Direct sequencing for comprehensive screening of LDLR genetic polymorphisms among five ethnic populations

Genes and Genomics

Volumn 37, Issue 3, 2015, Pages 247-255

  Kim, Jeong Hyun ^a   Cheong, Hyun Sub ^b   Kim, Lyoung Hyo ^b   Shin, Hee Jung ^c   Na, Han Sung ^c   Chung, Myeon Woo ^c   Shin, Hyoung Doo ^a,b  

^a Sogang University   (South Korea)

^b SNP Genetics Inc   (South Korea)

^c National Institute of Food and Drug Safety Evaluation   (South Korea)

Author keywords

LDLR; Lipoprotein metabolism; Minor allele frequency; Pharmacogenetics; Single nucleotide polymorphism

Indexed keywords

DNA; LOW DENSITY LIPOPROTEIN RECEPTOR;

3' UNTRANSLATED REGION; AFRICAN AMERICAN; ALTERNATIVE RNA SPLICING; ARTICLE; CHINESE; DNA SEQUENCE; ETHNIC GROUP; EUROPEAN AMERICAN; EXON; GENE FREQUENCY; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; INTRON; JAPANESE (PEOPLE); KOREAN (PEOPLE); MAJOR CLINICAL STUDY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84925481183     PISSN: 19769571     EISSN: 20929293     Source Type: Journal    
DOI: 10.1007/s13258-014-0244-3     Document Type: Article

References (44)

