Sequence variation within the KIV-2 copy number polymorphism of the human LPA gene in African, Asian, and European populations

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Noureen, Asma ^a   Fresser, Friedrich ^a   Utermann, Gerd ^a   Schmidt, Konrad ^a,b,c  

^a Division of Genetic Epidemiology Department of Medical Genetics Molecular and Clinical Pharmacology ^*  (Austria)

^b ALBERT SCHWEITZER HOSPITAL   (Gabon)

^c UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; LIPOPROTEIN; LIPOPROTEIN A;

AFRICAN; ALLELE; AMPLICON; ARTICLE; ASIAN; COPY NUMBER VARIATION; DNA FLANKING REGION; EUROPEAN; GENE; GENE AMPLIFICATION; GENE FREQUENCY; GENE SEQUENCE; GENETIC ASSOCIATION; HUMAN; KRINGLE DOMAIN; LPA GENE; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; POPULATION GENETICS; PULSED FIELD GEL ELECTROPHORESIS; ASIAN CONTINENTAL ANCESTRY GROUP; BLACK PERSON; CAUCASIAN; ETHNIC GROUP; EXON; FEMALE; GENETIC VARIATION; GENETICS; INTRON; MALE; NUCLEOTIDE SEQUENCE;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; BASE SEQUENCE; CLONING, MOLECULAR; DNA COPY NUMBER VARIATIONS; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; EXONS; FEMALE; GENE FREQUENCY; GENETIC VARIATION; HUMANS; INTRONS; KRINGLES; LIPOPROTEIN(A); MALE;

EID: 84926320277     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121582     Document Type: Article

References (41)

