Trait: cognition

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003925
Description Intellectual or mental process whereby an organism becomes aware of or obtains knowledge.
Trait category
Biological process
Synonym cognitive function
Mapped terms 2 mapped terms
  • MeSH:D003071
  • NCIt:C16446
Child trait(s) intelligence

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:
Display options:
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
Note: This table shows PGS for child terms of "cognition" in the EFO hierarchy.
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)
PGS001232
(GBE_INI20016)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Fluid intelligence score intelligence 10,055
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001232/ScoringFiles/PGS001232.txt.gz
PGS001919
(portability-PLR_fluid_intelligence)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Fluid intelligence score intelligence 26,145
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001919/ScoringFiles/PGS001919.txt.gz
PGS002135
(portability-ldpred2_fluid_intelligence)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Fluid intelligence score intelligence 903,259
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002135/ScoringFiles/PGS002135.txt.gz
PGS003510
(cont-decay-fluid_intelligence)
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Fluid intelligence score intelligence 979,739
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003510/ScoringFiles/PGS003510.txt.gz
PGS003724
(IQ)
PGP000465 |
Hatoum AS et al. Biol Psychiatry (2022)
Intelligence quotient intelligence 6,683,248
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003724/ScoringFiles/PGS003724.txt.gz
PGS004427
(X20016.score)
PGP000561 |
Jung H et al. Commun Biol (2024)
Fluid intelligence score intelligence 1,059,939
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004427/ScoringFiles/PGS004427.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
PPM008669 PGS001232
(GBE_INI20016)
PSS004891|
African Ancestry|
3,281 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Fluid intelligence score : 0.01453 [0.00875, 0.0203]
Incremental R2 (full-covars): -0.01682
PGS R2 (no covariates): 0.00026 [-0.00053, 0.00105]
age, sex, UKB array type, Genotype PCs
PPM008670 PGS001232
(GBE_INI20016)
PSS004892|
East Asian Ancestry|
716 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Fluid intelligence score : 0.06194 [0.03982, 0.08407]
Incremental R2 (full-covars): -0.023
PGS R2 (no covariates): 0.00235 [-0.00223, 0.00694]
age, sex, UKB array type, Genotype PCs
PPM008671 PGS001232
(GBE_INI20016)
PSS004893|
European Ancestry|
10,867 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Fluid intelligence score : 0.12663 [0.11891, 0.13435]
Incremental R2 (full-covars): 0.02765
PGS R2 (no covariates): 0.03358 [0.02918, 0.03797]
age, sex, UKB array type, Genotype PCs
PPM008672 PGS001232
(GBE_INI20016)
PSS004894|
South Asian Ancestry|
3,933 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Fluid intelligence score : 0.04498 [0.03601, 0.05394]
Incremental R2 (full-covars): 0.01256
PGS R2 (no covariates): 0.01775 [0.01195, 0.02354]
age, sex, UKB array type, Genotype PCs
PPM008673 PGS001232
(GBE_INI20016)
PSS004895|
European Ancestry|
27,171 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Fluid intelligence score : 0.06613 [0.0625, 0.06975]
Incremental R2 (full-covars): 0.0502
PGS R2 (no covariates): 0.05073 [0.0475, 0.05395]
age, sex, UKB array type, Genotype PCs
PPM010231 PGS001919
(portability-PLR_fluid_intelligence)
PSS009406|
European Ancestry|
5,092 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1628 [0.1359, 0.1895] sex, age, birth date, deprivation index, 16 PCs
PPM010232 PGS001919
(portability-PLR_fluid_intelligence)
PSS009180|
European Ancestry|
984 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.0669 [0.0038, 0.1295] sex, age, birth date, deprivation index, 16 PCs
PPM010233 PGS001919
(portability-PLR_fluid_intelligence)
PSS008734|
European Ancestry|
1,846 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1731 [0.1282, 0.2172] sex, age, birth date, deprivation index, 16 PCs
PPM010235 PGS001919
(portability-PLR_fluid_intelligence)
PSS008286|
South Asian Ancestry|
653 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1605 [0.0836, 0.2354] sex, age, birth date, deprivation index, 16 PCs
PPM010236 PGS001919
(portability-PLR_fluid_intelligence)
PSS008063|
East Asian Ancestry|
345 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.0626 [-0.0465, 0.1703] sex, age, birth date, deprivation index, 16 PCs
PPM010237 PGS001919
(portability-PLR_fluid_intelligence)
PSS007850|
African Ancestry|
266 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1082 [-0.0171, 0.2302] sex, age, birth date, deprivation index, 16 PCs
PPM010238 PGS001919
(portability-PLR_fluid_intelligence)
PSS008954|
African Ancestry|
323 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.0768 [-0.0362, 0.1879] sex, age, birth date, deprivation index, 16 PCs
PPM010234 PGS001919
(portability-PLR_fluid_intelligence)
PSS008508|
Greater Middle Eastern Ancestry|
158 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1171 [-0.051, 0.2788] sex, age, birth date, deprivation index, 16 PCs
PPM011938 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS008954|
African Ancestry|
323 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.0494 [-0.0636, 0.1612] sex, age, birth date, deprivation index, 16 PCs
PPM011931 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS009406|
European Ancestry|
5,092 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1998 [0.1733, 0.2261] sex, age, birth date, deprivation index, 16 PCs
PPM011932 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS009180|
European Ancestry|
984 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1048 [0.0419, 0.1668] sex, age, birth date, deprivation index, 16 PCs
PPM011933 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS008734|
European Ancestry|
1,846 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1987 [0.1542, 0.2423] sex, age, birth date, deprivation index, 16 PCs
PPM011934 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS008508|
Greater Middle Eastern Ancestry|
158 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.0685 [-0.0997, 0.233] sex, age, birth date, deprivation index, 16 PCs
PPM011935 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS008286|
South Asian Ancestry|
653 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1703 [0.0936, 0.245] sex, age, birth date, deprivation index, 16 PCs
PPM011936 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS008063|
East Asian Ancestry|
345 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1364 [0.0281, 0.2416] sex, age, birth date, deprivation index, 16 PCs
PPM011937 PGS002135
(portability-ldpred2_fluid_intelligence)
PSS007850|
African Ancestry|
266 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Fluid intelligence score Partial Correlation (partial-r): 0.1361 [0.0112, 0.2568] sex, age, birth date, deprivation index, 16 PCs
PPM017438 PGS003510
(cont-decay-fluid_intelligence)
PSS010872|
European Ancestry|
5,148 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.06 sex, age, deprivation index, PC1-16
PPM017522 PGS003510
(cont-decay-fluid_intelligence)
PSS010788|
European Ancestry|
983 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.01 sex, age, deprivation index, PC1-16
PPM017606 PGS003510
(cont-decay-fluid_intelligence)
PSS010620|
European Ancestry|
1,785 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.04 sex, age, deprivation index, PC1-16
PPM017690 PGS003510
(cont-decay-fluid_intelligence)
PSS010536|
Greater Middle Eastern Ancestry|
158 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.0 sex, age, deprivation index, PC1-16
PPM017774 PGS003510
(cont-decay-fluid_intelligence)
PSS010200|
European Ancestry|
799 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.05 sex, age, deprivation index, PC1-16
PPM017858 PGS003510
(cont-decay-fluid_intelligence)
PSS010452|
South Asian Ancestry|
652 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.03 sex, age, deprivation index, PC1-16
PPM017942 PGS003510
(cont-decay-fluid_intelligence)
PSS010368|
East Asian Ancestry|
345 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.01 sex, age, deprivation index, PC1-16
PPM018026 PGS003510
(cont-decay-fluid_intelligence)
PSS010284|
African Ancestry|
266 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.01 sex, age, deprivation index, PC1-16
PPM018110 PGS003510
(cont-decay-fluid_intelligence)
PSS010704|
African Ancestry|
322 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Fluid intelligence score partial-R2: 0.0 sex, age, deprivation index, PC1-16
PPM018418 PGS003724
(IQ)
PSS010959|
European Ancestry|
916 individuals
PGP000465 |
Hatoum AS et al. Biol Psychiatry (2022)
Reported Trait: Intelligence quotient β: 0.149 : 0.121 PCs1-10, genotyping batch, cEF PGS cEF and IQ were genetically correlated (0.61) so were used as covariates in the PGS prediction model.
PPM020542 PGS004427
(X20016.score)
PSS011364|
European Ancestry|
56,192 individuals
PGP000561 |
Jung H et al. Commun Biol (2024)
Reported Trait: Fluid intelligence score PGS R2 (no covariates): 0.22342

