Lists of HumanMethylation450 BeadChip probes with nucleotide-variant information obtained from the Phase 3 data of the 1000 Genomes Project.
Lists of HumanMethylation450 BeadChip probes with nucleotide-variant information obtained from the Phase 3 data of the 1000 Genomes Project.
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DOI：
10.1016/j.gdata.2015.11.023
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发表时间：
2016-03
期刊：
影响因子：
--
通讯作者：
Nakabayashi K
中科院分区：
文献类型：
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作者：
Okamura K;Kawai T;Hata K;Nakabayashi K
Illumina的Infinium HumanMethylation 450（HM 450）BeadChip阵列可同时检测人类基因组中超过480，000个CpG位点的DNA甲基化状态。其相对简单的协议是通过采用杂交方法，然后单碱基延伸反应。然而，杂交探针序列中个体之间的核苷酸变异会影响结果，即甲基化水平的估计。为了研究母体营养状况对子宫内表观遗传改变程度的可能影响，我们检查了在日本收集的33个绒毛膜绒毛样本（GEO登录号GSE 62733）的全基因组DNA甲基化谱，并使用Smirnov-Grubbs离群值检验揭示了表观遗传改变在子宫内不良环境下在胎盘中积累。在该研究中，我们编制了一份与1000个基因组计划的3期数据集（发布20130502）中报告的核苷酸变体重叠的HM 450探针列表。我们从已鉴定的甲基化离群值中排除了其序列与日本人群中次要等位基因频率（MAF）高于1%的变异体重叠的探针，以减少由于靶CpG位点处/附近的变异体而可能被错误鉴定的离群值数量。我们在此汇编了具有非洲、欧洲、美洲、南亚和东亚人群以及日本人群MAF信息的HM 450探针列表。所提供的列表可用于使用HM 450 BeadChip阵列对人群进行甲基化组分析。
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.