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Dataset ID

NHA000195

Type of data
GWAS for autoimmune diseases
Access criteria
Unrestricted-access
Total data volume
147 MB
File formats
  • DOCX
  • ZIP
Research
hum0197
Date published
2024-10-28
Date modified
2024-10-28
Secondary ID
hum0197.v21.gwas-ehhv6.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Description_GWASsumstats_eHHV6B_Jap_T2T_maf005_SasaNatGent2024.docxDictionary file21.7 KB
hum0197.v21.gwas-ehhv6.v1.zip147 MB

Analysis method

genome wide SNPs

Materials and participants
Autoimmune diseases (ICD10: L400, M0690, M329, J840, G35): 238 cases
eHHV-6B-positive: 22 cases
eHHV-6B-negative: 216 cases
  • Health status
    Affected
  • Subject count
    238 (Individual)
Disease
Autoimmune diseases (L400, M069, M329, J840, G35)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq DNA PCR-Free Library Prep Kit
Platform
Illumina HiSeq X
Illumina NovaSeq 6000
Reference genome
T2T-CHM13
QC and filtering
Sample QC: Individuals were excluded if they showed conflicting sex assignments between genetically inferred sex by variants and WGS coverage, deviating heterozygosity rate (±3 standard deviations), or cryptic relatedness (pi-hat > 0.2). We included samples of the estimated Japanese ancestry using PCA. Four cases were excluded.
Variant QC: We excluded (1) non-autosomal variants, (2) multi-allelic sites and spanning deletions, and (3) variants with P-value for Hardy?Weinberg equilibrium < 1e-10 in cases and < 1e-6 in controls.
Analysis method
The FASTQ reads were aligned to T2T-CHM13v2.0 with BWA-MEM (v0.7.27), followed by GATK4 MarkDuplicates and Base Quality Score Recalibration (v4.2.6.1) according to the GATK Best Practice. Then, we performed per-sample SNP and indel calling using GATK4 HaplotypeCaller and joint genotyping using GATK4 GenomicsDBImport and GenotypeGVCF. We conducted LD-based genotype refinement for low-confidence genotypes and missing sites in WGS data using BEAGLE v5.4 with default settings.
PLINK v2.0 software was used with top two principal components and sex as covariates.
Variant count
6,464,509 SNPs
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)