PGS Publication: PGP000246

Publication Information (EuropePMC)
Title The trans-ancestral genomic architecture of glycemic traits.
PubMed ID 34059833(Europe PMC)
doi 10.1038/s41588-021-00852-9
Publication Date May 31, 2021
Journal Nat Genet
Author(s) Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M, Boutin TS, Mägi R, Waage J, Li-Gao R, Chan KHK, Yao J, Anasanti MD, Chu AY, Claringbould A, Heikkinen J, Hong J, Hottenga JJ, Huo S, Kaakinen MA, Louie T, März W, Moreno-Macias H, Ndungu A, Nelson SC, Nolte IM, North KE, Raulerson CK, Ray D, Rohde R, Rybin D, Schurmann C, Sim X, Southam L, Stewart ID, Wang CA, Wang Y, Wu P, Zhang W, Ahluwalia TS, Appel EVR, Bielak LF, Brody JA, Burtt NP, Cabrera CP, Cade BE, Chai JF, Chai X, Chang LC, Chen CH, Chen BH, Chitrala KN, Chiu YF, de Haan HG, Delgado GE, Demirkan A, Duan Q, Engmann J, Fatumo SA, Gayán J, Giulianini F, Gong JH, Gustafsson S, Hai Y, Hartwig FP, He J, Heianza Y, Huang T, Huerta-Chagoya A, Hwang MY, Jensen RA, Kawaguchi T, Kentistou KA, Kim YJ, Kleber ME, Kooner IK, Lai S, Lange LA, Langefeld CD, Lauzon M, Li M, Ligthart S, Liu J, Loh M, Long J, Lyssenko V, Mangino M, Marzi C, Montasser ME, Nag A, Nakatochi M, Noce D, Noordam R, Pistis G, Preuss M, Raffield L, Rasmussen-Torvik LJ, Rich SS, Robertson NR, Rueedi R, Ryan K, Sanna S, Saxena R, Schraut KE, Sennblad B, Setoh K, Smith AV, Sparsø T, Strawbridge RJ, Takeuchi F, Tan J, Trompet S, van den Akker E, van der Most PJ, Verweij N, Vogel M, Wang H, Wang C, Wang N, Warren HR, Wen W, Wilsgaard T, Wong A, Wood AR, Xie T, Zafarmand MH, Zhao JH, Zhao W, Amin N, Arzumanyan Z, Astrup A, Bakker SJL, Baldassarre D, Beekman M, Bergman RN, Bertoni A, Blüher M, Bonnycastle LL, Bornstein SR, Bowden DW, Cai Q, Campbell A, Campbell H, Chang YC, de Geus EJC, Dehghan A, Du S, Eiriksdottir G, Farmaki AE, Frånberg M, Fuchsberger C, Gao Y, Gjesing AP, Goel A, Han S, Hartman CA, Herder C, Hicks AA, Hsieh CH, Hsueh WA, Ichihara S, Igase M, Ikram MA, Johnson WC, Jørgensen ME, Joshi PK, Kalyani RR, Kandeel FR, Katsuya T, Khor CC, Kiess W, Kolcic I, Kuulasmaa T, Kuusisto J, Läll K, Lam K, Lawlor DA, Lee NR, Lemaitre RN, Li H, Lifelines Cohort Study, Lin SY, Lindström J, Linneberg A, Liu J, Lorenzo C, Matsubara T, Matsuda F, Mingrone G, Mooijaart S, Moon S, Nabika T, Nadkarni GN, Nadler JL, Nelis M, Neville MJ, Norris JM, Ohyagi Y, Peters A, Peyser PA, Polasek O, Qi