PGS Publication: PGP000348

Publication Information (EuropePMC)
Title Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program.
PubMed ID 35385699(Europe PMC)
doi 10.1016/j.ajhg.2022.03.007
Publication Date April 5, 2022
Journal Am J Hum Genet
Author(s) Hu X, Qiao D, Kim W, Moll M, Balte PP, Lange LA, Bartz TM, Kumar R, Li X, Yu B, Cade BE, Laurie CA, Sofer T, Ruczinski I, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Gabriel S, Gupta N, Dugan-Perez S, Cupples LA, Loehr LR, Jain D, Rotter JI, Wilson JG, Psaty BM, Fornage M, Morrison AC, Vasan RS, Washko G, Rich SS, O'Connor GT, Bleecker E, Kaplan RC, Kalhan R, Redline S, Gharib SA, Meyers D, Ortega V, Dupuis J, London SJ, Lappalainen T, Oelsner EC, Silverman EK, Barr RG, Thornton TA, Wheeler HE, TOPMed Lung Working Group, Cho MH, Im HK, Manichaikul A.
Released in PGS Catalog: Aug. 3, 2022

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:
Display options:
Ancestry legend
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

External PGS Evaluated 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)
PGS000210
(LF279)
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Lung function (FEV1/FVC) FEV/FVC ratio 279
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000210/ScoringFiles/PGS000210.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
PPM014853 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years ≥0) OR: 1.66 [1.55, 1.79]
β: 0.5096 (0.0372)		 — — — —
PPM014845 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years ≥0) OR: 1.57 [1.48, 1.67]
β: 0.4524 (0.0304)		 — — — —
PPM014846 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years ≥0) OR: 1.24 [1.14, 1.36]
β: 0.2191 (0.0436)		 — — — —
PPM014847 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years: [0,20)) OR: 1.69 [1.36, 2.11]
β: 0.5271 (0.1112)		 — — — —
PPM014848 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years: [0,20)) OR: 1.33 [1.05, 1.7]
β: 0.2872 (0.1233)		 — — — —
PPM014849 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years: [20,40)) OR: 1.64 [1.49, 1.82]
β: 0.4971 (0.0506)		 — — — —
PPM014854 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years ≥0) OR: 1.35 [1.2, 1.52]
β: 0.2994 (0.0609)		 — — — —
PPM014855 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years: [0,20)) OR: 1.85 [1.37, 2.5]
β: 0.6155 (0.1527)		 — — — —
PPM014856 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years: [0,20)) OR: 1.31 [0.87, 1.96]
β: 0.2667 (0.2061)		 — — — —
PPM014850 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years: [20,40)) OR: 1.35 [1.18, 1.53]
β: 0.2968 (0.0653)		 — — — —
PPM014851 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years ≥40) OR: 1.52 [1.4, 1.65]
β: 0.4211 (0.042)		 — — — —
PPM014859 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years ≥40) OR: 1.61 [1.46, 1.77]
β: 0.4762 (0.0488)		 — — — —
PPM014860 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years ≥40) OR: 1.18 [0.98, 1.41]
β: 0.1638 (0.0931)		 — — — —
PPM014861 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years ≥0) β: -2.8878 (0.1597) — R²: 0.0361 [0.0144, 0.0578] — —
PPM014862 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years ≥0) β: -1.2526 (0.1985) — R²: 0.0111 [-0.0214, 0.0436] — —
PPM014863 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years: [0,20)) β: -2.6173 (0.448) — R²: 0.0361 [-0.0337, 0.1059] — —
PPM014864 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years: [0,20)) β: -0.6558 (0.4221) — R²: 0.0036 [-0.0741, 0.0813] — —
PPM014865 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years: [20,40)) β: -3.2512 (0.2601) — R²: 0.0464 [0.0087, 0.0841] — —
PPM014866 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years: [20,40)) β: -1.5655 (0.2858) — R²: 0.0199 [-0.0285, 0.0683] — —
PPM014867 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years ≥40) β: -2.7449 (0.2221) — R²: 0.0315 [0.0028, 0.0602] — —
PPM014868 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1/FVC ratio (Smoking Pack-Years ≥40) β: -1.1647 (0.3587) — R²: 0.0083 [-0.045, 0.0616] — —
PPM014869 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years ≥0) β: -0.131 (0.0081) — R²: 0.0301 [0.0084, 0.0518] — —
PPM014870 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years ≥0) β: -0.036 (0.0105) — R²: 0.0028 [-0.0297, 0.0353] — —
PPM014872 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years: [0,20)) β: -0.0365 (0.024) — R²: 0.0036 [-0.0741, 0.0813] — —
PPM014873 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years: [20,40)) β: -0.1382 (0.0137) — R²: 0.0326 [-0.0051, 0.0703] — —
PPM014874 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years: [20,40)) β: -0.0518 (0.0153) — R²: 0.0063 [-0.0421, 0.0547] — —
PPM014875 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years ≥40) β: -0.1272 (0.0109) — R²: 0.0288 [0.0001, 0.0575] — —
PPM014876 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years ≥40) β: -0.0142 (0.0183) — R²: 0.0004 [-0.0529, 0.0537] — —
PPM014852 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Moderate to severe COPD (Smoking Pack-Years ≥40) OR: 1.1 [0.96, 1.26]
β: 0.0963 (0.0706)		 — — — —
PPM014857 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years: [20,40)) OR: 1.75 [1.54, 2.0]
β: 0.5621 (0.0664)		 — — — —
PPM014858 PGS000210
(LF279)
 PSS009914|
African Ancestry|
3,627 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Severe COPD (Smoking Pack-Years: [20,40)) OR: 1.5 [1.24, 1.8]
β: 0.4023 (0.0958)		 — — — —
PPM014871 PGS000210
(LF279)
 PSS009915|
European Ancestry|
8,144 individuals
 PGP000348 |
Hu X et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: FEV1 (Smoking Pack-Years: [0,20)) β: -0.1204 (0.0248) — R²: 0.0256 [-0.0442, 0.0954] — —

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
PSS009914 — — 3,627 individuals — African American or Afro-Caribbean
(African American)		 — COPDGene, SPIROMICS —
PSS009915 — — 8,144 individuals — European
(Non Hispanic White)		 — COPDGene, SPIROMICS —