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: July 1, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000210 LF279 PGP000086
Shrine N et al. Nat Genet (2019)
Lung function (FEV1/FVC) FEV/FEC ratio 279 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000210/ScoringFiles/PGS000210.txt.gz

PGS 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)
Evaluated Score 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
PPM000643 PGS000210 (LF279) PSS000353 PGP000086
Shrine N et al. (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 PGP000086
Shrine N et al. (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 PGP000086
Shrine N et al. (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 PGP000086
Shrine N et al. (2019)
Reported Trait: Lung Function (FEV1/FVC) β: -0.086[-0.116, -0.056] age, age^2, sex, height, smoking, 10 genetic PCs
PPM000638 PGS000210 (LF279) PSS000345 PGP000086
Shrine N et al. (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
PPM000637 PGS000210 (LF279) PSS000349 PGP000086
Shrine N et al. (2019)
Reported Trait: Chronic obstructive pulmonary disease OR: 1.506[1.325, 1.712] age, age^2, sex, height, smoking, 10 genetic PCs
PPM000636 PGS000210 (LF279) PSS000348 PGP000086
Shrine N et al. (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)
PPM000635 PGS000210 (LF279) PSS000350 PGP000086
Shrine N et al. (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 PGP000086
Shrine N et al. (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 PGP000086
Shrine N et al. (2019)
Reported Trait: Chronic obstructive pulmonary disease OR: 1.255[1.147, 1.374] age, age^2, sex, height, smoking, 10 genetic PCs
PPM000645 PGS000210 (LF279) PSS000351 PGP000086
Shrine N et al. (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 PGP000086
Shrine N et al. (2019)
Reported Trait: Chronic obstructive pulmonary disease OR: 1.546[1.476, 1.62] age, age^2, sex, height, smoking, 10 genetic PCs
PPM000644 PGS000210 (LF279) PSS000356 PGP000086
Shrine N et al. (2019)
Reported Trait: Lung Function (FEV1/FVC) β: -0.186[-0.211, -0.162] age, age^2, sex, height, smoking, 10 genetic PCs
PPM000642 PGS000210 (LF279) PSS000355 PGP000086
Shrine N et al. (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)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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