Published March 20, 2025
| Version v1
Dataset
Open
Data for paper: Sharapov et al (2025) "A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins" (European GWAMA, N=10172)
Authors/Creators
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Sharapov, Sodbo1, 2
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Timoshchuk, Anna3
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Zaytseva, Olga4
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Maslov, Denis2
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Soplenkova, Anna2
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Elgaeva, Elizaveta5, 6
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Tiys, Evgeny6
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Mangino, Massimo7, 8
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Wittenbecher, Clemens9
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Karssen, Lennart C.10
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Timofeeva, Maria11, 12
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Nostaeva, Arina6, 10
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Vučković, Frano13
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Trbojevic Akmacic, Irena14
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Štambuk, Tamara14
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Feoktistova, Sofia15
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Potapova, Nadezhda16
- Voroshilova, Viktoria6, 17
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Williams, Frances8
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Primorac, Dragan18
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Van Zundert, Jan19
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Georges, Michel20
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Suhre, Karsten21
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Allegri, Massimo22, 23
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Chaturvedi, Nishi24
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Dunlop, Malcolm25
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Schulze, Matthias B.26, 9
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Spector, Tim8
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Tsepilov, Yakov27
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Lauc, Gordan28, 29
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Aulchenko, Yurii2, 6
- 1. Human Technopole
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2.
Lomonosov Moscow State University
- 3. MSU Institute for Artificial Intelligence, Lomonosov Moscow State University
- 4. Genos Glycoscience Research Laboratory
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5.
Novosibirsk State University
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6.
Institute of Cytology and Genetics
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7.
BC Children's Hospital Foundation
- 8. King's College London
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9.
German Institute of Human Nutrition
- 10. PolyOmica
- 11. University of Southern Denmark
- 12. The University of Edinburgh
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13.
Genos (Croatia)
- 14. Genos Ltd
- 15. Federal research center for innovator and emerging biomedical and pharmaceutical technologies
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16.
Engelhardt Institute of Molecular Biology
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17.
Vavilov Institute of General Genetics
- 18. St. Catherine Hospital
- 19. Department of Anesthesiology and Multidisciplinary Paincentre
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20.
University of Liège
- 21. Weill Cornell Medicine
- 22. Ensemble hospitalier de la Côte
- 23. Gruppo Policlinico di Monza
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24.
University College London
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25.
University of Edinburgh
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26.
University of Potsdam
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27.
Wellcome Sanger Institute
- 28. Genos
- 29. University of Zagreb Faculty of Pharmacy and Biochemistry
Description
The dataset contains results of genome-wide association study of human blood plasma glycome.
The TPNG_GWAMA_eur_10k.tar.gz contains summary statistics for 117 glycome traits from the European GWAMA (Genome-Wide Association Meta-Analysis) conducted on participants of European ancestry, totaling 10,172 individuals.
The 117 files contain association summary statistics for 117 glycome traits, of which 36 were directly measured by UHPLC technology and 81 were derived glycome traits.
Funding
The work of S.Sh., A.T., D.M., A.S., Y.S.A. was supported by the Research Program at the Moscow State University (MSU) Institute for Artificial Intelligence. The study was conducted using the UK Biobank resource under application #59345. The work of E.E., Y.A.T was supported by the budget project of the Institute of Cytology and Genetics FWNR-2022-0020. European Community’s Seventh Framework Programme funded project PainOmics (602736). TwinsUK is funded by the Wellcome Trust, Medical Research Council, Versus Arthritis, European Union Horizon 2020, Chronic Disease Research Foundation (CDRF), Zoe Ltd and the National Institute for Health Research (NIHR) Clinical Research Network (CRN) and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. The TwinsUK Study was approved by London-Westminster Research Ethics Committee (REC reference EC04/015), and Guy’s and St Thomas’ NHS Foundation Trust Research and Development (R&D). The TwinsUK BioBank was approved by the HRA - Liverpool East Research Ethics Committee (REC reference 19/NW/0187), IRAS ID 258513. Glycan analysis performed in Genos was supported by Horizon Europe grants GlycanSwitch (ERC Synergy grant # 101071386), INITIALISE (grant # 101094099) and SynHealth (grant #101159018). All participants provide written, informed consent. We thank Toma Keser, Mirna Šimurina, Marija Vilaj, Jerko Štambuk, Ivan Gudelj, Thomas S. Klarić, Jasminka Krištić, Jelena Šimunović, Julija Jurić, Ana Momčilović, Najda Rudman, and Maja Hanić for their assistance with glycan analysis.
