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

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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.", "claims": [{"id": "claim-method", "statement": "In our aforementioned study [1], we excluded CpG sites whose probes overlapped with variants with > 1% MAF in the Japanese population from a list of methylation outliers that were detected to be differentially methylated with statistical significance in one sample compared with the others by Smirnov–Grubbs' outlier tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981364", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 5", "quote": "In our aforementioned study [1], we excluded CpG sites whose probes overlapped with variants with > 1% MAF in the Japanese population from a list of methylation outliers that were detected to be differentially methylated with statistical significance in one sample compared with the others by Smirnov–Grubbs' outlier tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data obtained using the manufacturer's standard protocol have been submitted to NCBI GEO under accession number GSE62733.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981364", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 2", "quote": "The data obtained using the manufacturer's standard protocol have been submitted to NCBI GEO under accession number GSE62733."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26981364"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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