Abstract
After completion of the human genome, genome-wide association studies were conducted to identify single nucleotide polymorphisms (SNPs) associated with cancer initiation and progression. Most of the studies identified SNPs that were located outside the coding region, and the odds ratios were too low to implement in clinical practice. Although the genome gives information about genome sequence and structure, the human epigenome provides functional aspects of the genome. Epigenome-wide association studies (EWAS) provide an opportunity to identify genome-wide epigenetic variants that are associated with cancer. However, there are problems and issues in implementing EWAS to establish an association between epigenetic profiles and cancer. Few challenges include selection and handling of samples, choice of population and sample size, accurate measurement of exposure, integrating data, and insufficient information about the role of repeat sequences. The current status of EWAS, challenges in the field, and their potential solutions are discussed in this article.
Highlights
Biology in general has been genocentric for decades, the fate of a gene is not defined by the DNA sequence but by how a gene is programmed by chromatin changes, DNA methylation, and noncoding RNAs
Following the completion of genome-wide association studies (GWAS) in several cancers, it was observed that disease-associated single nucleotide polymorphisms (SNPs) are not localized near any gene in the pathways involved in these cancers
Because DNA methyl transfer reactions occur on one strand at a time, de novo methylation leading to full doublestranded DNA methylation can be thought of as two sequential one-stranded reactions
Summary
Biology in general has been genocentric for decades, the fate of a gene is not defined by the DNA sequence but by how a gene is programmed by chromatin changes, DNA methylation, and noncoding RNAs. The functional importance of epigenetic changes lies in their ability to regulate gene expression. Four major steps in epigenetic regulation are promoter methylation, histone acetylation/deacetylation, noncoding mRNA expression, and chromatin conformational changes [3, 4]. Through their effects on chromatin structure, epigenetic changes can modulate transcriptional repression, X-chromosome inactivation, genomic imprinting, and suppression of the detrimental effects of repetitive and parasitic DNA sequences on genome integrity [5, 6]. Following the completion of genome-wide association studies (GWAS) in several cancers, it was observed that disease-associated single nucleotide polymorphisms (SNPs) are not localized near any gene in the pathways involved in these cancers. Are there issues concerning EWAS approaches that should be resolved before moving in that direction?
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