Haplotype differences for copy number variants in the 22q11.23 region among human populations: A pigmentation-based model for selective pressure

European Journal of Human Genetics

Volumn 23, Issue 1, 2015, Pages 116-123

  Polimanti, Renato ^a   Piacentini, Sara ^a   Iorio, Andrea ^b   De Angelis, Flavio ^a   Kozlov, Andrey ^c   Novelletto, Andrea ^a   Fuciarelli, Maria ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b SAN GIOVANNI CALIBITA FATEBENEFRATELLI HOSPITAL   (Italy)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

MACROPHAGE MIGRATION INHIBITION FACTOR; ISOMERASE; MIF PROTEIN, HUMAN;

ADULT; AFRICA; ARTICLE; ASIA; CHROMOSOME 22Q; COPY NUMBER VARIATION; ETHNIC DIFFERENCE; ETHNIC GROUP; EUROPE; FEMALE; GENE DOSAGE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; MELANOGENESIS; POPULATION GENETICS; PRIORITY JOURNAL; SKIN COLOR; SKIN PIGMENTATION; ULTRAVIOLET A RADIATION; ULTRAVIOLET B RADIATION; ALLELE; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMISTRY; CHROMOSOME 22; ENVIRONMENT; GENETIC ASSOCIATION STUDY; GENETIC SELECTION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; MOLECULAR GENETICS; MULTIGENE FAMILY; RISK FACTOR; SEQUENCE ALIGNMENT;

ALLELES; AMINO ACID SEQUENCE; CHROMOSOMES, HUMAN, PAIR 22; DNA COPY NUMBER VARIATIONS; ENVIRONMENT; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPES; HUMANS; INTRAMOLECULAR OXIDOREDUCTASES; MACROPHAGE MIGRATION-INHIBITORY FACTORS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; RISK FACTORS; SELECTION, GENETIC; SEQUENCE ALIGNMENT; SKIN PIGMENTATION;

EID: 84927060820     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2014.47     Document Type: Article

References (45)

