PGS Publication: PGP000410

Publication Information (EuropePMC)
Title Genetic diversity fuels gene discovery for tobacco and alcohol use.
PubMed ID 36477530(Europe PMC)
doi 10.1038/s41586-022-05477-4
Publication Date Dec. 7, 2022
Journal Nature
Author(s) Saunders GRB, Wang X, Chen F, Jang SK, Liu M, Wang C, Gao S, Jiang Y, Khunsriraksakul C, Otto JM, Addison C, Akiyama M, Albert CM, Aliev F, Alonso A, Arnett DK, Ashley-Koch AE, Ashrani AA, Barnes KC, Barr RG, Bartz TM, Becker DM, Bielak LF, Benjamin EJ, Bis JC, Bjornsdottir G, Blangero J, Bleecker ER, Boardman JD, Boerwinkle E, Boomsma DI, Boorgula MP, Bowden DW, Brody JA, Cade BE, Chasman DI, Chavan S, Chen YI, Chen Z, Cheng I, Cho MH, Choquet H, Cole JW, Cornelis MC, Cucca F, Curran JE, de Andrade M, Dick DM, Docherty AR, Duggirala R, Eaton CB, Ehringer MA, Esko T, Faul JD, Silva LF, Fiorillo E, Fornage M, Freedman BI, Gabrielsen ME, Garrett ME, Gharib SA, Gieger C, Gillespie N, Glahn DC, Gordon SD, Gu CC, Gu D, Gudbjartsson DF, Guo X, Haessler J, Hall ME, Haller T, Harris KM, He J, Herd P, Hewitt JK, Hickie I, Hidalgo B, Hokanson JE, Hopfer C, Hottenga J, Hou L, Huang H, Hung YJ, Hunter DJ, Hveem K, Hwang SJ, Hwu CM, Iacono W, Irvin MR, Jee YH, Johnson EO, Joo YY, Jorgenson E, Justice AE, Kamatani Y, Kaplan RC, Kaprio J, Kardia SLR, Keller MC, Kelly TN, Kooperberg C, Korhonen T, Kraft P, Krauter K, Kuusisto J, Laakso M, Lasky-Su J, Lee WJ, Lee JJ, Levy D, Li L, Li K, Li Y, Lin K, Lind PA, Liu C, Lloyd-Jones DM, Lutz SM, Ma J, Mägi R, Manichaikul A, Martin NG, Mathur R, Matoba N, McArdle PF, McGue M, McQueen MB, Medland SE, Metspalu A, Meyers DA, Millwood IY, Mitchell BD, Mohlke KL, Moll M, Montasser ME, Morrison AC, Mulas A, Nielsen JB, North KE, Oelsner EC, Okada Y, Orrù V, Palmer ND, Palviainen T, Pandit A, Park SL, Peters U, Peters A, Peyser PA, Polderman TJC, Rafaels N, Redline S, Reed RM, Reiner AP, Rice JP, Rich SS, Richmond NE, Roan C, Rotter JI, Rueschman MN, Runarsdottir V, Saccone NL, Schwartz DA, Shadyab AH, Shi J, Shringarpure SS, Sicinski K, Skogholt AH, Smith JA, Smith NL, Sotoodehnia N, Stallings MC, Stefansson H, Stefansson K, Stitzel JA, Sun X, Syed M, Tal-Singer R, Taylor AE, Taylor KD, Telen MJ, Thai KK, Tiwari H, Turman C, Tyrfingsson T, Wall TL, Walters RG, Weir DR, Weiss ST, White WB, Whitfield JB, Wiggins KL, Willemsen G, Willer CJ, Winsvold BS, Xu H, Yanek LR, Yin J, Young KL, Young KA, Yu B, Zhao W, Zhou W, Zöllner S, Zuccolo L, 23andMe Research Team, Biobank Japan Project, Batini C, Bergen AW, Bierut LJ, David SP, Gagliano Taliun SA, Hancock DB, Jiang B, Munafò MR, Thorgeirsson TE, Liu DJ, Vrieze S.
