Genetic influences on metabolite levels: A comparison across metabolomic platforms

PLoS ONE

Volumn 11, Issue 4, 2016, Pages

  Yet, Idil ^a   Menni, Cristina ^a   Shin, So Youn ^b,c   Mangino, Massimo ^a   Soranzo, Nicole ^b   Adamski, Jerzy ^d   Suhre, Karsten ^e   Spector, Tim D ^a   Kastenmüller, Gabi ^a,d   Bell, Jordana T ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c MEDICAL RESEARCH COUNCIL   (United Kingdom)

^d INSTITUTE OF EPIDEMIOLOGY   (Germany)

^e WEILL CORNELL MEDICAL COLLEGE   (Qatar)

Author keywords

[No Author keywords available]

Indexed keywords

1 STEAROLYGLYCEROL; CARNITINE; GLYCEROL DERIVATIVE; NONANOYLCARNITINE; UNCLASSIFIED DRUG;

ARTICLE; BLOOD ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HUMAN; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; TWINS; GENOME-WIDE ASSOCIATION STUDY; METABOLOME; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME-WIDE ASSOCIATION STUDY; HUMANS; METABOLOME; METABOLOMICS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84963837830     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0153672     Document Type: Article

References (37)

1. Holle R, Happich M, Lowel H, Wichmann HE, Group M K S (2005) KORA-a research platform for population based health research. Gesundheitswesen 67 Suppl 1:S19-25. PMID: 16032513
2. Wichmann HE, Gieger C, Illig T, Group M K S (2005) KORA-gen-resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen 67 Suppl 1:S26-30. PMID: 16032514
3. Moayyeri A, Hammond CJ, Hart DJ, Spector TD (2013) The UK Adult Twin Registry (TwinsUK Resource). Twin Res Hum Genet 16:144-149. doi:10.1017/thg.2012.89 PMID: 23088889
4. Silander K, Alanne M, Kristiansson K, Saarela O, Ripatti S, Auro K, et al. (2008) Gender differences in genetic risk profiles for cardiovascular disease. PLoSOne 3:e3615. doi:10.1371/journal.pone. 0003615 PMID: 18974842
5. Boomsma DI, de Geus EJ, Vink JM, Stubbe JH, Distel MA, Hottenga JJ, etal. (2006) Netherlands Twin Register: from twins to twin families. Twin Res Hum Genet 9:849-857. PMID: 17254420
6. Riboli E, Kaaks R (1997) The EPIC Project: rationale and study design. European Prospective Investigation into Cancer and Nutrition. Int J Epidemiol 26 Suppl 1:S6-14. PMID: 9126529
7. Suhre K, Meisinger C, Doring A, Altmaier E, Belcredi P, Gieger C, etal. (2010) Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting. PLoS One 5:e13953. doi:10.1371/journal.pone.0013953 PMID: 21085649
8. Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, etal. (2011) The human serum metabolome. PLoS One 6:e16957. doi:10.1371/journal.pone.0016957 PMID: 21359215
9. Adamski J, Suhre K (2013) Metabolomics platforms for genome wide association studies-linking the genome to the metabolome. CurrOpin Biotechnol 24:39-47. doi:10.1016/j.copbio.2012.10.003 PMID: 23102864
10. Mandal R, Guo AC, Chaudhary KK, Liu P, Yallou FS, Dong E, etal. (2012) Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update. Genome Med 4:38. PMID: 22546835
11. Büscher JM, Czernik D, Ewald JC, Sauer U, Zamboni N (2009) Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal Chem 81:2135-2143. doi:10.1021/ac8022857 PMID: 19236023
12. Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, etal. (2011) A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet 7:e1002270. doi:10.1371/journal.pgen. 1002270 PMID: 21931564
13. Raffler J, Römisch-Margl W, Petersen AK, Pagel P, Blöchl F, Hengstenberg C, etal. (2013) Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma. Genome Med 5:13. doi:10.1186/gm417 PMID: 23414815
14. Assfalg M, Bertini I, Colangiuli D, Luchinat C, Schäfer H, Schütz B, etal. (2008) Evidence of different metabolic phenotypes in humans. Proc Natl Acad Sci USA 105:1420-1424. doi:10.1073/pnas. 0705685105 PMID: 18230739
15. Dumas ME, Wilder SP, Bihoreau MT, Barton RH, Fearnside JF, Argoud K, etal. (2007) Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models. Nat Genet 39:666-672. PMID: 17435758
16. Vinayavekhin N, Homan EA, Saghatelian A (2010) Exploring disease through metabolomics. ACS Chem Biol 5:91-103. doi:10.1021/cb900271r PMID: 20020774
