NBDC Research ID: hum0442.v1
SUMMARY
Aims: To evaluate the performance of a prognosis prediction model based on the plasma-free amino acid concentration profile for advanced and/or recurrent non-small cell lung cancer patients who will receive anti-PD-1/PD-L1 antibody therapy
Methods: RNA-seq analysis
Participants/Materials: advanced or recurrent non-small cell lung cancer patients before administering anti-PD-1/PD-L1 antibody treatment
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000675 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/12/06 |
| E-GEAD-883 | NGS (RNA-seq) | Unrestricted-access | 2024/12/06 |
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MOLECULAR DATA
| Participants/Materials |
advanced or recurrent non-small cell lung cancer (ICD10: C349) before administering anti-PD-1/PD-L1 antibody treatment: 20 cases FFPE tumor tissue: 20 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Smart Seq Stranded kit |
| Fragmentation Methods | Nextera XT DNA Library Prep Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp x 2 |
| Mapping Methods | The count data was mapped to the reference genome using STAR aligner for calculation. |
| Reference Genome Sequence |
read count calculated by HTSeq: hg19 TPM caluclated by salmon: GRCh38 |
| Detecting method for read count (software) | HTSeq |
| QC Methods | Read count and TPM data calculated after adapter trimming of fastq files. |
| Gene Number |
Count data: 25559 TPM data: 14222 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000805 |
| Genomic Expression Archive ID | E-GEAD-883 |
| Total Data Volume |
JGAD000805: 116.8 GB (fastq) E-GEAD-883: 4.5 MB (csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Tetsuro Sasada
Affiliation: Division of Cancer Immunotherapy, Kanagawa Cancer Center Reserach Institute
Project / Group Name: Exploratory study for stratification marker of immune checkpoint inhibitor in patients with advanced or recurrent non-small cell lung cancer
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project Focused on Developing Key Technology for Discovering and Manufacturing Drugs for Next-Generation Treatment and Diagnosis, Japan Agency for Medical Research and Development (AMED) | Evaluation of metabolic reprogramming in tumor immune microenvironment through amino-acid profiling and its application for stratifying patients under cancer immunotherapy | JP19ae0101076 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multi-omics analysis-based clinical and functional significance of a novel prognostic and immunotherapeutic gene signature derived from amino acid metabolism pathways in lung adenocarcinoma |
JGAD000805 E-GEAD-883 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
