NBDC Research ID: hum0362.v1
SUMMARY
Aims: This study has following four objectives
1) We identify driver mutations, classify the disease by gene profiling, and evaluate biomarkers that predict treatment efficacy and genomic changes during recurrence or metastasis.
2) We identify biomarkers that predict therapeutic efficacy and toxicity by analyzing polymorphisms of genes related to pharmacokinetics and pharmacology in non-tumor tissues and genetic mutations related to familial tumors and by performing association analysis between germline gene profiling and clinical information.
3) We compare "Clinical Liquid Sequencing" using plasma-derived free DNA with tissue biopsy ("Clinical Sequencing") to evaluate its efficacy.
4) In thymic tumors, we will examine immune cell profiling. The relationship between thymic tumors and autoimmune diseases will also be examined.
Methods: RNA-seq analysis
Participants/Materials: 98 thymoma cases (97 thymoma samples and one normal thymus sample)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000552 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/04/01 |
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MOLECULAR DATA
| Participants/Materials |
Thymoma (ICD10: C37): 98 cases - thymoma: 97 samples - normal thymus: 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from frozen tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded Total RNA Library Prep Gold Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000672 |
| Total Data Volume | 249.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinichi Yachida
Affiliation: Affiliated institution and division, Osaka University Cancer Genome Informatics
Project / Group Name: The study on genomic profiling using clinical specimens (tissue, blood, etc.) from patients with lung and thymic tumors
Funds / Grants (Research Project Number):
-
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Metagenomic analysis of familial adenomatous polyposis and its implications for understanding the pathogenesis of colorectal cancer | JP20H033620 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Developmstent (AMED) | Research aimed at elucidating alterations in the intestinal microenvironment associated with colorectal cancer development in high-risk individuals, and the development of personalized preventive strategies based on these findings | JP21ck0106546 |
| Project for Cancer Research and Therapeutic Evolution, Japan Agency for Medical Research and Developmstent (AMED) | Research and development aimed at predicting the occurrence of adverse effects associated with anticancer drugs through comprehensive analysis of the gut microbiota | JP21cm0106477 |
| Research Program on the challenges of Global Health issues, Japan Agency for Medical Research and Developmstent (AMED) | Investigation of infection-associated cancers conducted within the framework of the Japan–U.S. Medical Cooperation Program | JP20jk0210009 |
| Project for Promotion of Cancer Research and Therapeutic Evolution, Japan Agency for Medical Research and Developmstent (AMED) | Development of biomarkers for early detection and susceptibility assessment of young-onset colorectal cancer through comprehensive analysis of the intestinal microenvironment | JP22ama221404 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Developmstent (AMED) | Collection and analysis of whole-genome sequencing data and clinical information on treatment-resistant gastrointestinal cancers, such as esophageal cancer, with the aim of facilitating drug development and establishing a nationwide infrastructure for genome-informed medical care in Japan | JP22ck0106690 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Developmstent (AMED) | Advancement of preventive, diagnostic, and therapeutic approaches through comprehensive genomic analysis of rare malignancies, including sarcomas and brain tumors | JP21ck0106693 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Developmstent (AMED) | Development of novel strategies for prevention, diagnosis, and treatment through comprehensive genomic analysis of rare cancers, including sarcomas and brain tumors | JP24ck0106877 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Developmstent (AMED) | Implementation of advanced cancer precision medicine through the timely and accurate return of patient-specific data, including whole-genome information, alongside the development of novel therapeutics | JP24ck0106872 |
| the National Cancer Center Research and Development Fund | - | 2023-A-06 |
| Japan Health Research Promotion Bureau Research Fund | - | JH2022-B-01 |
| Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University | - | - |
| Joint Research Project of the Institute Medical Science, the University of Tokyo | - | - |
| the Takeda Science Foundation | - | - |
| the Yasuda Medical Foundation | - | - |
| the Mitsubishi Foundation | - | - |
| the Princess Takamatsu Cancer Research Fund | - | - |
| Takara Bio Inc. | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Characterizing the Tumor Immune Environment in Thymic Epithelial Tumors Using T-cell Receptor Repertoire Analysis and Gene Expression Profiling | doi: 10.1016/j.xjon.2025.03.008 | JGAD000672 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
