A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Shim, Heejung ^a   Chasman, Daniel I ^b   Smith, Joshua D ^c   Mora, Samia ^b   Ridker, Paul M ^b   Nickerson, Deborah A ^c   Krauss, Ronald M ^d   Stephens, Matthew ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERMEDIATE DENSITY LIPOPROTEIN; LOW DENSITY LIPOPROTEIN; PRAVASTATIN; SIMVASTATIN; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR;

ADULT; AGED; APOE GENE; ARTICLE; CAUCASIAN; CETP GENE; CLINICAL TRIAL (TOPIC); COHORT ANALYSIS; CONTROLLED STUDY; FEMALE; GEL ELECTROPHORESIS; GENE; GENE IDENTIFICATION; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; LPA GENE; MALE; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM; SORT1 GENE; BAYES THEOREM; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME; MIDDLE AGED;

AGED; BAYES THEOREM; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; HYDROXYMETHYLGLUTARYL-COA REDUCTASE INHIBITORS; LIPOPROTEINS, LDL; MALE; MIDDLE AGED; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84928253865     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0120758     Document Type: Article

References (43)

1. Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature. 2010; 466:707-713. doi: 10.1038/nature09270 PMID: 20686565
2. Chasman DI, ParNi G, Mora S, Hopewell JC, Peloso G, Clarke R, et al. Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. PLoS Genet. 2009; 5(11):e1000730. doi: 10.1371/journal.pgen.1000730 PMID: 19936222
3. Tukiainen T, Kettunen J, Kangas AJ, Lyytiäainen LP, Soininen P, Sarin AP, et al. Detailed metabolic and genetic characterization reveals new associations for 30 known lipid loci. Human Molecular Genetics. 2012 Mar; 21(6):1444-55. doi: 10.1093/hmg/ddr581 PMID: 22156771
4. Kettunen J, Tukiainen T, Sarin AP, Ortega-Alonso A, Tikkanen E, Lyytikinen LP, et al. Genomewide association study identifies multiple loci influencing human serum metabolite levels. Nature Genetics. 2012; 44(3):269-76. doi: 10.1038/ng.1073 PMID: 22286219
5. Thompson JF, Hyde CL, Wood LS, Paciga SA, Hinds DA, Cox DR, et al. Comprehensive wholegenome and candidate gene analysis for response to statin therapy in the Treating to New Targets (TNT) cohort. Circulation Cardiovascular genetics. 2009 Apr; 2(2):173-81. doi: 10.1161/CIRCGENETICS.108.818062 PMID: 20031582
6. Barber MJ, Mangravite LM, Hyde CL, Chasman DI, Smith JD, McCarty Ca, et al. Genome-wide association of lipid-lowering response to statins in combined study populations. PloS one. 2010 Jan; 5(3): e9763. doi: 10.1371/journal.pone.0009763 PMID: 20339536
7. Chasman DI, Giulianini F, Macfadyen J, Barratt BJ, Nyberg F, Ridker PM. Genetic Determinants of Statin Induced LDL-C Reduction: The JUPITER Trial. Circulation Cardiovascular Genetics. 2012 Feb; 5:257-264. doi: 10.1161/CIRCGENETICS.111.961144 PMID: 22331829
8. Simon Ja, Lin F, Hulley SB, Blanche PJ, Waters D, Shiboski S, et al. Phenotypic predictors of response to simvastatin therapy among African-Americans and Caucasians: the Cholesterol and Pharmacogenetics (CAP) Study. The American journal of cardiology. 2006 Mar; 97(6):843-50. doi: 10.1016/j.amjcard.2005.09.134 PMID: 16516587
9. Albert MA, Danielson E, Rifai N, Ridker PM. Effect of Statin Therapy on C-Reactive Protein Levels: The Pravastatin Inammation/CRP Evaluation (PRINCE): A Randomized Trial and Cohort Study. The Journal of the American Medical Association. 2001; 286:64-70. doi: 10.1001/jama.286.1.64
10. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS genetics. 2009 Jun; 5(6):e1000529. doi: 10.1371/journal.pgen.1000529 PMID: 19543373
11. Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS genetics. 2007 Jul; 3(7):e114. doi: 10.1371/journal.pgen.0030114 PMID: 17676998
12. Mangravite LM, Engelhardt BE, Medina MW, Smith JD, Brown CD, Chasman DI, et al. A statindependent QTL for GATM expression is associated with statin-induced myopathy. Nature. 2013 Oct; 502 (7471):377-80. doi: 10.1038/nature12508 PMID: 23995691
13. Durbin RM, Altshuler DL, Abecasis GR, Bentley DR, et al AC. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct; 467(7319):1061-73. doi: 10.1038/nature09534 PMID: 20981092
14. The International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct; 437 (7063):1299-320. doi: 10.1038/nature04226 PMID: 16255080
15. Friedewald WT, Levy RI, Fredrickson DS. Estimation of the concentration of low-density lipoprotein cholesterol in plasma, without use of the preparative ultracentrifuge. Clin Chem. 1972; 18:499-502. PMID: 4337382
16. Williams PT, Vranizan KM, Krauss RM. Correlations of plasma lipoproteins with LDL subfractions by particle size in men and women. J Lipid Res. 1992; 33:765-774. PMID: 1619368
17. Rainwater DL, Mitchell BD, Comuzzie AG, Haffner SM. Relationship of low-density lipoprotein particle size and measures of adiposity. Int J Obes Relat Metab Disord. 1999; 23:180189. doi: 10.1038/sj.ijo.0800813
18. Berneis K, Krauss RM. Metabolic origins and clinical significance of LDL heterogeneity. J Lipid Res. 2002; 43:1363-1379. doi: 10.1194/jlr.R200004-JLR200 PMID: 12235168
19. Ridker PM, Danielson E, Fonseca FAH, Genest J, Gotto AM, Kastelein JJP, et al. Rosuvastatin to prevent vascular events in men and women with elevated C-reactive protein. The New England journal of medicine. 2008 Nov; 359(21):2195-207. doi: 10.1056/NEJMoa0807646 PMID: 18997196
20. Caulfield MP, Li S, Lee G, Blanche PJ, Salameh WA, Benner WH, et al. Direct determination of lipoprotein particle sizes and concentrations by ion mobility analysis. Clinical chemistry. 2008 Aug; 54 (8):1307-16. doi: 10.1373/clinchem.2007.100586 PMID: 18515257
21. Musunuru K, Orho-Melander M, Caulfield MP, Li S, Salameh Wa, Reitz RE, et al. Ion mobility analysis of lipoprotein subfractions identifies three independent axes of cardiovascular risk. Arteriosclerosis, thrombosis, and vascular biology. 2009 Nov; 29(11):1975-80. doi: 10.1161/ATVBAHA.109.190405 PMID: 19729614
22. Stephens M. A unified framework for association analysis with multiple related phenotypes. PloS one. 2013 Jan; 8(7):e65245. doi: 10.1371/journal.pone.0065245 PMID: 23861737
23. Wakefield J. Bayes factors for genome-wide association studies: comparison with P-values. Genetic epidemiology. 2009 Jan; 33(1):79-86. doi: 10.1002/gepi.20359 PMID: 18642345
24. Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nature reviews Genetics. 2009 Oct; 10(10):681-90. doi: 10.1038/nrg2615 PMID: 19763151
25. Campos H, Arnold KS, Balestra ME, Innerarity TL, Krauss RM. Differences in receptor binding of LDL subfractions. Arteriosclerosis, Thrombosis, and Vascular Biology. 1996 Jun; 16(6):794-801. doi: 10.1161/01.ATV.16.6.794 PMID: 8640407
26. Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature. 2010 Aug; 466(7307):714-9. doi: 10.1038/nature09266 PMID: 20686566
27. Deshmukh HA, Colhoun HM, Johnson T, Mckeigue PM, John D, Durrington PN, et al. Genomewide Association Study of Genetic Determinants of LDL-c Response to Atorvastatin Therapy: Importance of Lp (a). Journal of lipid research. 2012; 53(5):1000-11. doi: 10.1194/jlr.P021113 PMID: 22368281
