Polygenic Score (PGS) ID: PGS000320

Predicted Trait
Reported Trait Body mass index (BMI)
Mapped Trait(s) body mass index (EFO_0004340)
Released in PGS Catalog: Sept. 4, 2020
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Score Details

Score Construction
PGS Name PRS_BMI
Development Method
Name PRSice
Parameters p < 0.5; r2 < 0.8; MAF > 5%; INFO > 0.4
Variants
Original Genome Build NR
Number of Variants 263,640
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000096
Citation (link to publication) Chami N et al. PLoS Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 99.1%
Hispanic or Latin American: 0.5%
African: 0.4%
238,944 individuals (100%)
Score Development/Training
European: 100%
20,000 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002783
Europe PMC: 25673413
 1,276 individuals Hispanic or Latin American NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 236,781 individuals European NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 887 individuals African American or Afro-Caribbean NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 20,000 individuals European UKB Body mass index measured at baseline visit. Range = [40.0, 69.0] years — — Used to select p-value threshold

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) 		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
PPM000860 PSS000411|
European Ancestry|
104 individuals
 PGP000096 |
Chami N et al. PLoS Med (2020)
 Reported Trait: Body mass index (BMI; kg/m^2) in MC4R carriers — — Higher PRS in obese vs. normal weight MC4R mutation carriers (p-value): 1.70e-06 age, sex, 10 genetic PCs —
PPM000859 PSS000412|
European Ancestry|
256,770 individuals
 PGP000096 |
Chami N et al. PLoS Med (2020)
 Reported Trait: Body mass index (BMI; kg/m^2) in MC4R non-carriers — — Higher PRS in obese vs. normal weight MC4R non-carriers (p-value): 2.00e-16 age, sex, 10 genetic PCs —
PPM000858 PSS000413|
European Ancestry|
451,508 individuals
 PGP000096 |
Chami N et al. PLoS Med (2020)
 Reported Trait: Body mass index (BMI; kg/m^2) β: 1.29 — R²: 0.0676 age, sex, 10 genetic 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
PSS000412 59 MC4R mutations that had previously been reported to play a role in obesity were included in our analyses (Table S2) All phenotypic data used for analyses were collected at the baseline visit. We provide a brief description here; more details can be found in S1 Text and elsewhere [18–21]. BMI, calculated as weight (kg) divided by height squared (m2), was used to categorize individuals with underweight (BMI < 18.5 kg/m2), normal weight (18.5 kg/m2 ≤ BMI < 25 kg/m2), overweight (25 kg/m2 ≤ BMI < 30 kg/m2), or obesity (BMI ≥ 30 kg/m2). —
[
  • 109,216 cases
  • , 147,554 controls
]
 — European — UKB —
PSS000413 All phenotypic data used for analyses were collected at the baseline visit. We provide a brief description here; more details can be found in S1 Text and elsewhere [18–21]. BMI, calculated as weight (kg) divided by height squared (m2), was used to categorize individuals with underweight (BMI < 18.5 kg/m2), normal weight (18.5 kg/m2 ≤ BMI < 25 kg/m2), overweight (25 kg/m2 ≤ BMI < 30 kg/m2), or obesity (BMI ≥ 30 kg/m2). — 206,612 individuals,
100.0 % Male samples
 Mean = 57.0 years
Sd = 8.1 years		 European — UKB —
PSS000413 All phenotypic data used for analyses were collected at the baseline visit. We provide a brief description here; more details can be found in S1 Text and elsewhere [18–21]. BMI, calculated as weight (kg) divided by height squared (m2), was used to categorize individuals with underweight (BMI < 18.5 kg/m2), normal weight (18.5 kg/m2 ≤ BMI < 25 kg/m2), overweight (25 kg/m2 ≤ BMI < 30 kg/m2), or obesity (BMI ≥ 30 kg/m2). — 244,896 individuals,
0.0 % Male samples
 Mean = 57.0 years
Sd = 7.9 years		 European — UKB —
PSS000411 59 MC4R mutations that had previously been reported to play a role in obesity were included in our analyses (Table S2) All phenotypic data used for analyses were collected at the baseline visit. We provide a brief description here; more details can be found in S1 Text and elsewhere [18–21]. BMI, calculated as weight (kg) divided by height squared (m2), was used to categorize individuals with underweight (BMI < 18.5 kg/m2), normal weight (18.5 kg/m2 ≤ BMI < 25 kg/m2), overweight (25 kg/m2 ≤ BMI < 30 kg/m2), or obesity (BMI ≥ 30 kg/m2). —
[
  • 76 cases
  • , 28 controls
]
 — European — UKB —