NBDC Research ID: hum0169.v2
SUMMARY
Aims: to compare genomic alterations between tumor tissues from Primary Central Nervous System Lymphoma (PCNSL) patients and xenograft samples derived from PCNSL patients
Methods: whole exome sequencing
Participants/Materials: Nine samples, including patient derived xenograft (PDX) mice, tumor samples and peripheral blood cells from PCNSL patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000178 | NGS (Exome) | Controlled-access (Type I) | 2019/06/01 |
| JGAS000178 (Data addition) | NGS (Exome) | Controlled-access (Type I) | 2020/07/14 |
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MOLECULAR DATA
| Participants/Materials |
PCNSL (ICD10: C859): 9 cases YML9: PDX (first and second passages), tumor samples and peripheral blood cells from PCNSL patients YML11: PDX (first passages), tumor samples and peripheral blood cells from PCNSL patients YML3: PDX (second passages), tumor samples and peripheral blood cells from PCNSL patients YML4: PDX (first and fourth passages), tumor samples and peripheral blood cells from PCNSL patients YML8: PDX (first passages), tumor samples and peripheral blood cells from PCNSL patients YML12: PDX (first and second passages), tumor samples and peripheral blood cells from PCNSL patients YML15: PDX (first passages), tumor samples and peripheral blood cells from PCNSL patients YML16: PDX (first, second and third passages), tumor samples and peripheral blood cells from PCNSL patients YML17: PDX (first passages), tumor samples and peripheral blood cells from PCNSL patients |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor tissues and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra™ DNA Library Prep Kit for Illumina®, SureSelect Human All Exon V6 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| QC | nucleotides with Quality Value ＜20 were masked |
| Mapping Methods | bwa-mem, bowtie2 |
| Coverage (Depth) | 84% (≧20X) |
| Algorithm for detecting CNVs (software) | Log-R ratio (calculated with in-house pipline) |
| Filtering Methods | Log-R ratio ≧1.0, −1.0≧ |
| Genotype Call Methods (software) | Mutect2, Varscan2 |
| Filtering Methods | read length ≧20, mutation rate ≧10% |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000259 |
| Total Data Volume |
101 GB + 150 GB Data files: 7 (bam) + 25 (bam [ref: hg38]) Analysis files: 10 (tab [ref: hg38]) + 36 (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Tetsuya Yamamoto
Affiliation: Department of Neurosurgery, Yokohama City University
Project / Group Name: Neurosurgical-Oncology lab, Yokohama City University
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Development of novel therapeutic target for IDH mutant gliomas with DNA hypermutation | 19K09488 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | A Rapid Genotyping Panel for Detection of Primary Central Nervous System Lymphoma | doi: 10.1182/blood.2020010137 | JGAD000259 |
| 2 | A Hyperactive RelA/p65-Hexokinase 2 Signaling Axis Drives Primary Central Nervous System Lymphoma | doi: 10.1158/0008-5472.CAN-20-2425 | JGAD000259 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