Q, Raven D, Reilly DF, Reiner A, Rivideneira F, Roll K, Rudan I, Sabanayagam C, Sandow K, Sattar N, Schürmann A, Shi J, Stringham HM, Taylor KD, Teslovich TM, Thuesen B, Timmers PRHJ, Tremoli E, Tsai MY, Uitterlinden A, van Dam RM, van Heemst D, van Hylckama Vlieg A, van Vliet-Ostaptchouk JV, Vangipurapu J, Vestergaard H, Wang T, Willems van Dijk K, Zemunik T, Abecasis GR, Adair LS, Aguilar-Salinas CA, Alarcón-Riquelme ME, An P, Aviles-Santa L, Becker DM, Beilin LJ, Bergmann S, Bisgaard H, Black C, Boehnke M, Boerwinkle E, Böhm BO, Bønnelykke K, Boomsma DI, Bottinger EP, Buchanan TA, Canouil M, Caulfield MJ, Chambers JC, Chasman DI, Chen YI, Cheng CY, Collins FS, Correa A, Cucca F, de Silva HJ, Dedoussis G, Elmståhl S, Evans MK, Ferrannini E, Ferrucci L, Florez JC, Franks PW, Frayling TM, Froguel P, Gigante B, Goodarzi MO, Gordon-Larsen P, Grallert H, Grarup N, Grimsgaard S, Groop L, Gudnason V, Guo X, Hamsten A, Hansen T, Hayward C, Heckbert SR, Horta BL, Huang W, Ingelsson E, James PS, Jarvelin MR, Jonas JB, Jukema JW, Kaleebu P, Kaplan R, Kardia SLR, Kato N, Keinanen-Kiukaanniemi SM, Kim BJ, Kivimaki M, Koistinen HA, Kooner JS, Körner A, Kovacs P, Kuh D, Kumari M, Kutalik Z, Laakso M, Lakka TA, Launer LJ, Leander K, Li H, Lin X, Lind L, Lindgren C, Liu S, Loos RJF, Magnusson PKE, Mahajan A, Metspalu A, Mook-Kanamori DO, Mori TA, Munroe PB, Njølstad I, O'Connell JR, Oldehinkel AJ, Ong KK, Padmanabhan S, Palmer CNA, Palmer ND, Pedersen O, Pennell CE, Porteous DJ, Pramstaller PP, Province MA, Psaty BM, Qi L, Raffel LJ, Rauramaa R, Redline S, Ridker PM, Rosendaal FR, Saaristo TE, Sandhu M, Saramies J, Schneiderman N, Schwarz P, Scott LJ, Selvin E, Sever P, Shu XO, Slagboom PE, Small KS, Smith BH, Snieder H, Sofer T, Sørensen TIA, Spector TD, Stanton A, Steves CJ, Stumvoll M, Sun L, Tabara Y, Tai ES, Timpson NJ, Tönjes A, Tuomilehto J, Tusie T, Uusitupa M, van der Harst P, van Duijn C, Vitart V, Vollenweider P, Vrijkotte TGM, Wagenknecht LE, Walker M, Wang YX, Wareham NJ, Watanabe RM, Watkins H, Wei WB, Wickremasinghe AR, Willemsen G, Wilson JF, Wong TY, Wu JY, Xiang AH, Yanek LR, Yengo L, Yokota M, Zeggini E, Zheng W, Zonderman AB, Rotter JI, Gloyn AL, McCarthy MI, Dupuis J, Meigs JB, Scott RA, Prokopenko I, Leong A, Liu CT, Parker SCJ, Mohlke KL, Langenberg C, Wheeler E, Morris AP, Barroso I, Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC).
