NBDC Research ID: hum0348.v1

 

SUMMARY

Aims: To elucidate the mechanism of the tumorigenic process involving genomic aberrations by CD30 signaling in HTLV-1–infected T-cells

Methods: CD30+ATL cells, CD30-ATL cells, and HTLV-1 uninfected lymphocytes were sorted by FACS AriaIII. DNA was extracted from each sorted cell and used for whole exome sequencing analysis and array-CGH analysis. 

Participants/Materials: Adult T-cell leukemia/lymphoma (ATL): 8 cases

 

Dataset IDType of DataCriteriaRelease Date
JGAS000537

NGS (Exome)

array-CGH

Controlled-access (Type I) 2023/05/15

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

Exome

Participants/Materials

ATL (ICD10: C91.5): 8 cases

    CD30+ATL cells: 8 samples

    CD30-ATL cells: 8 samples

    HTLV-1 uninfected lymphocytes: 8 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source DNAs extracted from sorted cells
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V6 Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Mapping Methods Trimmomatic (v.0.38), DRAGEN Bio-IT Platform (v.3.7.5)
Mapping Quality -
Reference Genome Sequence hg38
Coverage (Depth) 83.6
Japanese Genotype-phenotype Archive Dataset ID JGAD000656
Total Data Volume 118.1 GB (bam)
Comments (Policies) NBDC policy

 

Array CGH

Participants/Materials ATL (ICD10: C91.5): 8 cases
Targets array-CGH
Target Loci for Capture Methods -
Platform Agilent Technologies [GenetiSure Cancer Research CGH+SNP Microarray 2 x 400K]
Source DNAs extracted from sorted cells
Cell Lines -
Reagents (Kit, Version) SureTag Complete DNA Labeling Kit
Genotype Call Methods (software) Cytogenomics v5.0
Filtering ADM-2 algorithm, Threshokd value: 5.5
Japanese Genotype-phenotype Archive Dataset ID JGAD000656
Total Data Volume 118.1 GB (txt)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Makoto Nakashima

Affiliation: Graduate School of Frontier Sciences, The University of Tokyo

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Early-Career Scientists Analysis of ATL progression by CD30 signaling and its biomarkers 19K16580
KAKENHI Grant-in-Aid for Early-Career Scientists The oncogenic driving force of CD30 signaling-induced chromosomal instability in adult T-cell leukemia/lymphoma 22K15420

 

PUBLICATIONS

TitleDOIDataset ID
1 The oncogenic driving force of CD30 signaling-induced chromosomal instability in adult T-cell leukemia/lymphoma doi: 10.1111/cas.15706 JGAD000656

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use