Implementation of individualised polygenic risk score analysis: a test case of a family of four

BMC Medical Genomics

Table 4 Our set of bioinformatic filtering criteria applied to the remaining phenotypes

Phenotype Group	Phenotype (PheWAS Code)	Source (ID/PheWAS)	GWAS Consortium	# SNPs	Missing SNPs	% Missing SNPs	Validation	Status	Reason for filtering out
Autoimmune	Inflammatory Bowel Disease	PGS Catalog (PGS000017)	[3]	69,07,112	–		UKB	Selected
Autoimmune	Lupus	PGS Catalog (PGS000328)	[25]	57	32	56.14%	UKB	Unselected	Missing SNPs > 5%
Cancer	Breast Cancer	PGS Catalog (PGS000015)	[3]	5,218	–		UKB	Selected
	Prostate Cancer	PGS Catalog (PGS000333)	[22]	66,06,785	832	0.01%	FINRISK	Selected
	Glaucoma	PGS Catalog (PGS000137)	[28]	2,673	16	0.60%	UKB	Selected
	Testicular Cancer	Cancer-PRSweb (187.2)	[29,30,31,32,33,34,35,36]	43	–		UKB	Selected
	Chronic Lymph Leukaemia	Cancer-PRSweb (204.12)	[37,38,39,40,41,42,43]	27	–		UKB	Selected
	Thyroid cancer	Cancer-PRSweb (193)	[44,45,46,47]	5	–		UKB	Selected
	Glioma	Cancer-PRSweb (191.1)	[48,49,50,51,52,53]	19	–		UKB	Selected
	Melanoma	Cancer-PRSweb (172.1)	[54,55,56,57,58,59,60]	27	1	3.70%	UKB	Selected
	Colorectal Cancer	Cancer-PRSweb (153)	[61]	87	1	1.15%	UKB	Selected
	Basal Cell Carcinoma	Cancer-PRSweb (172.21)	[62,63,64,65,66,67,68]	24	1	4.17%	UKB	Selected
Cardiovascular	Atrial Fibrillation	PGS Catalog (PGS000016)	[3]	67,30,541	–		UKB	Selected
	Coronary Artery Disease	PGS Catalog (PGS000013)	[3]	66,30,150	–		UKB	Selected
	Ischaemic Stroke	PGS Catalog (PGS000039)	[109]	32,25,583	11,103	0.34%	UKB	Selected
Metabolic	Type 2 Diabetes	PGS Catalog (PGS000014)	[3]	69,17,436	–		UKB	Selected
	Testosterone Levels (female)	PGS Catalog (PGS000323)	[112]	7,168	–		UKB	Unselected	Missing SNPs > 5%
	Testosterone Levels (male)	PGS Catalog (PGS000322)	[112]	8,235	–		UKB	Unselected	Missing SNPs > 5%

ISSN: 1755-8794