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Dataset ID

NHA000199

Type of data
GWAS for PAF using whole exome sequencing data
Access criteria
Unrestricted-access
Total data volume
321 KB
File formats
  • DOCX
  • ZIP
Research
hum0495
Date published
2025-02-13
Date modified
2025-02-13
Secondary ID
hum0495.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0495.v1.gwas.v1.zip301 KB
hum0495_v1_gwas_v1.docxDictionary file20.1 KB

Analysis method

WES + Genotyping by array

Materials and participants
PAF (ICD10: I48.0): 1,176 cases
non-PAF (control) : 1,172 individuals
  • Health status
    Mixed
  • Subject count
    2348 (Individual)
Disease
PAF (I480)
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
WES
Target
N/A
Reagent kit
SureSelect XT Reagent Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
QC and filtering
Sample QC: We excluded samples with
(1) Sample call rate < 0.97
(2) Samples with sex mismatches
(3) One sample for each pair of second degree or closer relatives (kinship coefficient >0.088)
(4) Samples with outliers in sample size, heterozygosity and missing rates
Variant QC: We excluded variants with
(1) genotype quality < 2
(2) depth < 10
(3) allele imbalance
(4) variant call rate < 0.97
(5) Hardy-Weinberg equilibrium P-values =< 1 × 10−8
(6) PCA
Analysis method
GATK HaplotypeCaller
Variant count
518,621
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)