17. Watson AD (2006) Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res 47:2101-2111. PMID: 16902246
18. Homuth G, Teumer A, Völker U, Nauck M (2012) A description of large-scale metabolomics studies: increasing value by combining metabolomics with genome-wide SNP genotyping and transcriptional profiling. J Endocrinol 215:17-28. doi:10.1530/JOE-12-0144 PMID: 22782382
19. Kettunen J, Tukiainen T, Sarin AP, Ortega-Alonso A, Tikkanen E, Lyytikainen LP, etal. (2012) Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Nat Genet 44:269-276. doi:10.1038/ng.1073 PMID: 22286219
20. Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, etal. (2014) Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links. PLoS Genet 10:e1004132. doi:10.1371/journal.pgen. 1004132 PMID: 24586186
21. Gieger C, Geistlinger L, Altmaier E, Hrabede Angelis M, Kronenberg F, Meitinger T, etal. (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 4:e1000282. doi:10.1371/journal.pgen. 1000282 PMID: 19043545
22. Illig T, Gieger C, Zhai G, Romisch-Margl W, Wang-Sattler R, Prehn C, etal. (2010) A genome-wide perspective of genetic variation in human metabolism. Nat Genet 42:137-141. doi:10.1038/ng.507 PMID: 20037589
23. Suhre K, Shin SY, Petersen AK, Mohney RP, Meredith D, Wägele B, etal. (2011) Human metabolic individuality in biomedical and pharmaceutical research. Nature 477:54-60. doi:10.1038/nature10354 PMID: 21886157
24. Suhre K, Wallaschofski H, Raffler J, Friedrich N, Haring R, Michael K, etal. (2011) A genome-wide association study of metabolic traits in human urine. Nat Genet 43:565-569. doi:10.1038/ng.837 PMID: 21572414
25. Kastenmuller G, Raffler J, Gieger C, Suhre K (2015) Genetics of human metabolism: an update. Hum Mol Genet.
26. Moayyeri A, Hammond CJ, Valdes AM, Spector TD (2013) Cohort Profile: TwinsUK and healthy ageing twin study. Int J Epidemiol 42:76-85. doi:10.1093/ije/dyr207 PMID: 22253318
27. Römisch-Margl W, Prehn C, Bogumil R, Röhring C, Suhre K, Adamski J (2012) Procedure for tissue sample preparation and metabolite extraction for high-throughput targeted metabolomics. Metabolomics 8:133-142.
28. Mittelstrass K, Ried JS, Yu Z, Krumsiek J, Gieger C, Prehn C, etal. (2011) Discovery of sexual dimorphisms in metabolic and genetic biomarkers. PLoS Genet 7:e1002215. doi:10.1371/journal.pgen. 1002215 PMID: 21852955
29. Menni C, Zhai G, Macgregor A, Prehn C, Römisch-Margl W, Suhre K, etal. (2013) Targeted metabolomics profiles are strongly correlated with nutritional patterns in women. Metabolomics 9:506-514. PMID: 23543136
30. Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, etal. (2014) An atlas of genetic influences on human blood metabolites. Nat Genet 46:543-550. doi:10.1038/ng.2982 PMID: 24816252
31. Dehaven CD, Evans AM, Dai H, Lawton KA (2010) Organization of GC/MS and LC/MS metabolomics data into chemical libraries. J Cheminform 2:9. doi:10.1186/1758-2946-2-9 PMID: 20955607
32. Evans AM, De Haven CD, Barrett T, Mitchell M, Milgram E (2009) Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform forthe identification and relative quantification of the small-molecule complement of biological systems. Anal Chem 81:6656-6667. doi:10.1021/ac901536h PMID: 19624122
33. Yousri NA, Kastenmuller G, Gieger C, Shin SY, Erte I, Menni C, etal. (2014) Long term conservation of human metabolic phenotypes and link to heritability. Metabolomics 10:1005-1017. PMID: 25177233
34. Boker S, Neale M, Maes H, Wilde M, Spiegel M, Brick T, etal. (2011) OpenMx: An Open Source Extended Structural Equation Modeling Framework. Psychometrika 76:306-317. PMID: 23258944
35. Zhou X, Stephens M (2012) Genome-wide efficient mixed-model analysis for association studies. Nat Genet 44:821-824. doi:10.1038/ng.2310 PMID: 22706312
36. Krumsiek J, Suhre K, Evans AM, Mitchell MW, Mohney RP, Milburn MV, etal. (2012) Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information. PLoS Genet 8:e1003005. doi:10.1371/journal.pgen. 1003005 PMID: 23093944
37. Draisma HH, Pool R, Kobl M, Jansen R, Petersen AK, Vaarhorst AA, et al. (2015) Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. Nat Commun 6:7208. doi:10.1038/ncomms8208 PMID: 26068415