PGS Publication: PGP000084

Publication Information (EuropePMC)
Title Using polygenic scores for identifying individuals at increased risk of substance use disorders in clinical and population samples.
PubMed ID 32555147(Europe PMC)
doi 10.1038/s41398-020-00865-8
Publication Date June 18, 2020
Journal Transl Psychiatry
Author(s) Barr PB, Ksinan A, Su J, Johnson EC, Meyers JL, Wetherill L, Latvala A, Aliev F, Chan G, Kuperman S, Nurnberger J, Kamarajan C, Anokhin A, Agrawal A, Rose RJ, Edenberg HJ, Schuckit M, Kaprio J, Dick DM.
Released in PGS Catalog: July 1, 2020

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:
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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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000205
(RISK_PC_COGA)
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Risk-taking tendency (4-domain principal component model) risk-taking behaviour 1,110,737
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000205/ScoringFiles/PGS000205.txt.gz
PGS000202
(PROB_ALC_FT12)
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Problematic alcohol use alcohol dependence measurement 1,083,002
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000202/ScoringFiles/PGS000202.txt.gz
PGS000203
(GSCAN_DPW_COGA)
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Alcohol consumption (drinks per week) alcohol consumption measurement 1,110,910
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000203/ScoringFiles/PGS000203.txt.gz
PGS000206
(RISK_PC_FT12)
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Risk-taking tendency (4-domain principal component model) risk-taking behaviour 1,098,765
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000206/ScoringFiles/PGS000206.txt.gz
PGS000201
(PROB_ALC_COGA)
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Problematic alcohol use alcohol dependence measurement 1,094,954
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000201/ScoringFiles/PGS000201.txt.gz
PGS000204
(GSCAN_DPW_FT12)
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Alcohol consumption (drinks per week) alcohol consumption measurement 1,099,480
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000204/ScoringFiles/PGS000204.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
PPM000630 PGS000206
(RISK_PC_FT12)
 PSS000340|
European Ancestry|
1,251 individuals
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Reported Trait: Alcohol use disorder (DSM-5 criteria count, log-transformed) β: 0.1 (0.02) — ΔR-squared (vs. covariates alone): 0.02273 sex, age of last observation, 10 Genetic PCs —
PPM000629 PGS000202
(PROB_ALC_FT12)
 PSS000340|
European Ancestry|
1,251 individuals
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Reported Trait: Alcohol use disorder (DSM-5 criteria count, log-transformed) β: 0.043 (0.019) — ΔR-squared (vs. covariates alone): 0.00456 sex, age of last observation, 10 Genetic PCs —
PPM000628 PGS000204
(GSCAN_DPW_FT12)
 PSS000340|
European Ancestry|
1,251 individuals
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Reported Trait: Alcohol use disorder (DSM-5 criteria count, log-transformed) β: 0.114 (0.019) — ΔR-squared (vs. covariates alone): 0.0298 sex, age of last observation, 10 Genetic PCs —
PPM000627 PGS000205
(RISK_PC_COGA)
 PSS000339|
European Ancestry|
7,599 individuals
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Reported Trait: Alcohol use disorder (DSM-5 criteria count, log-transformed) β: 0.117 (0.011) — ΔR-squared (vs. covariates alone): 0.01613 sex, age of last observation, 10 Genetic PCs, genotyping array, data collection site —
PPM000626 PGS000201
(PROB_ALC_COGA)
 PSS000339|
European Ancestry|
7,599 individuals
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Reported Trait: Alcohol use disorder (DSM-5 criteria count, log-transformed) β: 0.099 (0.01) — ΔR-squared (vs. covariates alone): 0.01192 sex, age of last observation, 10 Genetic PCs, genotyping array, data collection site —
PPM000625 PGS000203
(GSCAN_DPW_COGA)
 PSS000339|
European Ancestry|
7,599 individuals
 PGP000084 |
Barr PB et al. Transl Psychiatry (2020)
 Reported Trait: Alcohol use disorder (DSM-5 criteria count, log-transformed) β: 0.121 (0.01) — ΔR-squared (vs. covariates alone): 0.01734 sex, age of last observation, 10 Genetic PCs, genotyping array, data collection site —

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
PSS000340 — — 1,251 individuals,
45.6 % Male samples
 Mean = 21.9 years
Sd = 0.77 years
Range = [21.0, 26.0] years		 European
(Finnish)		 — FinnTwin12 Twin Study
PSS000339 — — 7,599 individuals,
47.16 % Male samples
 Mean = 36.94 years
Sd = 14.77 years
Range = [12.0, 91.0] years		 European — COGA —