Trait: coffee consumption measurement

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 questionnaire
Trait category
Other measurement

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
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)
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

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
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
PPM008358 PGS001126
(GBE_INI1498)
 PSS004856|
African Ancestry|
5,753 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.02026 [0.01348, 0.02704]
Incremental R2 (full-covars): -0.00015
PGS R2 (no covariates): 0.00245 [0.00005, 0.00484]		 age, sex, UKB array type, Genotype PCs —
PPM008359 PGS001126
(GBE_INI1498)
 PSS004857|
East Asian Ancestry|
1,455 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.05298 [0.03232, 0.07363]
Incremental R2 (full-covars): 0.00443
PGS R2 (no covariates): 0.00591 [-0.00133, 0.01315]		 age, sex, UKB array type, Genotype PCs —
PPM008360 PGS001126
(GBE_INI1498)
 PSS004858|
European Ancestry|
23,191 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.02284 [0.01917, 0.02651]
Incremental R2 (full-covars): 0.00663
PGS R2 (no covariates): 0.00615 [0.00421, 0.00809]		 age, sex, UKB array type, Genotype PCs —
PPM008361 PGS001126
(GBE_INI1498)
 PSS004859|
South Asian Ancestry|
6,844 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.02847 [0.02121, 0.03573]
Incremental R2 (full-covars): -0.00336
PGS R2 (no covariates): 0.00187 [-0.00004, 0.00379]		 age, sex, UKB array type, Genotype PCs —
PPM008362 PGS001126
(GBE_INI1498)
 PSS004860|
European Ancestry|
62,965 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Coffee intake — — R²: 0.01573 [0.01387, 0.01759]
Incremental R2 (full-covars): 0.00848
PGS R2 (no covariates): 0.00833 [0.00697, 0.0097]		 age, sex, UKB array type, Genotype PCs —

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
PSS003815 — —
[
  • 1,999 cases
  • , 1,488 controls
]
 — African unspecified — UKB —
PSS003816 — —
[
  • 619 cases
  • , 440 controls
]
 — East Asian — UKB —
PSS003817 — —
[
  • 8,877 cases
  • , 10,636 controls
]
 — European non-white British ancestry UKB —
PSS003818 — —
[
  • 2,481 cases
  • , 1,267 controls
]
 — South Asian — UKB —
PSS003819 — —
[
  • 30,561 cases
  • , 22,963 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004856 — — 5,753 individuals — African unspecified — UKB —
PSS004857 — — 1,455 individuals — East Asian — UKB —
PSS004858 — — 23,191 individuals — European non-white British ancestry UKB —
PSS004859 — — 6,844 individuals — South Asian — UKB —
PSS004860 — — 62,965 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS003607 — —
[
  • 962 cases
  • , 1,129 controls
]
 — African unspecified — UKB —
PSS003608 — —
[
  • 370 cases
  • , 243 controls
]
 — East Asian — UKB —
PSS003609 — —
[
  • 8,832 cases
  • , 2,643 controls
]
 — European non-white British ancestry UKB —
PSS003610 — —
[
  • 1,099 cases
  • , 1,232 controls
]
 — South Asian — UKB —
PSS003611 — —
[
  • 22,541 cases
  • , 6,503 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003874 — —
[
  • 417 cases
  • , 3,070 controls
]
 — African unspecified — UKB —
PSS003875 — —
[
  • 275 cases
  • , 784 controls
]
 — East Asian — UKB —
PSS003876 — —
[
  • 8,000 cases
  • , 11,513 controls
]
 — European non-white British ancestry UKB —
PSS003877 — —
[
  • 606 cases
  • , 3,142 controls
]
 — South Asian — UKB —
PSS003878 — —
[
  • 12,738 cases
  • , 40,786 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)