28. Qi Q, Workalemahu T, Zhang C, Hu FB, Qi L. Genetic variants, plasma lipoprotein(a) levels, and risk of cardiovascular morbidity and mortality among two prospective cohorts of type 2 diabetes. European heart journal. 2012 Feb; 33(3):325-34. doi: 10.1093/eurheartj/ehr350 PMID: 21900290
29. Dreon DM, Fernstrom HA, Williams PT, Krauss RM. LDL subclass patterns and lipoprotein response to a low-fat, high-carbohydrate diet in women. Arteriosclerosis, Thrombosis, and Vascular Biology. 1997; 17(4):707-714. doi: 10.1161/01.ATV.17.4.707 PMID: 9108784
30. Rader DJ, DeGoma EM. Future of cholesteryl ester transfer protein inhibitors. Annual review of medicine. 2014 Jan; 65:385-403. doi: 10.1146/annurev-med-050311-163305 PMID: 24422575
31. Williams PT, Zhao XQ, Marcovina SM, Otvos JD, Brown BG, Krauss RM. Comparison of four methods of analysis of lipoprotein particle subfractions for their association with angiographic progression of coronary artery disease. Atherosclerosis. 2014 Apr; 233(2):713-20. doi: 10.1016/j.atherosclerosis.2014.01.034 PMID: 24603218
32. Hindorff L, MacArthur J, Morales J, Junkins H, Hall P, Klemm A, et al. A Catalog of Published Genome-Wide Association Studies.;. Available at: www.genome.gov/gwastudies. Accessed [date of access].
33. Krauss RM, Wojnooski K, Orr J, Geaney JC, Pinto CA, Liu Y, et al. Changes in lipoprotein subfraction concentration and composition in healthy individuals treated with the CETP inhibitor anacetrapib. Journal of lipid research. 2012 Mar; 53(3):540-7. doi: 10.1194/jlr.M018010 PMID: 22180633
34. Sakai N, Matsuzawa Y, Hirano K, Yamashita S, Nozaki S, Ueyama Y, et al. Detection of Two Species of Low Density Lipoprotein Particles in Cholesteryl Ester Transfer Protein Deficiency. Arteriosclerosis, thrombosis, and vascular biology. 1991; 11:71-79. doi: 10.1161/01.ATV.11.1.71
35. Verzilli CJ, Stallard N, Whittaker JC. Bayesian modelling of multivariate quantitative traits using seemingly unrelated regressions. Genet Epidemiol. 2005 May; 28(4):313-25. doi: 10.1002/gepi.20072 PMID: 15789447
36. Banerjee S, Yandell BS, Yi N. Bayesian quantitative trait loci mapping for multiple traits. Genetics. 2008 Aug; 179(4):2275-89. doi: 10.1534/genetics.108.088427 PMID: 18689903
37. Kim S, Sohn KA, Xing EP. A multivariate regression approach to association analysis of a quantitative trait network. Bioinformatics. 2009 Jun; 25(12):i204-12. doi: 10.1093/bioinformatics/btp218 PMID: 19477989
38. Kim S, Xing EP. Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet. 2009 Aug; 5(8):e1000587. doi: 10.1371/journal.pgen.1000587 PMID: 19680538
39. Baker AR, Goodloe RJ, Larkin EK, Baechle DJ, Song YE, Phillips LS, et al. Multivariate association analysis of the components of metabolic syndrome from the Framingham Heart Study. BMC Proc. 2009; 3 Suppl 7:S42. doi: 10.1186/1753-6561-3-s7-s42 PMID: 20018034
40. Zhang L, Pei YF, Li J, Papasian CJ, Deng HW. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. PLoS One. 2009; 4(8):e6502. doi: 10.1371/journal.pone.0006502 PMID: 19652719
41. Ferreira MAR, Purcell SM. A multivariate test of association. Bioinformatics. 2009 Jan; 25(1):132-3. doi: 10.1093/bioinformatics/btn563 PMID: 19019849
42. O 'Reilly PF, Hoggart CJ, Pomyen Y, Calboli FCF, Elliott P, Jarvelin MR, et al. MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS. PLoS One. 2012; 7(5):e34861. doi: 10.1371/journal.pone.0034861 PMID: 22567092
43. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics (Oxford, England). 2010 Sep; 26 (18):2336-7. doi: 10.1093/bioinformatics/btq419