Polygenic Score (PGS) ID: PGS000027

Predicted Trait
Reported Trait Body Mass Index
Mapped Trait(s) body mass index (EFO_0004340)
Released in PGS Catalog: Oct. 14, 2019
Download Score FTP directory
Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_BMI
Variants
Original Genome Build hg19
Number of Variants 2,100,302
Development Method
Name LDpred
Parameters ρ = 0.03; LD reference panel = 503 European samples from 1000 Genomes phase 3
PGS Source
PGS Catalog Publication (PGP) ID PGP000017
Citation (link to publication) Khera AV et al. Cell (2019)
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%
119,951 individuals (100%)
PGS Evaluation
European: 90%
Greater Middle Eastern: 10%
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002783
Europe PMC: 25673413
236,781 individuals European
GWAS Catalog: GCST002783
Europe PMC: 25673413
887 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002783
Europe PMC: 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
119,951 individuals European UKB UKB Phase 1

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
PPM000054 PSS000037|
European Ancestry|
288,016 individuals
PGP000017 |
Khera AV et al. Cell (2019)
Reported Trait: Body mass index β: 1.41 : 0.08526 First 10 genetic PCs Beta is in units of kg/m^2
PPM001725 PSS000885|
European Ancestry|
19,588 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between male siblings OR: 2.21 [1.92, 2.54] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001726 PSS000886|
European Ancestry|
21,499 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within female siblings OR: 2.09 [1.74, 2.51] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001727 PSS000886|
European Ancestry|
21,499 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between female siblings OR: 2.13 [1.87, 2.43] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001728 PSS000887|
European Ancestry|
26,323 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within male siblings OR: 2.15 [1.91, 2.41] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001730 PSS000888|
European Ancestry|
29,527 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within female siblings OR: 1.87 [1.68, 2.09] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001731 PSS000888|
European Ancestry|
29,527 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between female siblings OR: 2.05 [1.89, 2.22] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001732 PSS000889|
European Ancestry|
21,187 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within male siblings OR: 2.0 [1.79, 2.23] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001733 PSS000889|
European Ancestry|
21,187 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between male siblings OR: 2.12 [1.96, 2.3] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001734 PSS000890|
European Ancestry|
25,096 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within female siblings OR: 2.0 [1.8, 2.21] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001735 PSS000890|
European Ancestry|
25,096 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between female siblings OR: 2.03 [1.88, 2.19] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001736 PSS000891|
European Ancestry|
14,487 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within male siblings OR: 1.9 [1.68, 2.14] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001769 PSS000911|
Greater Middle Eastern Ancestry|
13,989 individuals
PGP000147 |
Thareja G et al. Nat Commun (2021)
|Ext.
Reported Trait: Body mass index Pearson correlation coefficent (r): 0.22
PPM001737 PSS000891|
European Ancestry|
14,487 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between male siblings OR: 2.0 [1.83, 2.19] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001738 PSS000892|
European Ancestry|
17,740 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within female siblings OR: 1.72 [1.53, 1.93] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001739 PSS000892|
European Ancestry|
17,740 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between female siblings OR: 1.89 [1.74, 2.05] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001724 PSS000885|
European Ancestry|
19,588 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity within male siblings OR: 2.02 [1.66, 2.46] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).
PPM001729 PSS000887|
European Ancestry|
26,323 individuals
PGP000141 |
Brandkvist M et al. PLoS Med (2020)
|Ext.
Reported Trait: Obesity between male siblings OR: 2.15 [1.97, 2.34] Sex, time of measurement, age, PCs (1-20), genotyping batch 2.07 million of the 2.1 milliion common variants (excluding those with insufficient quality of genotyping or imputation (r^2 < 0.8) in the HUNT cohort) were included in the polygenic score previously developed by Khera et al (2019).

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
PSS000892 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 17,740 cases
]
,
0.0 % Male samples
Mean = 58.9 years
Sd = 11.9 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000890 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 25,108 cases
]
,
0.0 % Male samples
Mean = 51.2 years
Sd = 15.0 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000911 13,989 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)
QBB
PSS000885 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 19,588 cases
]
,
100.0 % Male samples
Mean = 42.4 years
Sd = 12.6 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000886 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 21,499 cases
]
,
0.0 % Male samples
Mean = 42.6 years
Sd = 12.8 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000887 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 26,336 cases
]
,
100.0 % Male samples
Mean = 47.6 years
Sd = 16.1 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000888 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 29,545 cases
]
,
0.0 % Male samples
Mean = 47.1 years
Sd = 16.5 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000889 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 21,192 cases
]
,
100.0 % Male samples
Mean = 52.3 years
Sd = 14.5 years
European HUNT number o cases = number of observations (more than 1 pp)
PSS000037 288,016 individuals,
45.0 % Male samples
European UKB
PSS000891 Body mass index (BMI) measurements were standardized with weight measured to the nearest half kilogram with the participants wearing light clothes and no shoes, and height was measured to the nearest centimeter. BMI was calculated using the formula weight in kilograms per meter squared. As defined by the World Health Organization (WHO), the authors rrefer to overweight as having BMI greater than or equal to 25 and obesity as having BMI greater than or equal to 30. Severe obesity was defined as having BMI greater than or equal to 35.
[
  • 14,487 cases
]
,
100.0 % Male samples
Mean = 60.2 years
Sd = 11.5 years
European HUNT number o cases = number of observations (more than 1 pp)