1. Girirajan S, Campbell CD, Eichler EE: Human copy number variation and complex genetic disease. Annu Rev Genet 2011; 45: 203-226.
2. Zhang F, Gu W, Hurles ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 2009; 10: 451-481.
3. Pietilainen OP, Rehnstrom K, Jakkula E et al: Phenotype mining in CNV carriers from a population cohort. Hum Mol Genet 2011; 20: 2686-2695.
4. McCarroll SA, Altshuler DM: Copy-number variation and association studies of human disease. Nat Genet 2007; 39: S37-S42.
5. Campbell CD, Sampas N, Tsalenko A et al: Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet 2011; 88: 317-332.
6. Iskow RC, Gokcumen O, Lee C: Exploring the role of copy number variants in human adaptation. Trends Genet 2012; 28: 245-257.
7. Zhao Y, Marotta M, Eichler EE, Eng C, Tanaka H: Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes. PLoS Genet 2009; 5: e1000472.
8. Coggan M, Whitbread L, Whittington A, Board P: Structure and organization of the human theta-class glutathione S-transferase and D-dopachrome tautomerase gene complex. Biochem J 1998; 334:Pt 3 617-623.
9. Polimanti R, Piacentini S, Lazzarin N, Re MA, Manfellotto D, Fuciarelli M: Glutathione S-transferase variants as risk factor for essential hypertension in Italian patients. Mol Cell Biochem 2011; 357: 227-233.
10. Thorn CF, Ji Y, Weinshilboum RM, Altman RB, Klein TE: PharmGKB summary: very important pharmacogene information for GSTT1. Pharmacogenet Genomics 2012; 22: 646-651.
11. Savaskan NE, Fingerle-Rowson G, Buchfelder M, Eyupoglu IY: Brain miffed by macrophage migration inhibitory factor. Int J Cell Biol 2012; 2012: 139573.
12. Tobin DJ: Biochemistry of human skin-our brain on the outside. Chem Soc Rev 2005; 35: 52-67.
13. Merk M, Zierow S, Leng L et al: The D-dopachrome tautomerase (DDT) gene product is a cytokine and functional homolog of macrophage migration inhibitory factor (MIF). Proc Natl Acad Sci USA 2011; 108: E577-E585.
14. Merk M, Mitchell RA, Endres S, Bucala R: D-dopachrome tautomerase (D-DT or MIF-2): doubling the MIF cytokine family. Cytokine 2012; 59: 10-17.
15. Bozza M, Kolakowski Jr LF, Jenkins NA et al: Structural characterization and chromosomal location of the mouse macrophage migration inhibitory factor gene and pseudogenes. Genomics 1995; 27: 412-419.
16. Du J, Xie X, Chen H et al: Macrophage migration inhibitory factor (MIF) in chinese amphioxus as a molecular marker of immune evolution during the transition of invertebrate/vertebrate. Dev Comp Immunol 2004; 28: 961-971.
17. Parisi MG, Toubiana M, Mangano V, Parrinello N, Cammarata M, Roch P: MIF from mussel: coding sequence, phylogeny, polymorphism, 3D model and regulation of expression. Dev Comp Immunol 2012; 36: 688-696.
18. De Stefano GF, Martinez-Labarga C, Casalotti R et al: Analysis of three RFLPs of the COL1A2 (Type I Collagen) in the Amhara and the Oromo of Ethiopia. Ann Hum Biol 2002; 29: 432-441.
19. Luca F, Bubba G, Basile M et al: Multiple advantageous amino acid variants in the NAT2 gene in human populations. PLoS One 2008; 3: e3136.
20. Polimanti R, Piacentini S, Porreca F, Fuciarelli M: Glutathione S-transferase omega class (GSTO) polymorphisms in a sample from Rome (Central Italy). Ann Hum Biol 2010; 37: 585-592.
21. Polimanti R, Piacentini S, De Angelis F, De Stefano GF, Fuciarelli M: Human GST loci as markers of evolutionary forces: GSTO1∗E155del and GSTO1∗E208K polymorphisms may be under natural selection induced by environmental arsenic. Dis Markers 2011; 31: 231-239.
22. International HapMap Consortium, Altshuler DM, Gibbs RA et al: Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467: 52-58.
23. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D et al: A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061-1073.
24. Piacentini S, Polimanti R, De Angelis F, Iorio A, Fuciarelli M: Phenotype versus genotype methods for copy number variant analysis of glutathione S-transferases M1. Ann Hum Genet 2013; 77: 409-415.
25. McCarroll SA, Kuruvilla FG, Korn JM et al: Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008; 40: 1166-1174.
26. Mills RE, Walter K, Stewart C et al: Mapping copy number variation by populationscale genome sequencing. Nature 2011; 470: 59-65.
27. Biasutti R: Le Razze e i Popoli Della Terra. 4. Edizione riveduta e aggiornata. Torino: Unione Tipografico-Editrice Torinese, 1967.
28. Barsh GS: What controls variation in human skin color? PLoS Biol 2003; 1: E27.
29. Jablonski NG, Chaplin G: Colloquium paper: human skin pigmentation as an adaptation to UV radiation. Proc Natl Acad Sci USA 2010; 107:Suppl 2 8962-8968.
30. Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005; 21: 263-265.
31. Excoffier L, Lischer HE: Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010; 10: 564-567.
32. Hofer T, Ray N, Wegmann D, Excoffier L: Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann Hum Genet 2009; 73: 95-108.
33. Sturm RA: Molecular genetics of human pigmentation diversity. Hum Mol Genet 2009; 18: R9-17.
34. Candille SI, Absher DM, Beleza S et al: Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four european populations. PLoS One 2012; 7: e48294.
35. Norton HL, Kittles RA, Parra E et al: Genetic evidence for the convergent evolution of light skin in Europeans and East Asians. Mol Biol Evol 2007; 24: 710-722.
36. 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 USA 2005; 102: 15942-15947.
37. Shriver MD, Mei R, Parra EJ et al: Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics 2005; 2: 81-89.
38. Lohmueller KE, Indap AR, Schmidt S et al: Proportionally more deleterious genetic variation in European than in African populations. Nature 2008; 451: 994-997.
39. Shimizu T, Abe R, Ohkawara A, Nishihira J: Ultraviolet B radiation upregulates the production of macrophage migration inhibitory factor (MIF) in human epidermal keratinocytes. J Invest Dermatol 1999; 112: 210-215.
40. Sonesson B, Rosengren E, Hansson AS, Hansson C: UVB-induced inflammation gives increased d-dopachrome tautomerase activity in blister fluid which correlates with macrophage migration inhibitory factor. Exp Dermatol 2003; 12: 278-282.
41. Watanabe H, Shimizu T, Nishihira J et al: Ultraviolet A-induced production of matrix metalloproteinase-1 is mediated by macrophage migration inhibitory factor (MIF) in human dermal fibroblasts. J Biol Chem 2004; 279: 1676-1683.
42. Shimizu T: Role of macrophage migration inhibitory factor (MIF) in the skin. J Dermatol Sci 2005; 37: 65-73.
43. Enomoto A, Yoshihisa Y, Yamakoshi T et al: UV-B radiation induces macrophage migration inhibitory factor-mediated melanogenesis through activation of proteaseactivated receptor-2 and stem cell factor in keratinocytes. Am J Pathol 2011; 178: 679-687.
44. O'Rourke DH, Raff JA: The human genetic history of the Americas: the final frontier. Curr Biol 2010; 20: R202-R207.
45. Jablonski NG: Skin coloration; in Muehlenbein MP (ed) Human Evolutionary Biology. Cambridge, UK: Cambridge University Press, 2010.