1. Kronenberg F, Utermann G. Lipoprotein(a): resurrected by genetics. J Intern Med. 2013; 273: 6-30. doi: 10.1111/j.1365-2796.2012.02592.x PMID: 22998429
2. McLean JW, Tomlinson JE, Kuang WJ, Eaton DL, Chen EY, Fless GM, et al. cDNA sequence of human apolipoprotein(a) is homologous to plasminogen. Nature. 1987; 330: 132-137. PMID: 3670400
3. White AL, Guerra B, Lanford RE. Influence of allelic variation on apolipoprotein(a) folding in the endoplasmic reticulum. J Biol Chem. 1997; 272: 5048-5055. PMID: 9030568
4. Brunner C, Lobentanz EM, Petho-Schramm A, Ernst A, Kang C, Dieplinger H, et al. The number of identical kringle IV repeats in apolipoprotein(a) affects its processing and secretion by HepG2 cells. J Biol Chem. 1996; 271: 32403-32410. PMID: 8943305
5. Sandholzer C, Hallman DM, Saha N, Sigurdsson G, Lackner C, Császár A, et al. Effects of the apolipoprotein(a) size polymorphism on the lipoprotein(a) concentration in 7 ethnic groups. Hum Genet. 1991; 86: 607-614. PMID: 2026424
6. Rader DJ, Cain W, Zech LA, Usher D, Brewer HB Jr. Variation in lipoprotein(a) concentrations among individuals with the same apolipoprotein (a) isoform is determined by the rate of lipoprotein(a) production. J Clin Invest. 1993; 91: 443-447. PMID: 8432853
7. Gaw A, Brown EA, Ford I. Impact of apo(a) length polymorphism and the control of plasma Lp(a) concentrations: evidence for a threshold effect. Arterioscler Thromb Vasc Biol. 1998; 18: 1870-1876. PMID: 9848878
8. Lackner C, Boerwinkle E, Leffert CC, Rahmig T, Hobbs HH. Molecular basis of apolipoprotein (a) isoform size heterogeneity as revealed by pulsed-field gel electrophoresis. J Clin Invest. 1991; 87: 2153-2161. PMID: 1645755
9. Ogorelkova M, Gruber A, Utermann G. Molecular basis of congenital lp(a) deficiency: a frequent apo(a) 'null' mutation in caucasians. Hum Mol Genet. 1999; 8: 2087-2096. PMID: 10484779
10. Parson W, Kraft HG, Niederstatter H, Lingenhel AW, Kochl S, Fresser F, et al. A common nonsense mutation in the repetitive Kringle IV-2 domain of human apolipoprotein(a) results in a truncated protein and low plasma Lp(a). Hum Mutat. 2004; 24: 474-480. PMID: 15523644
11. Zysow BR, Lindahl GE, Wade DP, Knight BL, Lawn RM. C/T polymorphism in the 5' untranslated region of the apolipoprotein(a) gene introduces an upstream ATG and reduces in vitro translation. Arterioscler Thromb Vasc Biol. 1995; 15: 58-64. PMID: 7749816
12. Rosby O, Alestrom P, Berg K. High-degree sequence conservation in LPA kringle IV-type 2 exons and introns. Clin Genet. 1997; 52: 293-302. PMID: 9520119
13. Rosby O, Alestrom P, Berg K. Sequence conservation in kringle IV-type 2 repeats of the LPA gene. Atherosclerosis. 2000; 148: 353-364. PMID: 10657572
14. Kronenberg F, Lobentanz EM, Konig P, Utermann G, Dieplinger H. Effect of sample storage on the measurement of lipoprotein[a], apolipoproteins B and A-IV, total and high density lipoprotein cholesterol and triglycerides. J Lipid Res. 1994; 35: 1318-1328. PMID: 7964193
15. Kronenberg F, Kuen E, Ritz E, Junker R, Konig P, Kraatz G, et al. Lipoprotein(a) serum concentrations and apolipoprotein(a) phenotypes in mild and moderate renal failure. J Am Soc Nephrol. 2000; 11: 105-115. PMID: 10616846
16. Scholz M, Kraft HG, Lingenhel A, Delport R, Vorster EH, Bickeböller H, et al. Genetic control of lipoprotein(a) concentrations is different in Africans and Caucasians. Eur J Hum Genet. 1999; 7: 169-178. PMID: 10196700
17. Schmidt K, Kraft HG, Parson W, Utermann G. Genetics of the Lp(a)/apo(a) system in an autochthonous Black African population from the Gabon. Eur J Hum Genet. 2006; 14: 190-201. PMID: 16267501
18. Kraft HG, Kochl S, Menzel HJ, Sandholzer C, Utermann G. The apolipoprotein (a) gene: a transcribed hypervariable locus controlling plasma lipoprotein (a) concentration. Hum Genet. 1992; 90: 220-230. PMID: 1336760
19. Erdel M, Hubalek M, Lingenhel A, Kofler K, Duba HC, Utermann G. Counting the repetitive kringle-IV repeats in the gene encoding human apolipoprotein(a) by fibre-FISH. Nat Genet. 1999; 21: 357-358. PMID: 10192381
20. Li Y, Mitaxov V, Waksman G. Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc Natl Acad Sci U S A. 1999; 96: 9491-9496. PMID: 10449720
21. Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT. Inferring relative proportions of DNA variants from sequencing electropherograms. Bioinformatics. 2009; 25: 3244-3250. doi: 10.1093/bioinformatics/btp583 PMID: 19819885
22. Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics. 2012; 28: 2711-2718. doi: 10.1093/bioinformatics/bts535 PMID: 22942022
23. Kirby A, Gnirke A, Jaffe DB, Baresova V, Pochet N, Blumenstiel B, et al. Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet. 2013; 45: 299-303. doi: 10.1038/ng.2543 PMID: 23396133
24. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Clark AG, et al. A map of human genome variation from population-scale sequencing. Nature. 2010; 467: 1061-1073. doi: 10.1038/nature09534 PMID: 20981092
25. Crawford DC, Peng Z, Cheng JF, Boffelli D, Ahearn M, Nguyen D, et al. LPA and PLG Sequence Variation and Kringle IV-2 Copy Number in Two Populations. Hum Hered. 2008; 66: 199-209. doi: 10.1159/000143403 PMID: 18612205
26. Cline J, Braman JC, Hogrefe HH. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 1996; 24: 3546-3551. PMID: 8836181
27. Kraft HG, Lingenhel A, Pang RW, Delport R, Trommsdorff M, Vermaak H, et al. Frequency distributions of apolipoprotein(a) kringle IV repeat alleles and their effects on lipoprotein(a) levels in Caucasian, Asian, and African populations: the distribution of null alleles is non-random. Eur J Hum Genet. 1996; 4: 74-87. PMID: 8744025
28. Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, et al. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011; %19; 108: 11983-11988. doi: 10.1073/pnas.1019276108 PMID: 21730125
29. Chen JM, Cooper DN, Chuzhanova N, Ferec C, Patrinos GP. Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet. 2007; 8: 762-775. PMID: 17846636
30. Fawcett JA, Innan H. The role of gene conversion in preserving rearrangement hotspots in the human genome. Trends Genet. 2013; 29: 561-568. doi: 10.1016/j.tig.2013.07.002 PMID: 23953668
31. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A. 2005; 102: 15942-15947. PMID: 16243969
32. Keinan A, Mullikin JC, Patterson N, Reich D. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet. 2007; 39: 1251-1255. PMID: 17828266
33. Lanktree MB, Anand SS, Yusuf S, Hegele RA. Comprehensive analysis of genomic variation in the LPA locus and its relationship to plasma lipoprotein(a) in South Asians, Chinese, and European Caucasians. Circ Cardiovasc Genet. 2010; 3: 39-46. doi: 10.1161/CIRCGENETICS.109.907642 PMID: 20160194
34. Veeramah KR, Wegmann D, Woerner A, Mendez FL, Watkins JC, Destro-Bisol G, et al. An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data. Mol Biol Evol. 2012; 29: 617-630. doi: 10.1093/molbev/msr212 PMID: 21890477
35. Gaw A, Boerwinkle E, Cohen JC, Hobbs HH. Comparative analysis of the apo(a) gene, apo(a) glycoprotein, and plasma concentrations of Lp(a) in three ethnic groups. Evidence for no common "null" allele at the apo(a) locus. J Clin Invest. 1994; 93: 2526-2534. PMID: 8200989
36. Lavebratt C, Sengul S, Jansson M, Schalling M. Pyrosequencing-based SNP allele frequency estimation in DNA pools. Hum Mutat. 2004; 23: 92-97. PMID: 14695537
37. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009; 19: 1586-1592. doi: 10.1101/gr.092981.109 PMID: 19657104
38. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 2009; 19: 1527-1541. doi: 10.1101/gr.091868.109 PMID: 19546169
39. Ogorelkova M, Kraft HG, Ehnholm C, Utermann G. Single nucleotide polymorphisms in exons of the apo(a) kringles IV types 6 to 10 domain affect Lp(a) plasma concentrations and have different patterns in Africans and Caucasians. Hum Mol Genet. 2001; 10: 815-824. PMID: 11285247
40. Deo RC, Wilson JG, Xing C, Lawson K, Kao WH, Reich D, et al. Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. PLoS One. 2011; 6: e14581. doi: 10.1371/journal.pone.0014581 PMID: 21283670
41. Dumitrescu L, Glenn K, Brown-Gentry K, Shephard C, Wong M, Rieder MJ, et al. Variation in LPA is associated with Lp(a) levels in three populations from the Third National Health and Nutrition Examination Survey. PLoS One. 2011; 6: e16604. doi: 10.1371/journal.pone.0016604 PMID: 21305047