NBDC Research ID: hum0344.v2
SUMMARY
Aims: To investigate genomic alterations of Japanese biliary tract cancer
Methods: Whole genome sequencing analysis, transcriptome sequencing analysis, and amplicon sequencing analysis
Participants/Materials: Kidney cancer in endo-stage kidney disease, chronic kidney diseases, and HEK293 cell line
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000535 | Controlled-access (Type I) | 2022/08/04 | |
| JGAS000611 | NGS (Amplicon-seq) | Controlled-access (Type I) | 2023/05/16 |
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MOLECULAR DATA
| Participants/Materials |
Kidney cancer (ICD10: C64) in endo-stage kidney disease: 38 cases (of these, 26 cases also underwent RNA-seq analysis) tumor tissues: 38 samples non-tumor tissues/peripheral blood cells: 37 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | MGI Tech [MGISEQ-2000RS] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues/peripheral blood cells from kidney cancer in endo-stage kidney disease |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II FS DNA Module and MGIEasy DNA library prep kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp or 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000652 |
| Total Data Volume | 9.1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
Kidney cancer (ICD10: C64) in endo-stage kidney disease: 26 cases (These were also undergone WGS analysis) tumor tissues: 26 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues from kidney cancer in endo-stage kidney disease |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000652 |
| Total Data Volume | 9.1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Chronic kidney disease, CKD stage G1, G2, G4, G5 (ICD10: N18.1, N18.2, N18.4, N18.5): 77 cases (78 samples) HEK293 cell line: 1 sample |
| Targets | Amplicon-seq |
| Target Loci for Capture Methods | mitochondrial genome |
| Platform | Illumina [HiSeq 2500] |
| Library Source | mitochondrial DNAs extracted from non-tumor tissues from chronic kidney disease patients and HEK293 cell line |
| Cell Lines | 293 [HEK-293] (American Type Culture Collection, CRL-1573™) |
| Library Construction (kit name) |
KAPA Hyper Prep Kit Illumina Adapter Indexes (TruSeq DNA CD Indexes, TruSeq DNA Single Indexes) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000740 |
| Total Data Volume | 54 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hidewaki Nakagawa
Affiliation: Laboratory of Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences
Project / Group Name: Laboratory for Cancer Genomics
URL: https://www.riken.jp/en/research/labs/ims/genome_seq_anl/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis | doi: 10.1093/hmg/ddac180 | JGAD000652 |
| 2 | Mitochondrial DNA Mutations at Low-level Heteroplasmy in Chronic Kidney Disease | JGAD000740 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
