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Description
Cell type- and sex-specific DNA methylation summary data for autosomes (chr1-22) consists of 132 BED files. CpG sites overlapping with known genomic variants were removed. Genomic variation data were obtained from jMorp dataset, from which variations found from iMETHYL subjects were extracted. Each file contains 8 columns corresponding to:
- 1: Chromosome number
- 2-3: Chromosomal position of dinucleotides CpG
- 4: Number of sample with DNA methylation (DNAm) data on the CpG site
- 5: Mean DNAm level
- 6: Median of DNAm level
- 7: Standard deviation of DNAm level
- 8: Reference interval (RI; Hachiya et al., 2017)
Citation of Dataset
If you use our dataset in your publication or presentation, please cite our website and papers.
- Iwate Tohoku Medical Megabank Organization, iMETHYL Database; over 100 Japanese whole genome DNA methylation database from monocytes, CD4+ T cells, and neutrophils, http://imethyl.iwate-megabank.org
- T. Hachiya et al. "Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies" NPJ Genomic Medicine. 2017. 2:11
- S. Komaki et al. "iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation" Human Genome Variation. 2018. 5:18008
TERMS & CONDITIONS
The summary data will only be provided to persons who have agreed to the following Rules of Use. In other words, a person who has downloaded the data shall be deemed to have read and understood the contents stated in the provisions of the Rules of Use and to have agreed the stated obligations ((i) prohibition on identifying and contacting any person who has provided specimens which were used for constituting the summary data; (ii) use of the summary data for non-commercial purposes only; (iii) notification at the time of re-editing the summary data; (iv) stating and citing our institute and paper at the time of publication of article using our data. You are requested to download the summary only after having understood the foregoing. The copyrights in and to the summary data and the database are owned by IMM.
*The change in our policy for opening data of genomic analysis of cohort participants was made after sincere consideration by the members of Ethical, Legal, and Social Issues (ELSI) Committee and Sample and Data Access Committee for the Tohoku Medical Megabank Project regarding the following points.
- Protection of privacy of the participants and possibility of identification/specification of the participants.
- It is almost impossible to identify participants of the cohort study through only the summary data because no individual data is disclosed. Furthermore, users of the genomic data should agree to the following terms: prohibition of identification/specification of the participants by combining the data and other possibly available social, biological, and clinical data.
- To exclude the possibility that a participant is identified by the summary data in combination with epidemiological data (social, biological, or clinical information), epidemiological data would be released in a way that disallows easy connection of the genomic and epidemiological data.
- Variations associated with the diseases
- The summary data leased at this time may prove to be strongly associated with a certain disease. At the same time, we recognize that such data in our panel inevitably include a certain amount of error as a natural consequence of using next-generation sequencers and statistical methods. We think that our current data set has not yet met the quality required to estimate and report an individual's risk for the disease as is present in clinical settings. We have to accurately inform users of the data set to the current limitation of the genomic analysis data.
- The Medical Megabank Project seeks the possible return of reliable and beneficial genetic analysis results to the cohort participants. However, we must establish validation processes before we begin to inform participants of the genotype results, because as stated above, our current data were derived from a pipeline of next generation sequencer analysis, and such data are not accurate enough for individual return of the DNA methylation data.
*Any personal information registered by you with IMM for the use of the database shall be used solely for the purpose of managing the User's use of the database and shall not be provided or disclosed to any third parties.
*If you have any inquiries on the information stored in the database or if you find any person who is improperly using such information, please contact us at the following e-mail address: imethylATiwate-megabankDOTorg (Please replace "AT" with "@" and "DOT" with ".").
*We plan to improve the database in the future by adding further information, provided, however, that, in such case, you may be requested to use such information under stricter conditions in terms of ensuring the protection of personal information.
