Polygenic Score (PGS) ID: PGS000320

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

Score Details

Score Construction
PGS Name PRS_BMI
Variants
Original Genome Build NR
Number of Variants 263,640
Development Method
Name PRSice
Parameters p < 0.5; r2 < 0.8; MAF > 5%; INFO > 0.4
PGS Source
PGS Catalog Publication (PGP) ID PGP000096
Citation (link to publication) Chami N et al. PLoS Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002783
EuropePMC: 25673413
236,781 individuals European
GWAS Catalog: GCST002783
EuropePMC: 25673413
887 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002783
EuropePMC: 25673413
1,276 individuals Hispanic or Latin American
Score Development/Training
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
Body mass index measured at baseline visit. 20,000 individuals Range = [40.0, 69.0] years European UKB 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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000858 PSS000413 PGP000096
Chami N et al. (2020)
Reported Trait: Body mass index (BMI; kg/m^2) β: 1.29 : 0.0676 age, sex, 10 genetic PCs
PPM000859 PSS000412 PGP000096
Chami N et al. (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): 2e-16 age, sex, 10 genetic PCs
PPM000860 PSS000411 PGP000096
Chami N et al. (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): 1.7e-06 age, sex, 10 genetic PCs

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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