Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0006781 |
Description | the quantification of some coffee consumption or coffee consumption-related behaviour, usually self-... reported via a questionnaireShow more |
Trait category |
Other measurement
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Polygenic Score ID & Name
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PGS Publication ID (PGP)
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Reported Trait
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Mapped Trait(s) (Ontology)
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Number of Variants
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Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link)
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PGS001123 (GBE_BIN100240) | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Coffee consumption | coffee consumption measurement | 48 | - | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001123/ScoringFiles/PGS001123.txt.gz |
PGS001124 (GBE_BIN_FC30001508) | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Coffee consumption (ground coffee) | coffee consumption measurement | 9,694 | - | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001124/ScoringFiles/PGS001124.txt.gz |
PGS001125 (GBE_BIN_FC20001508) | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Coffee consumption (instant coffee) | coffee consumption measurement | 432 | - | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001125/ScoringFiles/PGS001125.txt.gz |
PGS001126 (GBE_INI1498) | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Coffee intake | coffee consumption measurement | 3,154 | - | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001126/ScoringFiles/PGS001126.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score
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PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
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PPM008343 | PGS001123 (GBE_BIN100240) | PSS003607| African Ancestry| 2,091 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee consumed | — | AUROC: 0.56543 [0.54078, 0.59007] | R²: 0.02152 Incremental AUROC (full-covars): 0.00175 PGS R2 (no covariates): 0.00286 PGS AUROC (no covariates): 0.52506 [0.50028, 0.54984] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008344 | PGS001123 (GBE_BIN100240) | PSS003608| East Asian Ancestry| 613 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee consumed | — | AUROC: 0.60702 [0.56152, 0.65252] | PGS R2 (no covariates): 0.00015 R²: 0.06384 Incremental AUROC (full-covars): 0.00101 PGS AUROC (no covariates): 0.50685 [0.46035, 0.55335] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008345 | PGS001123 (GBE_BIN100240) | PSS003609| European Ancestry| 11,475 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee consumed | — | AUROC: 0.60041 [0.58833, 0.61249] | R²: 0.03144 Incremental AUROC (full-covars): 0.00304 PGS R2 (no covariates): 0.00129 PGS AUROC (no covariates): 0.51901 [0.50649, 0.53153] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008346 | PGS001123 (GBE_BIN100240) | PSS003610| South Asian Ancestry| 2,331 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee consumed | — | AUROC: 0.61704 [0.5943, 0.63978] | R²: 0.05335 Incremental AUROC (full-covars): 0.00112 PGS R2 (no covariates): 0.0008 PGS AUROC (no covariates): 0.51646 [0.49302, 0.53991] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008347 | PGS001123 (GBE_BIN100240) | PSS003611| European Ancestry| 29,044 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee consumed | — | AUROC: 0.57876 [0.57089, 0.58662] | R²: 0.01993 Incremental AUROC (full-covars): 0.00268 PGS R2 (no covariates): 0.00154 PGS AUROC (no covariates): 0.52002 [0.51203, 0.52801] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008348 | PGS001124 (GBE_BIN_FC30001508) | PSS003874| African Ancestry| 3,487 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) | — | AUROC: 0.60248 [0.57445, 0.6305] | R²: 0.02526 Incremental AUROC (full-covars): -0.00838 PGS R2 (no covariates): 0.00112 PGS AUROC (no covariates): 0.51847 [0.48874, 0.54821] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008349 | PGS001124 (GBE_BIN_FC30001508) | PSS003875| East Asian Ancestry| 1,059 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) | — | AUROC: 0.62271 [0.58544, 0.65999] | R²: 0.06183 Incremental AUROC (full-covars): -0.00244 PGS R2 (no covariates): 0.00176 PGS AUROC (no covariates): 0.52394 [0.48401, 0.56387] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008350 | PGS001124 (GBE_BIN_FC30001508) | PSS003876| European Ancestry| 19,513 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) | — | AUROC: 0.6398 [0.632, 0.64761] | R²: 0.07694 Incremental AUROC (full-covars): 2e-05 PGS R2 (no covariates): 0.01506 PGS AUROC (no covariates): 0.55973 [0.55158, 0.56789] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008351 | PGS001124 (GBE_BIN_FC30001508) | PSS003877| South Asian Ancestry| 3,748 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) | — | AUROC: 0.57148 [0.54785, 0.59512] | R²: 0.01345 Incremental AUROC (full-covars): -0.00658 PGS R2 (no covariates): 0.00195 PGS AUROC (no covariates): 0.52707 [0.50259, 0.55154] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008352 | PGS001124 (GBE_BIN_FC30001508) | PSS003878| European Ancestry| 53,524 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Ground coffee (include espresso, filter etc) | — | AUROC: 0.584 [0.57837, 0.58964] | R²: 0.02384 Incremental AUROC (full-covars): 0.02525 PGS R2 (no covariates): 0.01318 PGS AUROC (no covariates): 0.56269 [0.55703, 0.56835] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008353 | PGS001125 (GBE_BIN_FC20001508) | PSS003815| African Ancestry| 3,487 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Instant coffee | — | AUROC: 0.56676 [0.54763, 0.58589] | R²: 0.01807 Incremental AUROC (full-covars): 0.00096 PGS R2 (no covariates): 0.00043 PGS AUROC (no covariates): 0.50852 [0.48917, 0.52787] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008354 | PGS001125 (GBE_BIN_FC20001508) | PSS003816| East Asian Ancestry| 1,059 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Instant coffee | — | AUROC: 0.58603 [0.55141, 0.62065] | R²: 0.04389 Incremental AUROC (full-covars): -0.00701 PGS R2 (no covariates): 0.00663 PGS AUROC (no covariates): 0.46336 [0.42819, 0.49853] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008355 | PGS001125 (GBE_BIN_FC20001508) | PSS003817| European Ancestry| 19,513 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Instant coffee | — | AUROC: 0.62091 [0.61307, 0.62875] | R²: 0.05743 Incremental AUROC (full-covars): 0.00079 PGS R2 (no covariates): 0.00216 PGS AUROC (no covariates): 0.52276 [0.51464, 0.53088] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008356 | PGS001125 (GBE_BIN_FC20001508) | PSS003818| South Asian Ancestry| 3,748 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Instant coffee | — | AUROC: 0.56461 [0.54534, 0.58388] | R²: 0.01489 Incremental AUROC (full-covars): 0.00295 PGS R2 (no covariates): 0.00158 PGS AUROC (no covariates): 0.52329 [0.50344, 0.54314] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008357 | PGS001125 (GBE_BIN_FC20001508) | PSS003819| European Ancestry| 53,524 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: Coffee type: Instant coffee | — | AUROC: 0.55986 [0.55497, 0.56475] | R²: 0.01438 Incremental AUROC (full-covars): 0.00115 PGS R2 (no covariates): 0.00071 PGS AUROC (no covariates): 0.51308 [0.50814, 0.51802] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods
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Participant Follow-up Time
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Sample Numbers
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Age of Study Participants
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Sample Ancestry
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Additional Ancestry Description
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Cohort(s)
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Additional Sample/Cohort Information
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PSS003607 | — | — | [
| — | African unspecified | — | UKB | — |
PSS003608 | — | — | [
| — | East Asian | — | UKB | — |
PSS003609 | — | — | [
| — | European | non-white British ancestry | UKB | — |
PSS003610 | — | — | [
| — | South Asian | — | UKB | — |
PSS003611 | — | — | [
| — | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS003815 | — | — | [
| — | African unspecified | — | UKB | — |
PSS003816 | — | — | [
| — | East Asian | — | UKB | — |
PSS003817 | — | — | [
| — | European | non-white British ancestry | UKB | — |
PSS003818 | — | — | [
| — | South Asian | — | UKB | — |
PSS003819 | — | — | [
| — | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS003874 | — | — | [
| — | African unspecified | — | UKB | — |
PSS003875 | — | — | [
| — | East Asian | — | UKB | — |
PSS003876 | — | — | [
| — | European | non-white British ancestry | UKB | — |
PSS003877 | — | — | [
| — | South Asian | — | UKB | — |
PSS003878 | — | — | [
| — | European | white British ancestry | UKB | Testing cohort (heldout set) |