GWAS summary statistics of autoimmune pulmonary alveolar proteinosis in Japanese

General information:

Sample size: 198 cases vs. 395 controls
Genotyping array: Infinium Asian Screening Array
Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) and in close genetic relation (PI_HAT > 0.175). We included samples of the estimated East Asian ancestry.
Variant QC: We excluded variants with (1) genotyping call rate < 98%, (2) P value for Hardy–Weinberg equilibrium < 1.0 × 10−6, and (3) minor allele count < 5, or (4) > 10% frequency difference with the imputation reference panel.
Phasing and imputation: shapeit2 and minimac3
Imputation reference: Combined panel of WGS data from the BioBank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504).
Post-imputation QC: We here report results of whole-genome imputed variants with Rsq > 0.7.
Association test: Logistic regression was performed with age, sex, and top 20 principal components as covariates by using PLINK2 software.

Uploaded files

File name	Descriptions
GWASsummary_PAP_Japanese_SakaueNatCommun2020.autosome.txt.gz	Results for 12,153,232 autosomal variants
GWASsummary_PAP_Japanese_SakaueNatCommun2020.chrX.txt.gz	Results for 242,876 X-chromosomal variants (males, females, and meta-analysis of males and females)

Columns

Autosomal variants

#	column name	Descriptions
1	SNP	marker name (CHR:POS:REF:ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	A1	effect allele (ALT)
5	A2	other allele (REF)
6	N_CASE	number of cases
7	N_CONTROL	number of controls
8	FREQ_A1_CASE	effect allele frequency in cases
9	FREQ_A1_CONTROL	effect allele frequency in controls
10	RSQ	imputation Rsq value
11	BETA	beta for effect allele
12	SE	standard error of beta for effect allele
13	P	P value

X-chromosomal variants

#	column name	Descriptions
1	SNP	marker name (CHR:POS:REF:ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	A1	effect allele (ALT)
5	A2	other allele (REF)
6	M_N_CASE	number of cases in males
7	M_N_CONTROL	number of controls in males
8	M_FREQ_A1_CASE	effect allele frequency in cases in males
9	M_FREQ_A1_CONTROL	effect allele frequency in controls in males
10	M_RSQ	imputation Rsq value in males
11	MBETA	beta for effect allele in males
12	MSE	standard error of beta for effect allele in males
13	MP	P value in males
14	F_N_CASE	number of cases in females
15	F_N_CONTROL	number of controls in females
16	F_FREQ_A1_CASE	effect allele frequency in cases in females
17	F_FREQ_A1_CONTROL	effect allele frequency in controls in females
18	F_RSQ	imputation Rsq value in females
19	FBETA	beta for effect allele in females
20	FSE	standard error of beta for effect allele in females
21	FP	P value in females
22	BETA	beta for effect allele in meta-analysis of sexes
23	SE	standard error of beta for effect allele in meta-analysis of sexes
24	P	P value in meta-analysis of sexes

Reference

If you use these summary statistics, please cite the following paper;
Sakaue S et al. Genetic determinants of risk in autoimmune pulmonary alveolar proteinosis. Nat Commun 2020.