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)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000139
(MDDRecur)
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Lifetime Major Depressive Disorder (with recurrence) recurrent,
major depressive disorder		 21,980
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000139/ScoringFiles/PGS000139.txt.gz
PGS000145
(ICD10Dep)
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Depression (ICD-10 defined) major depressive disorder 21,510
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000145/ScoringFiles/PGS000145.txt.gz
PGS000144
(SelfRepDep)
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Self-reported depression or depression symptoms depressive symptom measurement,
self-reported trait		 21,828
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000144/ScoringFiles/PGS000144.txt.gz
PGS000138
(LifetimeMDD)
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Lifetime Major Depressive Disorder major depressive disorder 22,274
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000138/ScoringFiles/PGS000138.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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000140/ScoringFiles/PGS000140.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
-
 https://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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000142/ScoringFiles/PGS000142.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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000143/ScoringFiles/PGS000143.txt.gz

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) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000435 PGS000143
(GPNoDep)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.53441 R²: 0.00471 Cohort —
PPM000433 PGS000141
(Psypsy)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.52988 R²: 0.00438 Cohort —
PPM000437 PGS000145
(ICD10Dep)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.5251 R²: 0.0032 Cohort —
PPM000436 PGS000144
(SelfRepDep)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.51641 R²: 0.00117 Cohort —
PPM000434 PGS000142
(DepAll)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.5333 R²: 0.00492 Cohort —
PPM000432 PGS000140
(GPpsy)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.53193 R²: 0.00481 Cohort —
PPM000431 PGS000139
(MDDRecur)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.54874 R²: 0.01097 Cohort —
PPM000430 PGS000138
(LifetimeMDD)
 PSS000250|
European Ancestry|
36,709 individuals
 PGP000068 |
Cai N et al. Nat Genet (2020)
 Reported Trait: Major Depressive Disorder status — AUROC: 0.5611 R²: 0.01817 Cohort —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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)