NBDC Research ID: hum0358.v1
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SUMMARY
Aims: To identify molecular markers involved in the development and prognosis of cervical adenocarcinoma, we would like to elucidate the molecular biological characteristics of cervical adenocarcinoma in relation to the carcinogenesis of other cervical cancers (squamous cell carcinoma), vaginal and vulvar cancers.
Methods: Whole exome sequencing, RNA-seq
Participants/Materials: cervical cancer total of 19 cases
[Whole exome sequencing] 1 case: 3 samples of tumor/tumor-derived organoids/peripheral blood cell, 4 cases: 8 tumor samples, 2 peripheral blood samples, 2 normal areas near the tumors
[RNA-seq] 1 case: 2 samples of tumor/tumor-derived organoids, 13 cases: 13 tumor samples, 5 cases: multiple sampling from within the same tumor for a total of 77 samples
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000582 JGAS000586 |
NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2022/12/20 |
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MOLECULAR DATA
| Participants/Materials |
cervical cancer (ICD10: C539) [JGAS000582] 4 cases: 8 tumor samples, 2 peripheral blood samples, 2 normal areas near the tumor [JGAS000586] 1 case: 3 samples of tumor/tumor-derived organoids/peripheral blood |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumors, tumor-derived organoids, peripheral blood cells, or normal areas near the tumor |
| Cell Lines | - |
| Library Construction (kit name) | Twist Comprehenive exome |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | bwa, bowtie2 |
| Mapping Quality | ≧30 |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 168x (39x-318x) |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000708: 76 GB (bam) JGAD000713: 25.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
cervical cancer (ICD10: C539) [JGAS000582] 5 cases: multiple sampling each from within the same tumor for a total of 77 samples [JGAS000586] 1 case: 2 samples of tumor/tumor-derived organoids [JGAS000586] 13 cases: 13 samples of tumors |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [MiSeq] |
| Library Source | RNAs extracted from tumor and tumor-derived organoids |
| Cell Lines | - |
| Library Construction (kit name) | Nextera XT DNA Library Preparation Kit |
| Fragmentation Methods | Nextera XT transposome |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000708: 76 GB (bam) JGAD000713: 25.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kenbun Sone
Affiliation: Department of obstetrics and gynecology, The university of Tokyo Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Japan Program for Infectious Diseases Research and Infrastructure, Japan Agency for Medical Research and Development (AMED) | Study of HPV-18 persistent infection and carcinogenesis in the squamocolumnar junction cells using novel culture technologies | JP22wm0325014 |
| Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), Japan Agency for Medical Research and Development (AMED) | Transcriptome analysis of single cell and micro tissue sections for supporting of drug discovery | JP21am0101104 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Cells with stem-like properties are associated with the development of HPV18-positive cervical cancer | doi: 10.1111/cas.15664 | JGAD000708 |
| 2 | Application of organoid culture from HPV18-positive small cell carcinoma of the uterine cervix for precision medicine | doi: 10.1002/cam4.5588 | JGAD000713 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
