NBDC Research ID: hum0236.v1
SUMMARY
Aims: Identifying aberrant splicing isoforms and potential neoantigens in non-small cell lung cancer
Methods: Full-length cDNA sequencing using a long-read sequencer MinION, short-read RNA sequencing, and whole-exome sequencing were performed to detect aberrant splicing isoforms and neoantigens expressed in non-small cell lung cancer specimens.
Participants/Materials: Seven non-small cell lung cancer specimens (tumor and matched-non tumor pair)
URL: http://kero.hgc.jp/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000245 | Controlled-access (Type I) | 2020/12/14 |
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MOLECULAR DATA
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 7 cases tumor tissues: 7 samples non-tumor tissues: 7 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from clinical specimens (tumor tissues and matched non-tumor tissues) |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V5 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000345 |
| Total Data Volume | 249 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 7 cases tumor tissues: 7 samples non-tumor tissues: 7 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Nanopore［MinION］ |
| Library Source | RNAs extracted from clinical specimens (tumor tissues and matched non-tumor tissues) |
| Cell Lines | - |
| Library Construction (kit name) | SQK-LSK308 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | full-length cDNA (1614 bp on average) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000345 |
| Total Data Volume | 249 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 7 cases tumor tissues: 7 samples non-tumor tissues: 7 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from clinical specimens (tumor tissues and matched non-tumor tissues) |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000345 |
| Total Data Volume | 249 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Tetsuya Nakatsura
Affiliation: Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science | 16H06279 |
| Grant-in-Aid for Early-Career Scientists | Development of novel measurement methods for RNA synthesis and degradation using nanopore sequencing | 19K16108 |
| Grant-in-Aid for Early-Career Scientists | Development of novel methods for detection of neoantigens in cancers by full-length transcriptome sequencing using nanopore sequencers | 19K16792 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Takashi Kohno | Division of Genome Biology, National Cancer Center Research Institute | Identification of genetic risk factors in AYA (Adolescence and Young Adult) cancer | JGAD000345 | 2021/11/29-2025/03/31 | |
| Hirofumi Nakaoka | Department of Cancer Genome Research, Sasaki Institute | Japan | Genetic analysis of lung cancer | JGAD000345 | 2022/08/06-2023/03/31 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000345 | 2022/12/26-2025/03/31 |
