Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma

Genome Medicine

Volumn 5, Issue 2, 2013, Pages

  Raffler, Johannes ^a,b   Römisch Margl, Werner ^a   Petersen, Ann Kristin ^a   Pagel, Philipp ^c   Blöchl, Florian ^c   Hengstenberg, Christian ^d   Illig, Thomas ^a,e   Meisinger, Christa ^a   Stark, Klaus ^d   Wichmann, H Erich ^a   Adamski, Jerzy ^a   Gieger, Christian ^a   Kastenmüller, Gabi ^a   Suhre, Karsten ^a,f  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c NUMARES AG   (Germany)

^d UNIVERSITY OF REGENSBURG   (Germany)

^e HANNOVER MEDICAL SCHOOL   (Germany)

^f WEILL CORNELL MEDICAL COLLEGE   (Qatar)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL COENZYME A DESATURASE 1; APOLIPOPROTEIN A1; BIOLOGICAL MARKER; CARBAMOYL PHOSPHATASE 1; CARBAMOYL PHOSPHATE; CHOLESTEROL ESTER; CHOLESTEROL ESTER TRANSFER PROTEIN; GLUCOKINASE; GLUCOKINASE REGULATOR; LIPOPROTEIN CHOLESTEROL; OXIDOREDUCTASE; PYRIDINE NUCLEOTIDE DISULFIDE OXIDOREDUCTASE 2; UNCLASSIFIED DRUG;

ARTICLE; BLOOD CHEMISTRY; BLOOD SAMPLING; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC VARIABILITY; HUMAN; HUMAN EXPERIMENT; MASS SPECTROMETRY; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLASMA; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SIGNAL NOISE RATIO; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84873714655     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm417     Document Type: Article

References (28)

