NBDC Research ID: hum0342.v2
SUMMARY
Aims: Recent advances in somatic mutation and expression analysis in tumors have revealed the molecular pathological background of various gastrointestinal tumors. In the future, it is expected that these findings will be used to improve the accuracy of histopathological and grade diagnoses, as well as to further advance such searches. In this study, we conducted an integrated analysis of somatic mutations, gene expression, and protein expression, mainly in gastrointestinal tumors. By correlating these findings with histopathological and clinicopathological findings, we will search for new tissue-specific markers and prognostic factors that can be applied to histopathological and molecular pathological diagnoses.
Methods: Whole exome sequencing (WES) was conducted using tumor and non-tumor tissues obtained from RSPO fusion-positive cases. Whole exome sequencing (WES) and transcriptome analysis (RNA-seq) were conducted using tumor and non-tumor tissues obtained from small intestine cancer cases.
Participants/Materials: colorectal cancer, small intestine cancer
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000538 | NGS (Exome) | Controlled-access (Type I) | 2022/06/27 |
| JGAS000868 | NGS（Exome, RNA-seq） | Controlled-access (Type I) | 2026/01/05 |
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MOLECULAR DATA
| Participants/Materials |
Colorectal cancer (ICD10: C18): 29 cases tumor tissues: 29 samples, non-tumor tissues: 29 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 2ｘ150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000657 |
| Total Data Volume | 512.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Small intestine cancer (ICD10: C17): 11 cases tumor and non-tumor tissue pairs: total 22 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Twist Comprehensive Exome Panel, Exome2.0 plus Comprehensive Exome Spike-in |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001011 |
| Total Data Volume | 275.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Small intestine cancer (ICD10: C17): 15 cases (4 cases are also used in Exome) tumor tissues: 10 samples, non-tumor tissues: 5 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SMART-Seq Stranded Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001011 |
| Total Data Volume | 275.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shigeki Sekine
Affiliation: Department of Diagnostic Pathology, National Cancer Center Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Clinicopathological analysis of RSPO fusion-positive colorectal carcinoma | 20K07382 |
| Kurozumi Medical Foundation | Efficient detection of RSPO gene fusion/overexpression in colorectal and gastric cancers using RNA in situ hybridization | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Clinicopathological and molecular characteristics of RSPO fusion-positive colorectal cancer | doi: 10.1038/s41416-022-01880-w | JGAD000657 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