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
PSS010788 983 individuals,
35.0 % Male samples
Mean = 54.1 years
Sd = 7.4 years
European Polish UKB
PSS010536 158 individuals,
56.0 % Male samples
Mean = 54.5 years
Sd = 7.6 years
Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB
PSS010284 266 individuals,
34.0 % Male samples
Mean = 50.4 years
Sd = 7.1 years
African American or Afro-Caribbean Caribbean UKB
PSS009180 984 individuals European Poland (NE Europe) UKB
PSS008286 653 individuals South Asian India (South Asia) UKB
PSS010704 322 individuals,
47.0 % Male samples
Mean = 50.6 years
Sd = 7.4 years
African unspecified Nigerian UKB
PSS008954 323 individuals African unspecified Nigeria (West Africa) UKB
PSS010452 652 individuals,
54.0 % Male samples
Mean = 52.5 years
Sd = 8.3 years
South Asian Indian UKB
PSS010200 799 individuals,
43.0 % Male samples
Mean = 57.7 years
Sd = 6.9 years
European Ashkenazi UKB
PSS008063 345 individuals East Asian China (East Asia) UKB
PSS010959 916 individuals European COL_Twin
PSS008734 1,846 individuals European Italy (South Europe) UKB
PSS010872 5,148 individuals,
46.0 % Male samples
Mean = 56.4 years
Sd = 7.6 years
European white British UKB
PSS011364 56,192 individuals European UKB
PSS010620 1,785 individuals,
42.0 % Male samples
Mean = 54.1 years
Sd = 8.1 years
European Italian UKB
PSS004891 3,281 individuals African unspecified UKB
PSS004892 716 individuals East Asian UKB
PSS004893 10,867 individuals European non-white British ancestry UKB
PSS004894 3,933 individuals South Asian UKB
PSS004895 27,171 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS010368 345 individuals,
27.0 % Male samples
Mean = 52.1 years
Sd = 7.6 years
East Asian Chinese UKB
PSS007850 266 individuals African American or Afro-Caribbean Carribean UKB
PSS008508 158 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009406 5,092 individuals European UK (+ Ireland) UKB