NBDC Research ID: hum0294.v1
SUMMARY
Aims: The objective is to analyze tumor and normal cell whole exome sequencing (WES) of esophageal cancer patients participating in the TENERGY-TR before treatment and RNA-seq specimens of tumor biopsy specimens at three points before treatment, after radiation chemotherapy, and after Atezolizumab administration, to search for biomarkers to predict treatment response.
Methods: DNA/RNA was extracted from frozen tumor or blood samples using an AllPrep DNA/RNA Mini kit (Qiagen) at each time point. Whole exome sequencing and RNA sequencing analyses were performed.
Participants/Materials:
- WES: tumor tissue (27 samples) and normal tissue (27 samples) from esophageal cancer patients
- RNA-seq: tumor biopsy specimens at three-time points before treatment (28 samples), after radiation chemotherapy (25 samples) and after Atezolizumab administration (25 samples)
URL： https://doi.org/10.1186/s12885-020-06716-5
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000708 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2024/05/29 |
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MOLECULAR DATA
| Participants/Materials |
esophageal cancer (ICD10: C159): 27 cases tumor tissue before treatment: 27 samples non-tumor tissue (blood): 27 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X] |
| Library Source | DNAs extracted from tumor and matched non-tumor tissues (blood samples) |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000841 |
| Total Data Volume | 974.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
esophageal cancer (ICD10: C159): 28 cases tumor tissue before treatment: 28 samples tumor tissue after radiation chemotherapy: 25 samples tumor tissue after atezolizumab administration: 25 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Access Library Prep Kit |
| Fragmentation Methods | |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000841 |
| Total Data Volume | 974.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shogo Kumagai
Affiliation: Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | A phase II, multicenter study to investigate the safety, efficacy, and proof-of-concept (POC) of Anti PD-L1 antibody monotherapy following radical chemoradiotherapy in patients with inoperable locally advanced esophageal squamous cell cancer | JP21ck0106420 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Atezolizumab monotherapy following dCRT indicated a promising cCR rate in patients with unresectable locally advanced esophageal squamous cell carcinoma (EPOC1802) | JGAD000841 |
USRES (Controlled-access Data)
| 研究代表者 | 所属機関 | 国・州名 | 研究題目 | 利用データID | 利用期間 |
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