NBDC Research ID: hum0295.v1
SUMMARY
Aims: DNA extracted from tumor and normal tissue (blood or saliva) was collected from patients with skin tumors. Tumor was primary lesion only (9 cases), metastatic lesion only (5), or both (7). 21 patients with melanoma and 1 patient with sebaceous nevus were enrolled. 29 tumor and 21 normal tissues were analyzed. From the case with sebaceous nevus, DNA was extracted from three parts of a tumor (sebaceous nevus, trichoblastoma and poroma).
Methods: To detect tumor driver mutations, DNAs from tumor and non-tumor tissues were sequenced with a custom panel. Tumor DNA was extracted from patients’ formalin-fixed paraffin-embedded sections. The panel contains 3,336 primer-pair for 95 gene regioins.
Participants/Materials: 98 patients with melanoma and one patient with sebaceous nevus were enrolled.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000351 | NGS (Amplicon-seq) | Controlled-access (Type I) | 2024/10/25 |
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MOLECULAR DATA
| Participants/Materials |
melanoma (ICD10: C21.0, C30.0, C31.9, C43.1, C43.3, C43.4, C43.5, C43.6, C43.7, C51.1, C52, C53.9, C60.9, C67.9, C69.0): 98 cases tumor tissues: 121 samples (one primary tumor sample: 65 cases, two primary tumor samples: 2 cases, metastatic lesion only: 10 cases, both primary and metastatic samples: 21 cases) non-tumor tissues: 98 samples (blood or saliva) sebaceous nevus (ICD10: D23.7): 1 case tumor tissues: 3 samples (sebaceous nevus, trichoblastoma and poroma) |
| Targets | Amplicon-seq |
| Target Loci for Capture Methods | 95 genes |
| Platform | Thermo Fisher Scientific [Ion S5] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Ion Ampliseq Library Kit Plus |
| Fragmentation Methods | PCR |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000465 |
| Total Data Volume | 311.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Hisashi Uhara
Affiliation: Dermatology, Sapporo Medical University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science | 16H06279 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Characterization of the intratumoral ecosystem in melanoma by single-cell RNA-seq analysis | 19K08752 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Comprehensive analysis of genetic mutations and fusions in Japanese melanoma | 21K08304 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Establishment of a personalized liquid biopsy method targeting multiple candidate mutated genes in melanoma | 22K08388 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Preemptive medicine for Japanese melanoma through comprehensive analysis of tumor genome and circulating tumor cells | 24K11477 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic analyses of a secondary poroma and trichoblastoma in a HRAS-mutated sebaceous nevus | doi: 10.1111/1346-8138.15919 | JGAD000465 |
| 2 | Genetic characteristics of cutaneous, acral, and mucosal melanoma in Japan. | doi: 10.1002/cam4.70360 | JGAD000465 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
