NBDC Research ID: hum0064.v1
SUMMARY
Aims:
To construct a Geriatric Oncology Database of genotype, methylation, gene expression, clinical data, and questionnaire survey results in Japanese elderly cancer patients and attempt to establish truly effective treatment strategy
Methods:
1. Genome & Genetic research
Direct sequencing, TaqMan analysis, qRT-PCR, COBRA assay, cDNA microarray. Collection of clinical data and digitalization of them.
2. Retrospective study
Collection of clinical data and digitalization of them. Collection of questionnaires and digitalization of them.
Participants/Materials:
1. Genome & Genetic research
colorectal cancer: 106 cases, gastric cancer: 62 cases, lung cancer: 173 cases
2. Retrospective study
colorectal cancer: 313 cases, gastric cancer: 166 cases, lung cancer: 344 cases
diabetes and nephropathy: 300 cases, cardiovascular disorder: 357 cases, respiratory dysfunction: 49 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000061 |
genotype, methylation, gene expression, clinical data for colorectal, gastric, or lung cancer patients. clinical data for colorectal cancer, gastric cancer, lung cancer, cardiovascular disorders, respiratory dysfunction, diabetes, or nephropathy patients. |
Controlled-access (Type I) | 2016/08/26 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials⋆１ |
colorectal cancer: 106 cases gastric cancer: 62 cases lung cancer: 173 cases |
| Targets |
-Direct sequencing XRCC1-1449delGGCC, TYMS_3UTR_6R_INS, TYMS_5UTR_3R_VNTR, EGFR, KRAS, BRAF, ERBB2, TP53 -TaqMan analysis ABCB1, ABCC1, ABCC2, CYP1B1, CYP2A6, CYP2C8, CYP3A4, CYP3A5, DPYD, ERCC1, ERCC2, GSTP1, UGT1A1, XRCC1, XRCC3 Genetic mutation List (Gene name, chromosomal positon, rs ID) -GSTM1 GSTT1 deletion mutant multiplex PCR⋆2 GSTM1, GSTT1 -qRT-PCR ABCB1, ABCC1, ABCC2, ABCG2, ACTB, ALAD, ASPRV1, BCL2, BRCA1, C20orf43, DMKN, DPYD, ERCC1, GAPDH, GDA, GSTP1, HPRT1, KRAS, MFTHR, OPRT, RRM1, TMEM18, TOP1, TUBB3, TYMS, UGT2B10, UMPS -COBRA assay APC, CDKN2A, MLH1 -cDNA microarray 41,000 probes⋆3 (control: 27,934 genes, gastric cancer: 23,288 genes, colorectal cancer: 23,295 genes) -Clinical data |
| Target Loci for Capture Methods | - |
| Platform |
-Direct sequencing Sequencer: Genetic Analyzer 3130 (Applied Biosystems) -TaqMan analysis Analysis kit: TaqMan® SNP Genotyping Assays (Thermo Fisher Scientific) qPCR instrument: LightCycler 480II (Roche) -qRT-PCR qPCR kit: ABsolute QPCR Mix (Thermo Fisher Scientific) qPCR instrument: LightCycler 480II (Roche) -COBRA assay Bisulfite Treatment: EZ DNA Methylation-Gold Kit (ZYMO Research) PCR kit: AmpliTaqGold (Thermo Fisher Scientific) -cDNA microarray Labeling: Quick-Amp Labeling Kit (Agilent Technologies) Chip: Whole Human Genome Microarray 4x44K (Agilent Technologies) Scanner: G2565BA (Agilent Technologies) |
| Library Source |
-Direct sequencing DNAs extracted from tumors or non-cancerous tissues -TaqMan analysis DNAs extracted from tumors or non-cancerous tissues -qRT-PCR RNAs extracted from tumors -COBRA assay DNAs extracted from tumors -cDNA microarray RNAs extracted from tumors |
| Normalization of microarray | Refer to JGA000061 experimental support information |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000061 |
| Total Data Volume | 37 MB (txt) |
| Comments (Policies) | NBDC policy |
*1: Details about Participants
Written informed consent was obtained from all patients or the proxy. They agreed to provide tissue specimens and clinical data for this and other medical research including genetic analysis when the study could be approved by the Institutional Review Board of the participating center and performed under anonymous condition. The eligibility criteria of this study were:
1) Patients with definite diagnosis of colorectal, gastric, or lung cancer.