Headers
rs_id - dbSNP ID.
chr - Chromosome number where the SNP is located.
bp - Base pair position of the SNP on the chromosome (build GRCh37/hg19).
ea - Effect allele.
ra - Reference allele.
eaf - Effect allele frequency.
af_ref - Frequency of the reference allele.
beta - Effect size estimate.
se - Standard error of the effect size estimate.
p - P-value for the association test.
n - Sample size used in the analysis.
z - Z-score for the association test.
info - Imputation information score.
Notes
| Harmonized code | Trait | Description |
| PGP1 | FA2 | The percentage of FA2 |
| PGP2 | FA2B | The percentage of FA2B |
| PGP3 | A2BG1 | The percentage of A2BG1 |
| PGP4 | FA2G1 | The percentage of FA2G1 |
| PGP5 | FA2G1 | The percentage of FA2G1 |
| PGP6 | FA2BG1 | The percentage of FA2BG1 |
| PGP7 | M6 | The percentage of M6 |
| PGP8 | A2G2 | The percentage of A2G2 |
| PGP9 | A2BG2 | The percentage of A2BG2 |
| PGP10 | FA2G2 | The percentage of FA2G2 |
| PGP11 | FA2BG2 | The percentage of FA2BG2 |
| PGP12 | M7 + A2G2S1 | The percentage of M7+A2G2S1 |
| PGP13 | FA2G1S1 | The percentage of FA2G1S1 |
| PGP14 | A2G2S1 | The percentage of A2G2S1+A2G2S1 |
| PGP15 | FA2G2S1 | The percentage of FA2G2S1 |
| PGP16 | FA2BG2S1 | The percentage of FA2BG2S1 |
| PGP17 | A2G2S2 | The percentage of A2G2S2 |
| PGP18 | M9 | The percentage of M9 |
| PGP19 | A2G2S2 | The percentage of A2G2S2 |
| PGP20 | FA2G2S2 | The percentage of FA2G2S2 |
| PGP21 | FA2BG2S2 | The percentage of FA2BG2S2 |
| PGP22 | A3G3S2 | The percentage of A3G3S2 |
| PGP23 | A3G3S2 | The percentage of A3G3S2 |
| PGP24 | A3F1G3S2 | The percentage of A3F1G3S2 |
| PGP25 | A3G3S3 | The percentage of A3G3S3 |
| PGP26 | A3G3S3 | The percentage of A3G3S3 |
| PGP27 | A3G3S3 | The percentage of A3G3S3 |
| PGP28 | FA3G3S3 | The percentage of FA3G3S3 |
| PGP29 | A3G3S3 | The percentage of A3G3S3 |
| PGP30 | A3F1G3S3 | The percentage of A3F1G3S3 |
| PGP31 | FA3G3S3 | The percentage of FA3G3S3 |
| PGP32 | FA3F1G3S3 | The percentage of FA3F1G3S3 |
| PGP33 | A4G4S3 | The percentage of A4G4S3 |
| PGP34 | A4G4S4 | The percentage of A4G4S4 |
| PGP35 | A4G4S4 | The percentage of A4G4S4 |
| PGP36 | A4F1G4S4 | The percentage of A4F1G4S4 |
| PGP37 | FGS/(FG+FGS) | The percentage of sialylation of core-fucosylated galactosylated structures without bisecting GlcNAc |
| PGP38 | FBGS/(FBG+FBGS) | The percentage of sialylation of core-fucosylated galactosylated structures with bisecting GlcNAc |
| PGP39 | FGS/(F+FG+FGS) | The percentage of sialylation of all core-fucosylated structures without bisecting GlcNAc |
| PGP40 | FBGS/(FB+FBG+FBGS) | The percentage of sialylation of all core-fucosylated structures with bisecting GlcNAc |
| PGP41 | FG1S1/(FG1+FG1S1) | The percentage of monosialylation of core-fucosylated monogalactosylated structures without bisecting GlcNAc |
| PGP42 | FG2S1/(FG2+FG2S1+FG2S2) | The percentage of monosialylation of core-fucosylated digalactosylated structures without bisecting GlcNAc |
| PGP43 | FG2S2/(FG2+FG2S1+FG2S2) | The percentage of disialylation of core-fucosylated digalactosylated structures without bisecting GlcNAc |
| PGP44 | FBG2S1/(FBG2+FBG2S1+FBG2S2) | The percentage of monosialylation of core-fucosylated digalactosylated structures with bisecting GlcNAc |
| PGP45 | FBG2S2/(FBG2+FBG2S1+FBG2S2) | The percentage of disialylation of core-fucosylated digalactosylated structures with bisecting GlcNAc |
| PGP46 | FtotalS1/FtotalS2 | Ratio of all fucosylated monosialylated and disialylated structures (+/- bisecting GlcNAc) |
| PGP47 | FS1/FS2 | Ratio of fucosylated monosialylated and disialylated structures (without bisecting GlcNAc) |
| PGP48 | FBS1/FBS2 | Ratio of fucosylated monosialylated and disialylated structures (with bisecting GlcNAc) |