1. Adeyemo A, Bentley AR, Meilleur KG, Doumatey AP, Chen G, Zhou J, Shriner D, Huang H, Herbert A, Gerry NP et al (2012) Transferability and fine mapping of genome-wide associated loci for lipids in African Americans. BMC Med Genet 13:88
2. Ahn YI, Kamboh MI, Aston CE, Ferrell RE, Hamman RF (1994) Role of common genetic polymorphisms in the LDL receptor gene in affecting plasma cholesterol levels in the general population. Arterioscler Thromb 14:663–670
3. Albers JJ, Day JR, Wolfbauer G, Kennedy H, Vuletic S, Cheung MC (2011) Impact of site-specific N-glycosylation on cellular secretion, activity and specific activity of the plasma phospholipid transfer protein. Biochim Biophys Acta 1814:908–911
4. Andreotti G, Chen J, Gao YT, Rashid A, Chen BE, Rosenberg P, Sakoda LC, Deng J, Shen MC, Wang BS et al (2008) Polymorphisms of genes in the lipid metabolism pathway and risk of biliary tract cancers and stones: a population-based case-control study in Shanghai, China. Cancer Epidemiol Biomark Prev 17:525–534
5. Benjannet S, Hamelin J, Chretien M, Seidah NG (2012) Loss- and gain-of-function PCSK9 variants: cleavage specificity, dominant negative effects, and low density lipoprotein receptor (LDLR) degradation. J Biol Chem 287:33745–33755
6. Bieghs V, Van Gorp PJ, Wouters K, Hendrikx T, Gijbels MJ, van Bilsen M, Bakker J, Binder CJ, Lutjohann D, Staels B et al (2012) LDL receptor knock-out mice are a physiological model particularly vulnerable to study the onset of inflammation in non-alcoholic fatty liver disease. PLoS One 7:e30668
7. Brown MS, Goldstein JL (1986) A receptor-mediated pathway for cholesterol homeostasis. Science 232:34–47
8. Cardona A, Pagani L, Antao T, Lawson DJ, Eichstaedt CA, Yngvadottir B, Shwe MT, Wee J, Romero IG, Raj S et al (2014) Genome-wide analysis of cold adaptation in indigenous Siberian populations. PLoS One 9:e98076
9. Chasman DI, Giulianini F, MacFadyen J, Barratt BJ, Nyberg F, Ridker PM (2012) Genetic determinants of statin-induced low-density lipoprotein cholesterol reduction: the justification for the use of statins in prevention: an intervention trial evaluating rosuvastatin (Jupiter) trial. Circ Cardiovasc Genet 5:257–264
10. Cheng D, Huang R, Lanham IS, Cathcart HM, Howard M, Corder EH, Poduslo SE (2005) Functional interaction between APOE4 and LDL receptor isoforms in Alzheimer’s disease. J Med Genet 42:129–131
11. Cross DS, Ivacic LC, Stefanski EL, McCarty CA (2010) Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project. BMC Genet 11:51
12. Dammerman M, Breslow JL (1995) Genetic basis of lipoprotein disorders. Circulation 91:505–512
13. Davis HR Jr, Lowe RS, Neff DR (2011) Effects of ezetimibe on atherosclerosis in preclinical models. Atherosclerosis 215:266–278
14. Di Lello FA, Caruz A, Rallon NI, Rivero-Juarez A, Neukam K, Barreiro P, Camacho A, Garcia-Rey S, Rivero A, Soriano V et al (2013) Effects of the genetic pattern defined by low-density lipoprotein receptor and IL28B genotypes on the outcome of hepatitis C virus infection. Eur J Clin Microbiol Infect Dis 32:1427–1435
15. Fouchier SW, Kastelein JJ, Defesche JC (2005) Update of the molecular basis of familial hypercholesterolemia in The Netherlands. Hum Mutat 26:550–556
16. Gao F, Ihn HE, Medina MW, Krauss RM (2013) A common polymorphism in the LDL receptor gene has multiple effects on LDL receptor function. Hum Mol Genet 22:1424–1431
17. Go GW, Mani A (2012) Low-density lipoprotein receptor (LDLR) family orchestrates cholesterol homeostasis. Yale J Biol Med 85:19–28
18. Guenard F, Houde A, Bouchard L, Tchernof A, Deshaies Y, Biron S, Lescelleur O, Biertho L, Marceau S, Perusse L et al (2012) Association of LIPA gene polymorphisms with obesity-related metabolic complications among severely obese patients. Obes (Silver Spring) 20:2075–2082
19. Hobbs HH, Brown MS, Goldstein JL (1992) Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum Mutat 1:445–466
20. Holla OL, Nakken S, Mattingsdal M, Ranheim T, Berge KE, Defesche JC, Leren TP (2009) Effects of intronic mutations in the LDLR gene on pre-mRNA splicing: comparison of wet-lab and bioinformatics analyses. Mol Genet Metab 96:245–252
21. Humphries S, Coviello DA, Masturzo P, Balestreri R, Orecchini G, Bertolini S (1991) Variation in the low density lipoprotein receptor gene is associated with differences in plasma low density lipoprotein cholesterol levels in young and old normal individuals from Italy. Arterioscler Thromb 11:509–516
22. Ishibashi S, Brown MS, Goldstein JL, Gerard RD, Hammer RE, Herz J (1993) Hypercholesterolemia in low density lipoprotein receptor knockout mice and its reversal by adenovirus-mediated gene delivery. J Clin Invest 92:883–893
23. Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS et al (2008) Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 40:189–197