1. Ward JL, Baker JM, Miller SJ, Deborde C, Maucourt M, Biais B, Rolin D, Moing A, Moco S, Vervoort J, Lommen A, Schafer H, Humpfer E, Beale MH. An inter-laboratory comparison demonstrates that [H]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection. Metabolomics 2010, 6:263-273. 10.1007/s11306-010-0200-4, 2874487, 20526352.
2. Viant MR, Bearden DW, Bundy JG, Burton IW, Collette TW, Ekman DR, Ezernieks V, Karakach TK, Lin CY, Rochfort S, de Ropp JS, Teng Q, Tjeerdema RS, Walter JA, Wu H. International NMR-based environmental metabolomics intercomparison exercise. Environ Sci Technol 2009, 43:219-225. 10.1021/es802198z, 19209610.
3. Gieger C, Geistlinger L, Altmaier E, Hrabe de Angelis M, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, Adamski J, Illig T, Suhre K. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 2008, 4:e1000282. 10.1371/journal.pgen.1000282, 2581785, 19043545.
4. Illig T, Gieger C, Zhai G, Romisch-Margl W, Wang-Sattler R, Prehn C, Altmaier E, Kastenmuller G, Kato BS, Mewes HW, Meitinger T, de Angelis MH, Kronenberg F, Soranzo N, Wichmann HE, Spector TD, Adamski J, Suhre K. A genome-wide perspective of genetic variation in human metabolism. Nat Genet 2010, 42:137-141. 10.1038/ng.507, 20037589.
5. Suhre K, Shin SY, Petersen AK, Mohney RP, Meredith D, Wagele B, Altmaier E, Deloukas P, Erdmann J, Grundberg E, Hammond CJ, de Angelis MH, Kastenmuller G, Kottgen A, Kronenberg F, Mangino M, Meisinger C, Meitinger T, Mewes HW, Milburn MV, Prehn C, Raffler J, Ried JS, Romisch-Margl W, Samani NJ, Small KS, Wichmann HE, Zhai G, Illig T, Spector TD, et al. Human metabolic individuality in biomedical and pharmaceutical research. Nature 2011, 477:54-60. 10.1038/nature10354, 21886157.
6. Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan KT, Spector TD, Nicholson JK, Lindon JC, Baunsgaard D, Holmes E, McCarthy MI, Holmes CC. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet 2011, 7:e1002270. 10.1371/journal.pgen.1002270, 3169529, 21931564.
7. Kettunen J, Tukiainen T, Sarin AP, Ortega-Alonso A, Tikkanen E, Lyytikainen LP, Kangas AJ, Soininen P, Wurtz P, Silander K, Dick DM, Rose RJ, Savolainen MJ, Viikari J, Kahonen M, Lehtimaki T, Pietilainen KH, Inouye M, McCarthy MI, Jula A, Eriksson J, Raitakari OT, Salomaa V, Kaprio J, Jarvelin MR, Peltonen L, Perola M, Freimer NB, Ala-Korpela M, Palotie A, Ripatti S. Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Nat Genet 2012, 44:269-276. 10.1038/ng.1073, 3605033, 22286219.
8. Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, Anderson CA, Bis JC, Bumpstead S, Ellinghaus D, Festen EM, Georges M, Green T, Haritunians T, Jostins L, Latiano A, Mathew CG, Montgomery GW, Prescott NJ, Raychaudhuri S, Rotter JI, Schumm P, Sharma Y, Simms LA, Taylor KD, Whiteman D, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010, 42:1118-1125. 10.1038/ng.717, 3299551, 21102463.
9. Kathiresan S, Willer CJ, Peloso GM, Demissie S, Musunuru K, Schadt EE, Kaplan L, Bennett D, Li Y, Tanaka T, Voight BF, Bonnycastle LL, Jackson AU, Crawford G, Surti A, Guiducci C, Burtt NP, Parish S, Clarke R, Zelenika D, Kubalanza KA, Morken MA, Scott LJ, Stringham HM, Galan P, Swift AJ, Kuusisto J, Bergman RN, Sundvall J, Laakso M, et al. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet 2009, 41:56-65. 10.1038/ng.291, 2881676, 19060906.
10. Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, Jackson AU, Wheeler E, Glazer NL, Bouatia-Naji N, Gloyn AL, Lindgren CM, Magi R, Morris AP, Randall J, Johnson T, Elliott P, Rybin D, Thorleifsson G, Steinthorsdottir V, Henneman P, Grallert H, Dehghan A, Hottenga JJ, Franklin CS, Navarro P, Song K, Goel A, Perry JR, Egan JM, Lajunen T, et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet 2010, 42:105-116. 10.1038/ng.520, 3018764, 20081858.
11. Kottgen A, Pattaro C, Boger CA, Fuchsberger C, Olden M, Glazer NL, Parsa A, Gao X, Yang Q, Smith AV, O'Connell JR, Li M, Schmidt H, Tanaka T, Isaacs A, Ketkar S, Hwang SJ, Johnson AD, Dehghan A, Teumer A, Pare G, Atkinson EJ, Zeller T, Lohman K, Cornelis MC, Probst-Hensch NM, Kronenberg F, Tonjes A, Hayward C, Aspelund T, et al. New loci associated with kidney function and chronic kidney disease. Nat Genet 2010, 42:376-384. 10.1038/ng.568, 2997674, 20383146.
12. Petersen AK, Krumsiek J, Wagele B, Theis FJ, Wichmann HE, Gieger C, Suhre K. On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. BMC Bioinformatics 2012, 13:120. 10.1186/1471-2105-13-120, 3537592, 22672667.