| PGP49 | FtotalS1/FtotalS3 | Ratio of all core-fucosylated monosialylated and trisialylated structures (+/- bisecting GlcNAc) |
| PGP50 | FS1/FS3 | Ratio of core-fucosylated monosialylated and trisialylated structures (without bisecting GlcNAc) |
| PGP51 | FtotalS2/FtotalS3 | Ratio of all core-fucosylated disialylated and trisialylated structures (+/- bisecting GlcNAc) |
| PGP52 | FS2/FS3 | Ratio of core-fucosylated disialylated and trisialylated structures (without bisecting GlcNAc) |
| PGP53 | FBStotal/FStotal | Ratio of all core-fucosylated sialylated structures with and without bisecting GlcNAc |
| PGP54 | FBS1/FS1 | Ratio of fucosylated monosialylated structures with and without bisecting GlcNAc |
| PGP55 | FBS1/(FS1+FBS1) | The incidence of bisecting GlcNAc in all fucosylated monosialylated structures |
| PGP56 | FBS2/FS2 | Ratio of fucosylated disialylated structures with and without bisecting GlcNAc |
| PGP57 | FBS2/(FS2+FBS2) | The incidence of bisecting GlcNAc in all fucosylated disialylated structures |
| PGP58 | FA2n | The percentage of FA2 in total neutral plasma glycans (GPn) |
| PGP59 | FA2Bn | The percentage of FA2B in total neutral plasma glycans (GPn) |
| PGP60 | A2BG1n | The percentage of A2BG1 in total neutral plasma glycans (GPn) |
| PGP61 | FA2G1n | The percentage of FA2G1 in total neutral plasma glycans (GPn) |
| PGP62 | FA2G1n | The percentage of FA2G1 in total neutral plasma glycans (GPn) |
| PGP63 | FA2BG1n | The percentage of FA2BG1 in total neutral plasma glycans (GPn) |
| PGP64 | M6n | The percentage of M6 in total neutral plasma glycans (GPn) |
| PGP65 | A2G2n | The percentage of A2G2 in total neutral plasma glycans (GPn) |
| PGP66 | A2BG2n | The percentage of A2BG2 in total neutral plasma glycans (GPn) |
| PGP67 | FA2G2n | The percentage of FA2G2 in total neutral plasma glycans (GPn) |
| PGP68 | FA2BG2n | The percentage of FA2BG2 in total neutral plasma glycans (GPn) |
| PGP69 | M9n | The percentage of M9 in total neutral plasma glycans (GPn) |
| PGP70 | G0n | The percentage of agalactosylated structures in total neutral plasma glycans |
| PGP71 | G1n | The percentage of monogalactosylated structures in total neutral plasma glycans |
| PGP72 | G2n | The percentage of digalactosylated structures in total neutral plasma glycans |
| PGP73 | Fn total | The percentage of all fucosylated structures (+/- bisecting GlcNAc) in total neutral plasma glycans |
| PGP74 | FG1n total/G1n | The percentage of fucosylation of monogalactosylated structures in total neutral plasma glycans |
| PGP75 | FG2n total /G2n | The percentage of fucosylation of digalactosylated structures in total neutral plasma glycans |
| PGP76 | Fn | The percentage of fucosylated structures (without bisecting GlcNAc) in total neutral plasma glycans |
| PGP77 | FG0n/G0n | The percentage of fucosylation of agalactosylated structures (without bisecting GlcNAc) in total neutral plasma glycans |
| PGP78 | FG1n/G1n | The percentage of fucosylation of monogalactosylated structures (without bisecting GlcNAc) in total neutral plasma glycans |
| PGP79 | FG2n/G2n | The percentage of fucosylation of digalactosylated structures (without bisecting GlcNAc) in total neutral plasma glycans |
| PGP80 | FBn | The percentage of fucosylated structures (with bisecting GlcNAc) in total neutral plasma glycans |
| PGP81 | FBG0n/G0n | The percentage of fucosylation of agalactosylated structures (with bisecting GlcNAc) in total neutral plasma glycans |
| PGP82 | FBG1n/G1n | The percentage of fucosylation of monogalactosylated structures (with bisecting GlcNAc) in total neutral plasma glycans |
| PGP83 | FBG2n/G2n | The percentage of fucosylation of digalactosylated structures (with bisecting GlcNAc) in total neutral plasma glycans |
| PGP84 | FBn/Fn | Ratio of fucosylated structures with and without bisecting GlcNAc in total neutral plasma glycans |
