PGS Catalog - Saunders GRB, Nature (2022) (Publication)

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)

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)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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	—	—
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	—	—
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	—	—
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	—	—
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)	—	∆ R^2: 0.007 ∆ AUC: 0.009	—	—
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	—	—
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	—	—

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	—	Add Health	—
PSS010061	—	—	1,132 individuals	—	Hispanic or Latin American	—	Add Health	—
PSS010062	—	—	525 individuals	—	East Asian	—	Add Health	—
PSS010063	—	—	6,092 individuals	—	European	—	Add Health	—