13. Petersen AK, Stark K, Musameh MD, Nelson CP, Romisch-Margl W, Kremer W, Raffler J, Krug S, Skurk T, Rist MJ, Daniel H, Hauner H, Adamski J, Tomaszewski M, Doring A, Peters A, Wichmann HE, Kaess BM, Kalbitzer HR, Huber F, Pfahlert V, Samani NJ, Kronenberg F, Dieplinger H, Illig T, Hengstenberg C, Suhre K, Gieger C, Kastenmuller G. Genetic associations with lipoprotein subfractions provide information on their biological nature. Hum Mol Genet 2012, 21:1433-1443. 10.1093/hmg/ddr580, 22156577.
14. Wichmann HE, Gieger C, Illig T. KORA-gen--resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen 2005, (Suppl 1):S26-30.
15. Smolinska A, Blanchet L, Buydens LM, Wijmenga SS. NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review. Anal Chim Acta 2012, 750:82-97.
16. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
17. Suhre K, Wallaschofski H, Raffler J, Friedrich N, Haring R, Michael K, Wasner C, Krebs A, Kronenberg F, Chang D, Meisinger C, Wichmann HE, Hoffmann W, Volzke H, Volker U, Teumer A, Biffar R, Kocher T, Felix SB, Illig T, Kroemer HK, Gieger C, Romisch-Margl W, Nauck M. A genome-wide association study of metabolic traits in human urine. Nat Genet 2011, 43:565-569. 10.1038/ng.837, 21572414.
18. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 2009, 37:D603-610. 10.1093/nar/gkn810, 2686599, 18953024.
19. Klaus V, Vermeulen T, Minassian B, Israelian N, Engel K, Lund AM, Roebrock K, Christensen E, Haberle J. Highly variable clinical phenotype of carbamylphosphate synthetase 1 deficiency in one family: an effect of allelic variation in gene expression?. Clin Genet 2009, 76:263-269. 10.1111/j.1399-0004.2009.01216.x, 19793055.
20. Dumont J, Huybrechts I, Spinneker A, Gottrand F, Grammatikaki E, Bevilacqua N, Vyncke K, Widhalm K, Kafatos A, Molnar D, Labayen I, Gonzalez-Gross M, Amouyel P, Moreno LA, Meirhaeghe A, Dallongeville J. FADS1 genetic variability interacts with dietary alpha-linolenic acid intake to affect serum non-HDL-cholesterol concentrations in European adolescents. J Nutr 2011, 141:1247-1253. 10.3945/jn.111.140392, 21593353.
21. Lu Y, Feskens EJ, Dolle ME, Imholz S, Verschuren WM, Muller M, Boer JM. Dietary n-3 and n-6 polyunsaturated fatty acid intake interacts with FADS1 genetic variation to affect total and HDL-cholesterol concentrations in the Doetinchem Cohort Study. Am J Clin Nutr 2010, 92:258-265. 10.3945/ajcn.2009.29130, 20484448.
22. van Schaftingen E, Veiga-da-Cunha M, Niculescu L. The regulatory protein of glucokinase. Biochem Soc Trans 1997, 25:136-140.
23. Vaxillaire M, Cavalcanti-Proenca C, Dechaume A, Tichet J, Marre M, Balkau B, Froguel P. The common P446L polymorphism in GCKR inversely modulates fasting glucose and triglyceride levels and reduces type 2 diabetes risk in the DESIR prospective general French population. Diabetes 2008, 57:2253-2257. 10.2337/db07-1807, 2494697, 18556336.
24. Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, Chen H, Roix JJ, Kathiresan S, Hirschhorn JN, Daly MJ, Hughes TE, Groop L, Altshuler D, Almgren P, Florez JC, Meyer J, Ardlie K, Bengtsson Bostrom K, Isomaa B, Lettre G, Lindblad U, Lyon HN, Melander O, Newton-Cheh C, Nilsson P, Orho-Melander M, Rastam L, Speliotes EK, Taskinen MR, Tuomi T, et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 2007, 316:1331-1336.
25. Horvatovich K, Bokor S, Polgar N, Kisfali P, Hadarits F, Jaromi L, Csongei V, Repasy J, Molnar D, Melegh B. Functional glucokinase regulator gene variants have inverse effects on triglyceride and glucose levels, and decrease the risk of obesity in children. Diabetes Metab 2011, 37:432-439. 10.1016/j.diabet.2011.02.003, 21511510.
26. Kristiansson K, Perola M, Tikkanen E, Kettunen J, Surakka I, Havulinna AS, Stancakova A, Barnes C, Widen E, Kajantie E, Eriksson JG, Viikari J, Kahonen M, Lehtimaki T, Raitakari OT, Hartikainen AL, Ruokonen A, Pouta A, Jula A, Kangas AJ, Soininen P, Ala-Korpela M, Mannisto S, Jousilahti P, Bonnycastle LL, Jarvelin MR, Kuusisto J, Collins FS, Laakso M, Hurles ME, et al. Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits. Circ Cardiovasc Genet 2012, 5:242-249. 10.1161/CIRCGENETICS.111.961482, 3378651, 22399527.
27. Krumsiek J, Suhre K, Evans AM, Mitchell MW, Mohney RP, Milburn MV, Wagele B, Romisch-Margl W, Illig T, Adamski J, Gieger C, Theis FJ, Kastenmuller G. Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information. PLoS Genet 2012, 8:e1003005. 10.1371/journal.pgen.1003005, 3475673, 23093944.
28. Wei SW, Zhang J, Liu LY, Ye T, Gowda GAN, Tayyari F, Raftery D. Ratio analysis nuclear magnetic resonance spectroscopy for selective metabolite identification in complex samples. Analytical Chemistry 2011, 83:7616-7623. 10.1021/ac201625f, 3193582, 21894988.