2) Patients who had received cancer treatment between September 2002 to June 2006.
3) Patients ≥40 years old.
4) Patients known their age, gender, stage, prognosis, and therapeutic response.
5) Patients who agreed enroll to this research project with written informed consent.
*2: Chen CL, Liu Q, Relling MV: Simultaneous characterization of glutathione S-transferase M1 and T1 polymorphisms by polymerase chain reaction in American whites and blacks. Pharmacogenetics. 1996 Apr;6(2):187-91. （PMID: 9156696）
*3: Refer to GGRNA (https://ggrna.dbcls.jp/en/) for positions of probes.
| Participants/Materials⋆4 |
2-1. Cancer cases colorectal cancer: 313 cases gastric cancer: 166 cases lung cancer: 344 cases
2-2. Non-cancerous cases diabetes and nephropathy: 300 cases cardiovascular disorder: 357 cases respiratory dysfunction: 49 cases |
| Targets |
Clinical data Treatment information (specific information of elderly people and test values) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000061 |
| Total Data Volume | 1 MB (txt) |
| Comments (Policies) | NBDC policy |
*4: Details about Participants
2-1. Cancer case
1) Patients with definite diagnosis of colorectal, gastric, and lung cancer.
2) Patients who had received cancer treatment between September 2002 to June 2006.
3) Patients ≥40 years old.
4) Patients known their age, gender, stage, prognosis, and therapeutic response.
2-2. Noncancerous case
1) Patients with definite diagnosis of cardiovascular disorder, respiratory dysfunction, diabetes and nephropathy.
2) Patients who had no medical record of cancer. And patients who achieved complete remission before September 2002 even if one had a medical record of cancer.
3) Patients who had received treatments for cardiovascular disorder, respiratory dysfunction, diabetes or nephropathy between September 2002 to June 2006.
4) Patients ≥40 years old.
5) Patients know their age, gender, prognosis, and therapeutic response.
DATA PROVIDER
Principal Investigator: Masahiko Nishiyama
Affiliation: Department of Molecular Pharmacology and Oncology, Gunma University Graduate School of Medicine
URL: https://www.giar.gunma-u.ac.jp/en/program/program_kawabata/
Project / Group Name: Third Term Comprehensive Control Research for Cancer Health and Labor Sciences Research Grants of the Ministry of Health, Labor and Welfare of Japan.
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Third Term Comprehensive Control Research for Cancer Health and Labor Sciences Research Grants of the Ministry of Health, Labor and Welfare of Japan. | Geriatric Oncology Database of genotypes and methylation, gene expression, clinical data, and survey results on psychosocial and physical conditions in Japanese elderly cancer patients to establish truly effective treatment strategy | General-010 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic and Prognostic Differences of Non-small Cell Lung Cancer between Elderly Patients and Younger Counterparts. | - | JGAS000061 |
| 2 | Impact of age on epidermal growth factor receptor mutation in lung cancer. | doi: 10.1016/j.lungcan.2012.09.006 | JGAS000061 |
| 3 | Association between a genome-wide association study-identified locus and the risk of lung cancer in Japanese population. | doi: 10.1097/JTO.0b013e3182475028 | JGAS000061 |
| 4 | Thoracic radiotherapy with or without daily low-dose carboplatin in elderly patients with non-small-cell lung cancer: a randomised, controlled, phase 3 trial by the Japan Clinical Oncology Group (JCOG0301) | doi: 10.1016/S1470-2045(12)70139-0 | JGAS000061 |
| 5 | Progression-free survival as a surrogate for overall survival in advanced/recurrent gastric cancer trials: a meta-analysis. | doi: 10.1093/jnci/djt269 | JGAS000061 |
| 6 | Risk factors associated with recurrence of surgically resected node-positive non-small cell lung cancer. | doi: 10.1007/s00595-015-1301-5 | JGAS000061 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
