PGS Publication: PGP000086

Publication Information (EuropePMC)
Title New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.
PubMed ID 30804560(Europe PMC)
doi 10.1038/s41588-018-0321-7
Publication Date Feb. 25, 2019
Journal Nat Genet
Author(s) Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Soler Artigas M, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV, Understanding Society Scientific Group.
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:
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

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)
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
PPM000638 PGS000210
(LF279)
 PSS000345|
East Asian Ancestry|
75,580 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.219 [1.182, 1.256] — — age, age^2, sex, height, smoking Models were stratified by geographical region and meta-analyzed. 12 Proxy SNPs were used
PPM000636 PGS000210
(LF279)
 PSS000348|
European Ancestry|
303,570 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.436 [1.411, 1.461] — — age, age^2, sex, height, smoking, 10 genetic PCs *Potential inflation (some weights are derived in a UKB GWAS)
PPM000645 PGS000210
(LF279)
 PSS000351|
East Asian Ancestry|
72,796 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.078 [-0.085, -0.071] — — age, age^2, sex, height, smoking Models were stratified by geographical region and meta-analyzed. 12 Proxy SNPs were used
PPM000647 PGS000210
(LF279)
 PSS000346|
European Ancestry|
10,894 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.546 [1.476, 1.62] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000642 PGS000210
(LF279)
 PSS000355|
European Ancestry|
303,570 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.224 [-0.227, -0.221] — — age, age^2, sex, height, smoking, 10 genetic PCs *Potential inflation (some weights are derived in a UKB GWAS)
PPM000643 PGS000210
(LF279)
 PSS000353|
Additional Diverse Ancestries|
1,208 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.176 [-0.231, -0.12] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000641 PGS000210
(LF279)
 PSS000354|
East Asian Ancestry|
1,607 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.142 [-0.191, -0.093] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000640 PGS000210
(LF279)
 PSS000357|
South Asian Ancestry|
6,358 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.181 [-0.205, -0.156] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000639 PGS000210
(LF279)
 PSS000352|
African Ancestry|
4,225 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.086 [-0.116, -0.056] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000644 PGS000210
(LF279)
 PSS000356|
Additional Diverse Ancestries|
6,033 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Lung Function (FEV1/FVC) β: -0.186 [-0.211, -0.162] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000637 PGS000210
(LF279)
 PSS000349|
Additional Diverse Ancestries|
6,033 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.506 [1.325, 1.712] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000635 PGS000210
(LF279)
 PSS000350|
South Asian Ancestry|
6,358 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.414 [1.254, 1.594] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000634 PGS000210
(LF279)
 PSS000347|
African Ancestry|
4,225 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.348 [1.152, 1.577] — — age, age^2, sex, height, smoking, 10 genetic PCs —
PPM000646 PGS000210
(LF279)
 PSS000344|
African Ancestry|
2,466 individuals
 PGP000086 |
Shrine N et al. Nat Genet (2019)
 Reported Trait: Chronic obstructive pulmonary disease OR: 1.255 [1.147, 1.374] — — age, age^2, sex, height, smoking, 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
PSS000352 — — 4,225 individuals — African unspecified — UKB —
PSS000353 — — 1,208 individuals — Other admixed ancestry
(Admixed African (unspecified) and European)		 — UKB —
PSS000354 — — 1,607 individuals — East Asian — UKB —
PSS000355 — — 303,570 individuals — European — UKB —
PSS000356 — — 6,033 individuals — Other admixed ancestry — UKB —
PSS000357 — — 6,358 individuals — South Asian — UKB —
PSS000344 — —
[
  • 910 cases
  • , 1,556 controls
]
 — African American or Afro-Caribbean — COPDGene —
PSS000345 FEV1/FVC<0.7 and FEV1<80% predicted (i.e. corresponding to GOLD 2-4 standards) —
[
  • 69,567 cases
  • , 6,013 controls
]
 — East Asian
(Chinese)		 — CKB —
PSS000346 — —
[
  • 6,979 cases
  • , 3,915 controls
]
 — European — 6 cohorts
  • COPDGene
  • ,ECLIPSE
  • ,GenKOLS
  • ,NAS
  • ,NETT
  • ,SPIROMICS
 —
PSS000347 FEV1/FVC<0.7 and FEV1<80% predicted (i.e. corresponding to GOLD 2-4 standards) —
[
  • 172 cases
  • , 4,053 controls
]
 — African unspecified — UKB —
PSS000348 FEV1/FVC<0.7 and FEV1<80% predicted (i.e. corresponding to GOLD 2-4 standards) —
[
  • 288,467 cases
  • , 15,103 controls
]
 — European — UKB —
PSS000349 FEV1/FVC<0.7 and FEV1<80% predicted (i.e. corresponding to GOLD 2-4 standards) —
[
  • 5,752 cases
  • , 281 controls
]
 — Other admixed ancestry — UKB —
PSS000350 FEV1/FVC<0.7 and FEV1<80% predicted (i.e. corresponding to GOLD 2-4 standards) —
[
  • 6,046 cases
  • , 312 controls
]
 — South Asian — UKB —
PSS000351 — — 72,796 individuals — East Asian
(Chinese)		 — CKB —