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 : 0.00471 Cohort
PPM000433 PGS000141
(Psypsy)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.52988 : 0.00438 Cohort
PPM000437 PGS000145
(ICD10Dep)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.5251 : 0.0032 Cohort
PPM000436 PGS000144
(SelfRepDep)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.51641 : 0.00117 Cohort
PPM000434 PGS000142
(DepAll)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.5333 : 0.00492 Cohort
PPM000432 PGS000140
(GPpsy)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.53193 : 0.00481 Cohort
PPM000431 PGS000139
(MDDRecur)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.54874 : 0.01097 Cohort
PPM000430 PGS000138
(LifetimeMDD)
PSS000250 PGP000068 Cai N et al. (2020) Reported Trait: Major Depressive Disorder status AUROC: 0.5611 : 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
[
  • 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)