Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes

Table 3 PheLEx discoveries identified for UK Biobank bipolar disorder phenotype

UK Biobank phenotype	SNP	Locus	p-value^a in original phenotype	p-value^a in corrected phenotype	r^2b	Genes^c	MAF^d
Bipolar Disorder	rs112071029	11:132129335	1.23e⁻⁵	6.74e⁻⁷	4e^− 4	NTM, OPCML, NTM-IT, C11orf39	0.0423
Bipolar Disorder	rs17028986	3:11913699	1.13e⁻⁵	1.58e^− 6	3.8e⁻⁴	TAMM41, SYN2, PPARG, TIMP4, ATG7, VGLL4	0.0925
Epilepsy	rs114011598	3:11913699	2.90e⁻⁵	1.55e⁻⁶	1e⁻⁴	ZLPD1, LOC152225, NXPE3, NFKBIZ	0.036

^a unadjusted p-values
^b Maximum r² with training SNPs
^c Genes with loci in linkage disequilibrium with loci where all annotations were performed using web-resource LDLink
^d MAF = Minor Allele Frequency

ISSN: 1471-2105