| PGP85 | FBn/Fn total | The incidence of bisecting GlcNAc in all fucosylated structures in total neutral plasma glycans |
| PGP86 | Fn/(Bn+FBn) | Ratio of fucosylated non-bisecting GlcNAc structures and all structures with bisecting GlcNAc in total neutral plasma glycans |
| PGP87 | Bn/(Fn+FBn) | Ratio of afucosylated structures with bisecting GlcNAc and all fucosylated structures (+/- bisecting GlcNAc) in total neutral plasma glycans |
| PGP88 | FBG2n/FG2n | Ratio of fucosylated digalactosylated structures with and without bisecting GlcNAc in total neutral plasma glycans |
| PGP89 | FBG2n /(FG2n+FBG2n ) | The incidence of bisecting GlcNAc in all fucosylated digalactosylated structures in total neutral plasma glycans |
| PGP90 | FG2n/(BG2n+FBG2n) | Ratio of fucosylated digalactosylated non-bisecting GlcNAc structures and all digalactosylated structures with bisecting GlcNAc in total neutral plasma glycans |
| PGP91 | BG2n/(FG2n+FBG2n) | Ratio of afucosylated digalactosylated structures with bisecting GlcNAc and all fucosylated digalactosylated structures (+/- bisecting GlcNAc) in total neutral plasma glycans |
| PGP92 | FUC-A | The percentage of antennary fucosylated structures in total plasma glycans |
| PGP93 | FUC-C | The percentage of core fucosylated structures in total plasma glycans |
| PGP94 | S0total | The percentage of neutral glycan structures in total plasma glycans |
| PGP95 | S1total | the percentage of monosialylated structures in total plasma glycans |
| PGP96 | S2total | the percentage of bisialylated structures in total plasma glycans |
| PGP97 | S3total | the percentage of trisialylated structures in total plasma glycans |
| PGP98 | S4total | the percentage of tetrasialylated structures in total plasma glycans |
| PGP99 | G0total | The percentage of agalactosylated structures in total plasma glycans |
| PGP100 | G1total | The percentage of monogalactosylated structures in total plasma glycans |
| PGP101 | G2total | The percentage of digalactosylated structures in total plasma glycans |
| PGP102 | G3total | The percentage of trigalactosylated structures in total plasma glycans |
| PGP103 | G4total | The percentage of tetragalactosylated structures in total plasma glycans |
| PGP104 | A2total | The percentage of biantennary structures in total plasma glycans |
| PGP105 | A3total | The percentage of triantennary structures in total plasma glycans |
| PGP106 | A4total | The percentage of tetraantennary structures in total plasma glycans |
| PGP107 | Mtotal | The percentage of high-mannose structures in total plasma glycans |
| PGP108 | Btotal | The percentage of glycan structures with bisecting GlcNAc in total plasma glycans |
| PGP109 | G3S2/G3S3 | Ratio of disialylated and trisialylated trigalactosylated structures |
| PGP110 | G4S3/G4S4 | Ratio of trisialylated and tetrasialylated tetragalactosylated structures |
| PGP111 | FG3/G3total | The percentage of core-fucosylation of trigalactosylated structures |
| PGP112 | G3Fa/G3total | The percentage of antennary-fucosylation of trigalactosylated structures |
| PGP113 | G4Fa/G4total | The percentage of antennary-fucosylation of tetragalactosylated structures |
| PGP114 | M7n | The percentage of M7 in total neutral plasma glycans (GPn) |
| PGP115 | Stotal | The percentage of sialylated structures in total plasma glycans |
| PGP116 | Gtotal | The percentage of galactosylated structures in total plasma glycans |
| PGP117 | Gntotal | The percentage of galactosylated structures in total neutral plasma glycans |
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Additional details
Identifiers
Related works
- Is metadata for
- Dataset: 10.1101/2024.07.08.24309967 (DOI)
Dates
- Created
-
2025-04-01
References
- 10.1101/2024.07.08.24309967