NBDC Research ID: hum0238.v1
SUMMARY
Aims: To determine human herpesvirus 6 (HHV-6) sequences in human genome sequences
Methods: Reconstruction of integrated HHV-6 sequences from whole genome sequencing data of BioBank Japan (BBJ) participants using unmapped reads
Participants/Materials: BBJ participants whose DNA sequences contain germline integration of HHV-6 sequences
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000240 | NGS (HHV-6 sequences in WGS) | Controlled-access (Type I) | 2020/07/28 |
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MOLECULAR DATA
| Participants/Materials | BBJ participants (WGS are included in JGAD000220 / AGDD_000005) whose DNA sequences contain germline integration of HHV-6 sequences: 10 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Preparation Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 160 bp |
| Human Sequence Exclusion Method |
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. |
| HHV-6 sequence construction 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. |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000340 |
| Total Data Volume | 1 MB (chromosome_fasta) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yukihide Momozawa / Nicholas Parrish
Affiliation: Laboratory for Genotyping Development / Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences
URL： https://www.riken.jp/en/research/labs/ims/genom_immunobiol_riken_hakubi/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Endogenization and excision of human herpesvirus 6 in human genomes | doi: 10.1101/2019.12.19.882522 | JGAD000340 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
