NBDC Research ID: hum0107.v2
SUMMARY
Aims: Identification of cause mutations and analysis of novel mutated genes of Gorlin syndrome
Methods: Exome sequence analysis, RNA sequence analysis
Participants/Materials: Patients with Gorlin syndrome : 4 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000099 | NGS (Exome) | Controlled-access (Type I) | 2017/10/02 |
| JGAS000218 | NGS (RNA-seq) | Controlled-access (Type I) | 2020/06/01 |
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MOLECULAR DATA
| Participants/Materials |
Gorlin syndrome (ICD10: Q859) : 4 cases oral mucosa fibroblast : 4 samples oral mucosa : 1 sample |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform |
oral mucosa fibroblast: Illumina [HiSeq 2500] oral mucosa: Illumina [HiSeq 4000] |
| Library Source | DNAs extracted from oral mucosa fibroblasts and oral mucosa |
| Cell Lines | - |
| Library Construction (kit name) | Sure Select Human All Exon v5 kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000099 |
| Total Data Volume | 2 GB (fastq [10 files]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Gorlin syndrome (ICD10: Q859) : 1 case osteoblast differentiated from iPS cells established from oral mucosa fibroblast : 3 samples osteoblast differentiated from iPS cells established from oral fibroblast cell line : 3 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from osteoblast differentiated from iPS cells established from oral mucosa fibroblast or fibroblast cell line |
| Cell Lines | - |
| Library Construction (kit name) | HiSeq SBS Kit v4 |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000304 |
| Total Data Volume |
13 GB Data files: 12 (fastq) Analysis files: 6 (bam [ref：GRCh38]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshifumi Azuma
Affiliation: Tokyo Dental Collage department of biochemistry
Project / Group Name: Tokyo Dental College Research Branding Project
URL: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Young Scientists (B) | Elucidation of the pathological mechanism of Gorlin syndrome using disease-specific iPS cells | 16K20427 |
| KAKENHI Grant-in-Aid for Young Scientists (B) | Elucidation of the pathophysiology of Cleidocranial dysplasia using disease-specific iPS cells | 16K20428 |
| Tokyo Dental College Research Branding Project |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multi-layered mutation in hedgehog-related genes in Gorlin syndrome may affect the phenotype | doi: 10.1371/journal.pone.0184702 | JGAD000099 |
| 2 | Hedgehog activation regulates human osteoblastogenesis. | doi: 10.1016/j.stemcr.2020.05.008 | JGAD000304 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000304 | 2022/12/26-2025/03/31 |
