NBDC Research ID: hum0169.v1
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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: Two PCNSL samples (YML9 and YML11), including patient derived xenograft (PDX) mice, tumor samples and peripheral blood cells from PCNSL patients
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000178 | NGS (Exome) | Controlled Access (Type I) | 2019/06/01 |
* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
PCNSL (ICD10: C859): 2 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 |
| 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 Data set ID | JGAD000259 |
| Total Data Volume |
101 GB Data files: 7 (bam) Analysis files: 10 (tab [ref: hg38]) |
| 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 |
|---|---|---|
| - | ||
PUBLICATIONS
| Title | DOI | Data Set ID | |
|---|---|---|---|
| 1 | - | ||
| 2 |
USRES (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