Released in PGS Catalog: Dec. 20, 2022

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

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS003369
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AFR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking cessation smoking cessation 1,193,789
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003369/ScoringFiles/PGS003369.txt.gz
PGS003357
(GSCAN_SmkInit_2022_PRS_WEIGHTS_AFR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking initiation smoking initiation 1,194,472
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003357/ScoringFiles/PGS003357.txt.gz
PGS003360
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EUR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking initiation smoking initiation 1,055,915
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003360/ScoringFiles/PGS003360.txt.gz
PGS003362
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_AMR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Age of smoking initiation age at initiation of smoking 1,073,689
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003362/ScoringFiles/PGS003362.txt.gz
PGS003367
(GSCAN_CigDay_2022_PRS_WEIGHTS_EAS)
PGP000410 |
Saunders GRB et al. Nature (2022)
Cigarettes smoked per day cigarettes per day measurement 858,414
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003367/ScoringFiles/PGS003367.txt.gz
PGS003373
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_AFR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Drinks per week alcohol consumption measurement 1,177,071
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003373/ScoringFiles/PGS003373.txt.gz
PGS003374
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_AMR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Drinks per week alcohol consumption measurement 1,109,568
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003374/ScoringFiles/PGS003374.txt.gz
PGS003368
(GSCAN_CigDay_2022_PRS_WEIGHTS_EUR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Cigarettes smoked per day cigarettes per day measurement 1,055,811
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003368/ScoringFiles/PGS003368.txt.gz
PGS003376
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_EUR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Drinks per week alcohol consumption measurement 1,055,988
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003376/ScoringFiles/PGS003376.txt.gz
PGS003358
(GSCAN_SmkInit_2022_PRS_WEIGHTS_AMR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking initiation smoking initiation 1,109,850
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003358/ScoringFiles/PGS003358.txt.gz
PGS003363
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_EAS)
PGP000410 |
Saunders GRB et al. Nature (2022)
Age of smoking initiation age at initiation of smoking 858,406
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003363/ScoringFiles/PGS003363.txt.gz
PGS003370
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AMR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking cessation smoking cessation 1,109,663
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003370/ScoringFiles/PGS003370.txt.gz
PGS003372
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EUR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking cessation smoking cessation 1,055,802
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003372/ScoringFiles/PGS003372.txt.gz
PGS003375
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_EAS)
PGP000410 |
Saunders GRB et al. Nature (2022)
Drinks per week alcohol consumption measurement 856,333
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003375/ScoringFiles/PGS003375.txt.gz
PGS003364
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_EUR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Age of smoking initiation age at initiation of smoking 1,055,960
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003364/ScoringFiles/PGS003364.txt.gz
PGS003365
(GSCAN_CigDay_2022_PRS_WEIGHTS_AFR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Cigarettes smoked per day cigarettes per day measurement 1,196,168
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003365/ScoringFiles/PGS003365.txt.gz
PGS003366
(GSCAN_CigDay_2022_PRS_WEIGHTS_AMR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Cigarettes smoked per day cigarettes per day measurement 1,112,206
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003366/ScoringFiles/PGS003366.txt.gz
PGS003359
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EAS)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking initiation smoking initiation 859,206
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003359/ScoringFiles/PGS003359.txt.gz
PGS003361
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_AFR)
PGP000410 |
Saunders GRB et al. Nature (2022)
Age of smoking initiation age at initiation of smoking 1,193,754
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003361/ScoringFiles/PGS003361.txt.gz
