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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)
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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

JGAD000340

Type of data
NGS (HHV-6 sequences in WGS)
Access criteria
Controlled-access (Type I)
Total data volume
1.5 MB
File formats
  • FASTA
Research
hum0238
Date published
2020-09-28
Date modified
2020-11-18
DDBJ Search
JGAD000340 (opens in a new tab)
JGA Study
JGAS000240 (opens in a new tab)

Analysis method

WGS

Materials and participants
BBJ participants (WGS are included in JGAD000220 / AGDD_000005) whose DNA sequences contain germline integration of HHV-6 sequences: 10 samples
  • Subject count
    10 (Sample)
  • Cohort
    BioBank Japan
  • Population
    Japanese
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
160 bp
Reference genome
GRCh37
HHV-6A
Analysis method
We aligned HHV-6 reads against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM.
Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8.
We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7.
We used reads that are unmappable to the human reference genome (hg19) and realign such reads against a HHV-6 reference.
Ten subjects with high depth of coverage of HHV-6 were selected.
Data use policy
NBDC data sharing policy (JGAP000001)