DNA Methylation Signatures in Development and Aging of the Human Prefrontal Cortex

Abstract

(The American Journal of Human Genetics, 90, 260–272; February 2012) This article contained errors related to the use of potentially nonspecific or polymorphic probes present on Infinium HumanMethylation27 BeadChips (Illumina). The lists of probes that might need to be removed because they target multiple sequences (particularly important for, but not limited to, loci showing sex-related differences) or contain SNPs in CpG loci are now available at Brain Cloud (see Web Resources). The authors thank Dr. RosannaWeksberg and colleagues (Hospital for Sick Children, Toronto, CA) as well as John Blair and Magda Price (University of British Columbia, Vancouver, CA) for bringing the issue of potential cross-reactivity of Illumina DNA microarray probes to their attention. Please note that the nonspecific probes differ from those reported by Chen et al.;1Chen Y.A. Choufani S. Ferreira J.C. Grafodatskaya D. Butcher D.T. Weksberg R. Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray.Genomics. 2011; 97: 214-222Crossref PubMed Scopus (56) Google Scholar see details of the identification methods in the downloadable spreadsheets at Brain Cloud. The URL for data presented herein is as follows:Brain Cloud, http://BrainCloud.jhmi.edu/downloads.htm DNA Methylation Signatures in Development and Aging of the Human Prefrontal CortexNumata et al.The American Journal of Human GeneticsFebruary 2, 2012In BriefThe human prefrontal cortex (PFC), a mastermind of the brain, is one of the last brain regions to mature. To investigate the role of epigenetics in the development of PFC, we examined DNA methylation in ∼14,500 genes at ∼27,000 CpG loci focused on 5′ promoter regions in 108 subjects range in age from fetal to elderly. DNA methylation in the PFC shows unique temporal patterns across life. The fastest changes occur during the prenatal period, slow down markedly after birth and continue to slow further with aging. Full-Text PDF Open ArchiveCross-Reactive DNA Microarray Probes Lead to False Discovery of Autosomal Sex-Associated DNA MethylationChen et al.The American Journal of Human GeneticsOctober 05, 2012In BriefTo the Editor: The majority of the significant sex-associated DNA-methylation sites at autosomal CpG loci reported by Numata et al.1 do not reflect a true biological phenomenon. Rather, the conclusions in this paper reflect a technical artifact created by the presence of cross-reactive autosomal probes hybridizing to both autosomal and sex chromosomes. Full-Text PDF Open ArchiveIlluminating Potential Technical Artifacts of DNA-Methylation Array ProbesBlair et al.The American Journal of Human GeneticsOctober 05, 2012In BriefTo the Editor: Recently, Numata et al.1 provided evidence of changes in DNA methylation in the human prefrontal cortex (PFC) through human development and aging. This study reported on three aspects of DNA methylation in 108 fetal, child, and adult PFC samples with the use of the Illumina Infinium HumanMethylation27 BeadChip array. These three aspects were (1) temporal changes in DNA methylation, (2) genetic polymorphisms in association with DNA methylation, and (3) a correlation between mRNA expression and DNA methylation. Full-Text PDF Open Archive