PGS003371
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EAS)
PGP000410 |
Saunders GRB et al. Nature (2022)
Smoking cessation smoking cessation 859,229
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003371/ScoringFiles/PGS003371.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
PPM016232 PGS003376
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_EUR)
PSS010063|
European Ancestry|
6,092 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Drinks per week β: 0.121 (0.016) ∆ R^2: 0.012
PPM016229 PGS003373
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_AFR)
PSS010064|
African Ancestry|
2,199 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Drinks per week β: 0.051 (0.028) ∆ R^2: 0.003
PPM016230 PGS003374
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_AMR)
PSS010061|
Hispanic or Latin American Ancestry|
1,132 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Drinks per week β: 0.078 (0.034) ∆ R^2: 0.006
PPM016231 PGS003375
(GSCAN_DrnkWk_2022_PRS_WEIGHTS_EAS)
PSS010062|
East Asian Ancestry|
525 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Drinks per week β: 0.089 (0.057) ∆ R^2: 0.007
PPM016213 PGS003357
(GSCAN_SmkInit_2022_PRS_WEIGHTS_AFR)
PSS010064|
African Ancestry|
2,199 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking initiation OR: 0.445 (0.112) ∆ AUC: 0.015
∆ R^2: 0.01
PPM016214 PGS003358
(GSCAN_SmkInit_2022_PRS_WEIGHTS_AMR)
PSS010061|
Hispanic or Latin American Ancestry|
1,132 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking initiation OR: 0.46 (0.078) ∆ AUC: 0.027
∆ R^2: 0.036
PPM016215 PGS003359
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EAS)
PSS010062|
East Asian Ancestry|
525 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking initiation OR: 0.339 (0.096) ∆ AUC: 0.03
∆ R^2: 0.041
PPM016216 PGS003360
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EUR)
PSS010063|
European Ancestry|
6,092 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking initiation OR: 0.846 (0.042) ∆ AUC: 0.118
∆ R^2: 0.096
PPM016217 PGS003361
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_AFR)
PSS010064|
African Ancestry|
2,199 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Age of smoking initiation β: 0.045 (0.06) ∆ R^2: 0.001
PPM016218 PGS003362
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_AMR)
PSS010061|
Hispanic or Latin American Ancestry|
1,132 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Age of smoking initiation β: 0.058 (0.047) ∆ R^2: 0.003
PPM016219 PGS003363
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_EAS)
PSS010062|
East Asian Ancestry|
525 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Age of smoking initiation β: 0.057 (0.088) ∆ R^2: 0.003
PPM016220 PGS003364
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_EUR)
PSS010063|
European Ancestry|
6,092 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Age of smoking initiation β: 0.12 (0.018) ∆ R^2: 0.014
PPM016221 PGS003365
(GSCAN_CigDay_2022_PRS_WEIGHTS_AFR)
PSS010064|
African Ancestry|
2,199 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Cigarettes smoked per day β: 0.016 (0.042) ∆ R^2: 0.00022
PPM016222 PGS003366
(GSCAN_CigDay_2022_PRS_WEIGHTS_AMR)
PSS010061|
Hispanic or Latin American Ancestry|
1,132 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Cigarettes smoked per day β: 0.111 (0.05) ∆ R^2: 0.012
PPM016223 PGS003367
(GSCAN_CigDay_2022_PRS_WEIGHTS_EAS)
PSS010062|
East Asian Ancestry|
525 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Cigarettes smoked per day β: -0.028 (0.091) ∆ R^2: 0.001
PPM016224 PGS003368
(GSCAN_CigDay_2022_PRS_WEIGHTS_EUR)
PSS010063|
European Ancestry|
6,092 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Cigarettes smoked per day β: 0.217 (0.02) ∆ R^2: 0.045
PPM016225 PGS003369
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AFR)
PSS010064|
African Ancestry|
2,199 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking cessation OR: 0.276 (0.206) ∆ AUC: 0.005
∆ R^2: 0.005
PPM016226 PGS003370
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AMR)
PSS010061|
Hispanic or Latin American Ancestry|
1,132 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking cessation OR: 0.767 (0.488) ∆ AUC: 0.009
∆ R^2: 0.007
PPM016227 PGS003371
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EAS)
PSS010062|
East Asian Ancestry|
525 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking cessation OR: 0.034 (0.166) ∆ AUC: -0.001
∆ R^2: 0.00039
PPM016228 PGS003372
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EUR)
PSS010063|
European Ancestry|
6,092 individuals
PGP000410 |
Saunders GRB et al. Nature (2022)
Reported Trait: Smoking cessation OR: 1.02 (0.139) ∆ AUC: 0.049
∆ R^2: 0.026

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
PSS010064 2,199 individuals African unspecified AddHealth
PSS010061 1,132 individuals Hispanic or Latin American AddHealth
PSS010062 525 individuals East Asian AddHealth
PSS010063 6,092 individuals European AddHealth