Released in PGS Catalog: Nov. 4, 2021

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)
PGS001350
(MAGICTA_EUR_PGS_FG)
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Fasting glucose fasting blood glucose measurement 1,023,373
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001350/ScoringFiles/PGS001350.txt.gz
PGS001352
(MAGICTA_EUR_PGS_HbA1c)
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Glycated haemoglobin levels (HbA1c) HbA1c measurement 1,018,836
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001352/ScoringFiles/PGS001352.txt.gz
PGS001351
(MAGICTA_EUR_PGS_FI)
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Fasting insulin fasting blood insulin measurement 1,025,098
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001351/ScoringFiles/PGS001351.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
PPM005137 PGS001350
(MAGICTA_EUR_PGS_FG)
 PSS003587|
European Ancestry|
45,038 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting glucose — — R²: 0.229 — —
PPM005138 PGS001351
(MAGICTA_EUR_PGS_FI)
 PSS003590|
European Ancestry|
29,123 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting insulin — — R²: 0.095 — —
PPM005139 PGS001352
(MAGICTA_EUR_PGS_HbA1c)
 PSS003594|
European Ancestry|
61,820 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.178 — —
PPM005140 PGS001350
(MAGICTA_EUR_PGS_FG)
 PSS003585|
African Ancestry|
16,579 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting glucose — — R²: 0.032 — —
PPM005141 PGS001351
(MAGICTA_EUR_PGS_FI)
 PSS003588|
African Ancestry|
8,101 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting insulin — — R²: 0.028 — —
PPM005142 PGS001352
(MAGICTA_EUR_PGS_HbA1c)
 PSS003591|
African Ancestry|
6,647 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.012 — —
PPM005143 PGS001350
(MAGICTA_EUR_PGS_FG)
 PSS003586|
East Asian Ancestry|
31,669 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting glucose — — R²: 0.027 — —
PPM005144 PGS001351
(MAGICTA_EUR_PGS_FI)
 PSS003589|
East Asian Ancestry|
26,691 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting insulin — — R²: 0.014 — —
PPM005145 PGS001352
(MAGICTA_EUR_PGS_HbA1c)
 PSS003593|
East Asian Ancestry|
31,236 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.026 — —
PPM005146 PGS001352
(MAGICTA_EUR_PGS_HbA1c)
 PSS003592|
African Ancestry|
4,441 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.006 — —

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
PSS003594 — — 61,820 individuals — European — EPIC, InterAct, LifeLines, METSIM, WGHS —
PSS003585 — — 16,579 individuals — African American or Afro-Caribbean — 10 cohorts
  • ARIC
  • ,BioMe
  • ,CHS
  • ,FamHS
  • ,GENOA
  • ,GeneSTAR
  • ,HANDLS
  • ,JHS
  • ,MESA
  • ,WHI
 —
PSS003586 — — 31,669 individuals — East Asian
(Japanese, Chinese, Malay, Filipino, Han Chinese)		 — 13 cohorts
  • AASC
  • ,CAGE
  • ,CHNS
  • ,CLHNS
  • ,CRC
  • ,KARE
  • ,Living-Biobank
  • ,MESA
  • ,NHAPC
  • ,Nagahama_Study
  • ,SBCS
  • ,SMHS
  • ,SP2
 —
PSS003587 — — 45,038 individuals — European — ARIC, LifeLines, METSIM, TwinGene Additional cases and controls were obtained from Fenland-OMICS.
PSS003588 — — 8,101 individuals — African American or Afro-Caribbean — 9 cohorts
  • ARIC
  • ,CHS
  • ,FamHS
  • ,GENOA
  • ,GeneSTAR
  • ,HANDLS
  • ,JHS
  • ,MESA
  • ,WHI
 —
PSS003589 — — 26,691 individuals — East Asian
(Japanese, Filipino, Chinese, Han Chinese)		 — 10 cohorts
  • AASC
  • ,CAGE
  • ,CHNS
  • ,CRC
  • ,KARE
  • ,MESA
  • ,NHAPC
  • ,Nagahama_Study
  • ,SMHS
  • ,SP2
 —
PSS003590 — — 29,123 individuals — European — ARIC, METSIM, NTR, PROCARDIS —
PSS003591 — — 6,647 individuals — African American or Afro-Caribbean — ARIC, BioMe, HANDLS, JHS, MESA —
PSS003592 — — 4,441 individuals — Sub-Saharan African
(Ugandan)		 — NR —
PSS003593 — — 31,236 individuals — East Asian
(Japanese, Chinese, Malay, Han Chinese)		 — 15 cohorts
  • AASC
  • ,BES
  • ,CAGE
  • ,CHNS
  • ,CRC
  • ,KARE
  • ,Living-Biobank
  • ,MESA
  • ,NHAPC
  • ,Nagahama_Study
  • ,SBCS
  • ,SCES
  • ,SIMES
  • ,SP2
  • ,TWSC
 —