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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000259

Type of data
NGS (Exome)
Access criteria
Controlled-access (Type I)
Total data volume
223 GB
File formats
  • BAM
  • TXT
Research
hum0169
Date published
2020-09-28
Date modified
2020-11-18
DDBJ Search
JGAD000259 (opens in a new tab)
JGA Study
JGAS000178 (opens in a new tab)

Analysis method

WES

Materials and participants
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
  • Health status
    Affected
  • Subject count
    9 (Individual)
Disease
PCNSL (C859)
Sample description
DNAs extracted from tumor tissues and peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
NEBNext Ultra DNA Library Prep Kit for Illumina
SureSelect Human All Exon V6
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
125 bp
Reference genome
GRCh38
Mapping
bwa-mem, bowtie2
QC and filtering
nucleotides with Quality Value ＜20 were masked
Analysis method
Log-R ratio (calculated with in-house pipline)
Coverage (breadth)
20x or more: 84%
Data use policy
NBDC data sharing policy (JGAP000001)