NBDC Research ID: hum0276.v1
SUMMARY
Aims: The responsible gene for Gorlin syndrome is PTCH1. Early diagnosis by genetic testing is necessary. In this study, we will create a generic genetic diagnostic panel for Gorlin syndrome. The following points will be verified. (1) To validate the usefulness of a general-purpose genetic diagnostic panel test that can detect genomic mutations in the four genes (PTCH1, PTCH2, SMO, and SUFU) that are thought to cause Gorlin syndrome. (2) Extract genomic DNA from peripheral blood samples, oral tissues, and cysts and analyze them with a next-generation sequencer to verify the usefulness of a genetic diagnostic panel test from blood samples, which is less invasive than pathological specimen collection, and whether the same results can be obtained from blood-derived DNA as from tissue-derived DNA.
Methods: Genomic DNA is extracted from a portion of tissues, oral tissues, and blood samples removed during surgery between October 2014 and March 2025 from patients with Gorlin syndrome who have given consent for this study. Similarly, genomic DNA is extracted from leftover blood samples taken by blood relatives of patients with Gorlin syndrome who have consented to participate in this study, when needed for the purpose of diagnosing other diseases or for preoperative testing for general anesthesia. Libraries are prepared from the extracted DNAs and they are subjected to the next-generation sequencing analysis. Four genes (PTCH1, PTCH2, SMO, and SUFU) that may cause the disease are targeted and mutation analysis was performed.
Participants/Materials: The research subjects are patients with Gorlin syndrome treated at the Chiba Dental Center of the Tokyo Dental University, Suidobashi Hospital, and Ichikawa General Hospital who have consented to participate in this study, and undiagnosed blood relatives.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000308 | NGS (Target Capture) | Controlled-access (Type I) | 2021/10/01 |
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| Participants/Materials |
Gorlin syndrome (ICD10: Q859): 12 cases (7 cyst samples, 12 gingival samples, and 5 blood samples) 3 blood relatives (3 blood samples) |
| Targets | Target Capture |
| Target Loci for Capture Methods | PTCH1, PTCH2, SMO, SUFU |
| Platform | Illumina [MiSeq] |
| Library Source | gDNA extracted from cysts, gingival, and blood samples |
| Cell Lines | - |
| Library Construction (kit name) | AmpliSeq Library PLUS for illumina |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 375 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000419 |
| Total Data Volume | 1.4 GB (fastq, bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshifumi Azuma
Affiliation: Department of Biochemistry, Tokyo Dental College
Project / Group Name: Tokyo dental College Research Branding Project
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Establishment and application of an odontogenic keratocyst model using Gorlin syndrome-derived iPS cells | 18K09753 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | The osteoblast differentiation and calcification mechanism of GNAS-cAMP pathway using diseased iPS cells | 18H03007 |
| Tokyo dental College Research Branding Project | Development of a diagnostic gene panel for Gorlin syndrome that can be applied in liquid biopsy | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Satoshi Yuhara | Bioinformatics section, SRL inc. | Japan | Validation of Rare Disease Clinical Reporting System | JGAD000419 | 2024/07/01-2027/03/31 |
