically relevant epigenetic changes in prostate cancer.

Changes in correlation between promoter methylation and gene expression in cancer

The results suggest that epigenetic reprogramming in cancer does not contribute to cancer development via direct inhibition of gene expression through promoter hypermethylation, but may instead modify how the expression of a few specific genes, particularly transcription factors, are associated with DNA methylation variations in a tissue-dependent manner.

Integrative epigenetic and genetic pan-cancer somatic alteration portraits

This work identified the global DNA methylation dysregulation patterns across 14 cancer types showing a higher impact for the non-CpG island areas and identified common clusters across cancer types that may have implications for future treatment and prevention measures.

SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions

This work implements a solution, P-value with out-of-band (OOB) array hybridization (pOOBAH), in the R package SeSAMe, which effectively masks deleted and hyperpolymorphic regions, reducing or eliminating spurious reports of epigenetic silencing at oft-deleted tumor suppressor genes.

Predicting tumor purity from methylation microarray data

In cancer samples, the distributions of data from Illumina Infinium 450 k methylation microarray are highly correlated with tumor purities, and a simple but effective method to estimate purities from the microarray data is developed.

A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform

The Elastic Net emerges as a powerful classification algorithm for large-scale DNA methylation studies, while NMF does well in the unsupervised context of cancer diagnosis and non-negative matrix factorisation clearly outperforms principal components analysis.

Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted

This work, using a novel and robust statistical approach, demonstrates that, although a “second hit” mechanism is not likely the predominant mode of action for epigenetic dysregulation in cancer, the patterns of methylation events are associated with the pattern of allele loss.

DNA Methylation Characteristics of Primary Melanomas with Distinct Biological Behaviour

The strong influence of promoter localized DNA methylation changes on melanoma initiation and how hypermethylation decreases in melanomas associated with less favourable clinical outcomes are demonstrated and established the methylation pattern as part of an integrated apparatus of somatic DNA alterations.

References

SHOWING 1-10 OF 35 REFERENCES

Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array

Results from this study provide a basis for a systematic and comprehensive cataloging of CN alterations associated with grades of prostate cancer, and the subsequent identification of specific genes that associated with initiation and progression of the disease.

Whole genome DNA copy number changes identified by high density oligonucleotide arrays

A novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA), to identify genome-wide chromosomal gains and losses at high resolution and can tolerate samples which contain a mixture of both tumour and normal DNA.

High-resolution analysis of DNA copy number using oligonucleotide microarrays.

The studies demonstrate that combining the genotype and copy number analyses gives greater insight into the underlying genetic alterations in cancer cells with identification of complex events including loss and reduplication of loci.

High-throughput DNA methylation profiling using universal bead arrays.

The results demonstrate the effectiveness of the method for reliably profiling many CpG sites in parallel for the discovery of informative methylation markers and should prove useful for DNA methylation analyses in large populations.

Comprehensive High‐Throughput Arrays for Relative Methylation (CHARM)

DNA methylation (DNAm) is a term used to describe the heritable covalent addition of a methyl group to cytosines at CpG dinucleotides in mammals. While methods for examining DNAm status at specific

Global DNA Methylation Level in Whole Blood as a Biomarker in Head and Neck Squamous Cell Carcinoma

DNA hypomethylation in nontarget tissue was independently associated with HNSCC and had a complex relationship with the known risk factors associated with the genesis of H NSCC.

Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers

We have performed a genome-wide analysis of copy number changes in breast and colorectal tumors using approaches that can reliably detect homozygous deletions and amplifications. We found that the

Algorithms for large-scale genotyping microarrays

The modified partitioning around medoids is proposed as a classification method for relative allele signals and a method to determine the gender of a sample based on the heterozygous call rate of SNPs on the X chromosome is provided.

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

A novel model-based recursive-partitioning algorithm to navigate clusters in a beta mixture model is proposed that is more reliable than competing nonparametric clustering approaches, and is at least as reliable as conventional mixture model methods.

Microarray tools for deciphering complex diseases.

  • R. Shai
  • Biology
    Frontiers in bioscience : a journal and virtual library
  • 2006
Through utilizing the colossal amount of microarray data findings, defining the structure, function, and dynamics of entire biological pathways and cellular networks under various physiological states, and the development of robust and efficient methods for analyzing and interpreting high dimensional data, it will be possible to connect combination of experimental results with individualized disease state.