24. Klausen IC, Hansen PS, Gerdes LU, Rudiger N, Gregersen N, Faergeman O (1993) A PvuII polymorphism of the low density lipoprotein receptor gene is not associated with plasma concentrations of low density lipoproteins including LP(a). Hum Genet 91:193–195
25. Leren TP (2014) Sorting an LDL receptor with bound PCSK9 to intracellular degradation. Atherosclerosis 237:76–81
26. Linsel-Nitschke P, Gotz A, Erdmann J, Braenne I, Braund P, Hengstenberg C, Stark K, Fischer M, Schreiber S, El Mokhtari NE et al (2008) Lifelong reduction of LDL-cholesterol related to a common variant in the LDL-receptor gene decreases the risk of coronary artery disease—a mendelian randomisation study. PLoS One 3:e2986
27. Mahley RW, Rall SC Jr (2000) Apolipoprotein E: far more than a lipid transport protein. Annu Rev Genomics Hum Genet 1:507–537
28. Martinelli N, Girelli D, Lunghi B, Pinotti M, Marchetti G, Malerba G, Pignatti PF, Corrocher R, Olivieri O, Bernardi F (2010) Polymorphisms at LDLR locus may be associated with coronary artery disease through modulation of coagulation factor VIII activity and independently from lipid profile. Blood 116:5688–5697
29. Miljkovic I, Yerges-Armstrong LM, Kuller LH, Kuipers AL, Wang X, Kammerer CM, Nestlerode CS, Bunker CH, Patrick AL, Wheeler VW et al (2010) Association analysis of 33 lipoprotein candidate genes in multi-generational families of African ancestry. J Lipid Res 51:1823–1831
30. Pineda JA, Caruz A, Di Lello FA, Camacho A, Mesa P, Neukam K, Rivero-juarez A, Macias J, Gomez-Mateos J, Rivero A (2011) Low-density lipoprotein receptor genotyping enhances the predictive value of IL28B genotype in HIV/hepatitis C virus-coinfected patients. Aids 25:1415–1420
31. Pullinger CR, Kane JP, Malloy MJ (2003) Primary hypercholesterolemia: genetic causes and treatment of five monogenic disorders. Expert Rev Cardiovasc Ther 1:107–119
32. Sanna S, Li B, Mulas A, Sidore C, Kang HM, Jackson AU, Piras MG, Usala G, Maninchedda G, Sassu A et al (2011) Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet 7:e1002198
33. Schaefer JR, Kurt B, Sattler A, Klaus G, Soufi M (2012) Pharmacogenetic aspects in familial hypercholesterolemia with the special focus on FHMarburg (FH p. W556R). Clin Res Cardiol Suppl 7:2–6
34. Seidelmann SB, De Luca C, Leibel RL, Breslow JL, Tall AR, Welch CL (2005) Quantitative trait locus mapping of genetic modifiers of metabolic syndrome and atherosclerosis in low-density lipoprotein receptor-deficient mice: identification of a locus for metabolic syndrome and increased atherosclerosis on chromosome 4. Arterioscler Thromb Vasc Biol 25:204–210
35. Skropeta D, Settasatian C, McMahon MR, Shearston K, Caiazza D, McGrath KC, Jin W, Rader DJ, Barter PJ, Rye KA (2007) N-Glycosylation regulates endothelial lipase-mediated phospholipid hydrolysis in apoE- and apoA-I-containing high density lipoproteins. J Lipid Res 48:2047–2057
36. Slimani A, Jelassi A, Jguirim I, Najah M, Rebhi L, Omezzine A, Maatouk F, Hamda KB, Kacem M, Rabes JP et al (2012) Effect of mutations in LDLR and PCSK9 genes on phenotypic variability in Tunisian familial hypercholesterolemia patients. Atherosclerosis 222:158–166
37. Thompson D, Stram D, Goldgar D, Witte JS (2003) Haplotype tagging single nucleotide polymorphisms and association studies. Hum Hered 56:48–55
38. Tishkoff SA, Williams SM (2002) Genetic analysis of African populations: human evolution and complex disease. Nat Rev Genet 3:611–621
39. Wang B, Zhao H, Zhou L, Dai X, Wang D, Cao J, Niu W (2009) Association of genetic variation in apolipoprotein E and low density lipoprotein receptor with ischemic stroke in Northern Han Chinese. J Neurol Sci 276:118–122
40. Willer CJ, Sanna S, Jackson AU, Scuteri A, Bonnycastle LL, Clarke R, Heath SC, Timpson NJ, Najjar SS, Stringham HM et al (2008) Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 40:161–169
41. Xue C, Liu X, Gong Y, Zhao Y, Fu YX (2013) Significantly fewer protein functional changing variants for lipid metabolism in Africans than in Europeans. J Transl Med 11:67
42. Zhang L, Yuan F, Liu P, Fei L, Huang Y, Xu L, Hao L, Qiu X, Le Y, Yang X et al (2013) Association between PCSK9 and LDLR gene polymorphisms with coronary heart disease: case-control study and meta-analysis. Clin Biochem 46:727–732
43. Zhu H, Tucker HM, Grear KE, Simpson JF, Manning AK, Cupples LA, Estus S (2007) A common polymorphism decreases low-density lipoprotein receptor exon 12 splicing efficiency and associates with increased cholesterol. Hum Mol Genet 16:1765–1772
44. Zou F, Gopalraj RK, Lok J, Zhu H, Ling IF, Simpson JF, Tucker HM, Kelly JF, Younkin SG, Dickson DW et al (2008) Sex-dependent association of a common low-density lipoprotein receptor polymorphism with RNA splicing efficiency in the brain and Alzheimer’s disease. Hum Mol Genet 17:929–935