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| Status |
Public on Nov 25, 2024 |
| Title |
Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome [cord_blood] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those
To address this deficiency, we developed a custom methylation array containing 22,819 probes. Among them, 9,757 probes map to 1,088 out of the 1,488 candidate ICRs recently described. To assess the performance of the array, we created matched samples processed with the Human Imprintome array and WGBS, which is the current standard method for assessing the methylation of the Human Imprintome. We compared the methylation levels from the shared CpG sites and obtained a mean R2 = 0.569. We also created matched samples processed with the Human Imprintome array and the Infinium Methylation EPIC v2 array and obtained a mean R2 = 0.796. Furthermore, replication experiments demonstrated high reliability (ICC: 0.799-0.945).
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| Overall design |
8 oord blood samples analyzed with the Human Imprintome array with two replicates each.
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| Contributor(s) |
Carreras-Gallo N, Dwaraka VB, Jima DD, Skaar DA, Mendez TL, Planchart A, Zhou W, Jirtle RL, Smith R, Hoyo C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 21, 2024 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Dereje Jima |
| E-mail(s) |
[email protected]
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| Organization name |
NCSU
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| Department |
CHHE
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| Street address |
850 Main Campus Drive
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| City |
RALEIGH |
| State/province |
NC |
| ZIP/Postal code |
27606 |
| Country |
USA |
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| Platforms (1) |
| GPL34511 |
Illumina Custom Human Imprintome array |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA1114301 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE268074_RAW.tar |
52.1 Mb |
(http)(custom) |
TAR (of IDAT) |
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