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Genom Data. 2015 Nov 28;7:67-9. doi: 10.1016/j.gdata.2015.11.023. eCollection 2016 Mar.

Lists of HumanMethylation450 BeadChip probes with nucleotide-variant information obtained from the Phase 3 data of the 1000 Genomes Project.

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1
Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan.
2
Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan.

Abstract

The Illumina's Infinium HumanMethylation450 (HM450) BeadChip array provides a simultaneous examination of DNA methylation status of more than 480,000 CpG sites in the human genome. Its relatively simple protocol is achieved by employing a hybridization methodology followed by single-base extension reactions. However, nucleotide variations among individuals in the hybridization probe sequences can affect the results, i.e. estimates of methylation levels. To investigate possible effects of maternal nutritional conditions on the extent of epigenetic alterations in utero, we examined genome-wide DNA methylation profiles of 33 chorionic villi samples collected in Japan (GEO accession number GSE62733), and revealed using Smirnov-Grubbs' outlier test that epigenetic alterations accumulate in placentas under adverse in utero environments. In that study, we compiled a list of HM450 probes overlapping with the reported nucleotide variants in the Phase 3 dataset (release 20130502) of the 1000 Genomes Project. We excluded the probes whose sequences overlapped with variants with minor allele frequency (MAF) higher than 1% in the Japanese population from identified methylation outliers, to diminish the number of outliers that could have been spuriously identified due to variants at/near the target CpG sites. We herein compiled lists of HM450 probes with MAF information of the African, European, American, South Asian and East Asian populations, in addition to the Japanese population. The provided lists are useful for methylome analyses for human populations using the HM450 BeadChip arrays.

KEYWORDS:

DNA methylation; Genetic variations; Methylation BeadChip; Minor allele frequency; The 1000 Genomes Project

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