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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000061

1. Genome & Genetic research

genotype, methylation, gene expression, clinical data for colorectal, gastric, or lung cancer patients.

2. Retrospective study

clinical data for colorectal cancer, gastric cancer, lung cancer, cardiovascular disorders, respiratory dysfunction, diabetes, or nephropathy patients.

Controlled Access (Type I) 2016/08/26

*Release Note 

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

1. Genome & Genetic research

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

  Dictionary file

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 JGA00000000061 experimental support information
Japanese Genotype-phenotype Archive Data set ID JGAD00000000061
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.

 

2. Retrospective study

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)

Dictionary file

Japanese Genotype-phenotype Archive Data set ID JGAD00000000061
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: http://www.med.gunma-u.ac.jp/en/med-organization/biosys/biosys-tumor/63.html

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):

NameTitleProject 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

TitleDOIData Set ID
1 Genetic and Prognostic Differences of Non-small Cell Lung Cancer between Elderly Patients and Younger Counterparts. - JGAS00000000061
2 Impact of age on epidermal growth factor receptor mutation in lung cancer. doi: 10.1016/j.lungcan.2012.09.006 JGAS00000000061
3 Association between a genome-wide association study-identified locus and the risk of lung cancer in Japanese population. doi: 10.1097/JTO.0b013e3182475028 JGAS00000000061
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 JGAS00000000061
5 Progression-free survival as a surrogate for overall survival in advanced/recurrent gastric cancer trials: a meta-analysis. doi: 10.1093/jnci/djt269 JGAS00000000061
6 Risk factors associated with recurrence of surgically resected node-positive non-small cell lung cancer. doi: 10.1007/s00595-015-1301-5 JGAS00000000061

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use