NBDC Research ID: hum0368.v1
SUMMARY
Aims: ICF (immunodeficiency, centromeric instability, facial anomaly) syndrome is a rare congenital autosomal recessive genetic disorder characterized by immunodeficiency, chromosomal instability with DNA hypomethylation, and facial anomalies. Previous studies have revealed that ICF patients can be divided into four subtypes according to their causative genes (DNMT3B, ZBTB24, CDCA7, or HELLS). However, there are still a few patients whose causative genes are unknown. In this study, we identified UHRF1 as a novel causative gene in one such patient and performed whole-genome bisulfite sequencing analysis of DNA extracted from peripheral blood cells of this patient to identify a DNA hypomethylation pattern characteristic of this patient.
Methods: DNA was extracted from peripheral blood cells, and prepared libraries by the post-bisulfite adaptor-tagging (PBAT) method. Then whole genome sequencing was performed and determined the methylation status of all cytosines.
Participants/Materials: ICF syndrome
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000559 | NGS (PBAT-seq) | Controlled-access (Type I) | 2022/11/29 |
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| Participants/Materials | ICF syndrome (ICD10: D800) : 1 case |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from peripheral blood cells (Amplification-free) |
| Cell Lines | - |
| Library Construction (kit name) | Post-Bisulfite Adaptor-Tagging (PBAT)*1 |
| Fragmentation Methods | Bisulfite Treatment |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000681 |
| Total Data Volume | 46.4 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Motoko Unoki
Affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Mechanisms underlying maintenance of genome integrity by DNA methylation | 19H05740 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Molecular pathogenesis of ICF syndrome | 18K06961 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | ICF syndrome and the molecular network regulating the human epigenome | 26253020 |
| Yamada Science Foundation | Novel DNA methylation maintenance mechanism for centromeric and pericentromeric repeats | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome with distinctive genome-wide DNA hypomethylation. | doi: 10.1093/hmg/ddac291 | JGAD000681 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
