PGS Catalog - Cai N, Nat Genet (2020) (Publication)

PGS Publication: PGP000068

Publication Information (EuropePMC)
Title	Minimal phenotyping yields genome-wide association signals of low specificity for major depression.
PubMed ID	32231276(Europe PMC)
doi	10.1038/s41588-020-0594-5
Publication Date	March 30, 2020
Journal	*Nat Genet*
Author(s)	Cai N, Revez JA, Adams MJ, Andlauer TFM, Breen G, Byrne EM, Clarke TK, Forstner AJ, Grabe HJ, Hamilton SP, Levinson DF, Lewis CM, Lewis G, Martin NG, Milaneschi Y, Mors O, Müller-Myhsok B, Penninx BWJH, Perlis RH, Pistis G, Potash JB, Preisig M, Shi J, Smoller JW, Streit F, Tiemeier H, Uher R, Van der Auwera S, Viktorin A, Weissman MM, MDD Working Group of the Psychiatric Genomics Consortium, Kendler KS, Flint J.

Released in PGS Catalog: April 29, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID	PGS Name	PGS Publication (PGP) ID	Reported Trait	Mapped Trait(s) (Ontology)	Number of Variants	PGS Scoring File (FTP Link)
PGS000138	LifetimeMDD	PGP000068 Cai N et al. Nat Genet (2020)	Lifetime Major Depressive Disorder	major depressive disorder	22,274	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000138/ScoringFiles/PGS000138.txt.gz
PGS000139	MDDRecur	PGP000068 Cai N et al. Nat Genet (2020)	Lifetime Major Depressive Disorder (with recurrence)	major depressive disorder recurrent	21,980	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000139/ScoringFiles/PGS000139.txt.gz
PGS000141	Psypsy	PGP000068 Cai N et al. Nat Genet (2020)	Seen a psychiatrist for nerves, anxiety, tension or depression	seeing a psychiatrist for nerves, anxiety, tension or depression, self-reported depressive disorder	22,728	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000141/ScoringFiles/PGS000141.txt.gz
PGS000142	DepAll	PGP000068 Cai N et al. Nat Genet (2020)	Probable Depression (low mood or anhedonia, and seen a GP or psychiatrist for nerves, anxiety, tension or depression)	seeing a general practitioner for nerves, anxiety, tension or depression, self-reported seeing a psychiatrist for nerves, anxiety, tension or depression, self-reported depressive disorder	21,908	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000142/ScoringFiles/PGS000142.txt.gz
PGS000144	SelfRepDep	PGP000068 Cai N et al. Nat Genet (2020)	Self-reported depression or depression symptoms	self-reported trait depressive symptom measurement	21,828	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000144/ScoringFiles/PGS000144.txt.gz
PGS000145	ICD10Dep	PGP000068 Cai N et al. Nat Genet (2020)	Depression (ICD-10 defined)	major depressive disorder	21,510	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000145/ScoringFiles/PGS000145.txt.gz
PGS000140	GPpsy	PGP000068 Cai N et al. Nat Genet (2020)	Broad Depression (seen a General Practitioner for nerves, anxiety, tension or depression)	seeing a general practitioner for nerves, anxiety, tension or depression, self-reported depressive disorder	24,665	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000140/ScoringFiles/PGS000140.txt.gz
PGS000143	GPNoDep	PGP000068 Cai N et al. Nat Genet (2020)	Seen a General Practitioner for nerves, anxiety, tension or depression (without report of low mood or anhedonia)	seeing a general practitioner for nerves, anxiety, tension or depression, self-reported	21,042	http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000143/ScoringFiles/PGS000143.txt.gz

PGS Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID (PPM ID)	Evaluated Score	PGS Sample Set ID (PSS ID)	Performance Source	Trait	PGS Effect Sizes (per SD change)	PGS Classification Metrics	Other Metrics	Covariates Included in the Model	PGS Performance: Other Relevant Information
PPM000435	PGS000143 (GPNoDep)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.53441	R²: 0.00471	Cohort	—
PPM000433	PGS000141 (Psypsy)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.52988	R²: 0.00438	Cohort	—
PPM000437	PGS000145 (ICD10Dep)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.5251	R²: 0.0032	Cohort	—
PPM000436	PGS000144 (SelfRepDep)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.51641	R²: 0.00117	Cohort	—
PPM000434	PGS000142 (DepAll)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.5333	R²: 0.00492	Cohort	—
PPM000432	PGS000140 (GPpsy)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.53193	R²: 0.00481	Cohort	—
PPM000431	PGS000139 (MDDRecur)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.54874	R²: 0.01097	Cohort	—
PPM000430	PGS000138 (LifetimeMDD)	PSS000250	PGP000068 Cai N et al. (2020)	Reported Trait: Major Depressive Disorder status	—	AUROC: 0.5611	R²: 0.01817	Cohort	—

Evaluated Samples

PGS Sample Set ID (PSS ID)	Phenotype Definitions and Methods	Participant Follow-up Time	Sample Numbers	Age of Study Participants	Sample Ancestry	Additional Ancestry Description	Cohort(s)	Additional Sample/Cohort Information
PSS000250	—	—	36,709 individuals [ 14,696 cases , 22,013 controls ]	—	European	—	15 cohorts BOMA ,CoLaus ,Edinburgh ,GenPOD ,GenRED ,MARS ,MPIP ,NESDA ,QIMR ,RADIANT ,RS ,SHIP ,STAR*D ,TwinGene ,i2b2	Part of PGC29 (PMID: 29700475)