Haplotype structure and positive selection at TLR1

European Journal of Human Genetics

Volumn 22, Issue 4, 2014, Pages 551-557

  Heffelfinger, Christopher ^a,b   Pakstis, Andrew J ^a   Speed, William C ^a   Clark, Allison P ^a   Haigh, Eva ^a   Fang, Rixun ^c   Furtado, Mahohar R ^c,d   Kidd, Kenneth K ^a   Snyder, Michael P ^e  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

^c Life Technologies Corporation   (United States)

^d Biology for Global Good   (United States)

^e STANFORD UNIVERSITY   (United States)

Author keywords

Evolution; Haplotypes; Selection; SNPs; TLR1

Indexed keywords

LIGAND; LIPOPROTEIN; RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B; TOLL LIKE RECEPTOR 1; TOLL LIKE RECEPTOR 2;

ALLELE; ARTICLE; GENE FREQUENCY; GENETIC RISK; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN CELL; IMMUNOSTIMULATION; INNATE IMMUNITY; LEPROSY; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RECEPTOR GENE; RISK REDUCTION; SEPSIS; TLR1 GENE; TUBERCULOSIS;

ALLELES; GENETIC LOCI; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MUTATION, MISSENSE; NF-KAPPA B; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, CELL SURFACE; SELECTION, GENETIC; TOLL-LIKE RECEPTOR 1;

EID: 84896545839     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2013.194     Document Type: Article

References (52)

1. Takeda K, Kaisho T, Akira S: Toll-like receptors. Annu Rev Immunol 2003; 21: 335-376
2. Medzhitov R: Toll-like receptors and innate immunity. Nat Rev Immunol 2001; 1: 135-145
3. Iwasaki A, Medzhitov R: Toll-like receptor control of the adaptive immune responses. Nat Immunol 2004; 5: 987-995
4. Lemaitre B, Nicolas E, Michaut L, Reichhart JM, Hoffmann JA: The dorsoventral regulatory gene cassette spatzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell 1996; 86: 973-983
5. Medzhitov R, Preston-Hurlburt P, Janeway CA Jr: A human homologue of the Drosophila Toll protein signals activation of adaptive immunity. Nature 1997; 388: 394-397
6. Yoshimura A, Lien E, Ingalls RR, Tuomanen E, Dziarski R, Golenbock D: Cutting edge: Recognition of Gram-positive bacterial cell wall components by the innate immune system occurs via Toll-like receptor 2. J Immunol 1999; 163: 1-5
7. Wlasiuk G, Nachman MW: Adaptation and constraint at Toll-like receptors in primates. Mol Biol Evol 2010; 27: 2172-2186
8. Enard D, Depaulis F, Roest Crollius H: Human and non-human primate genomes share hotspots of positive selection. PLoS Genet 2010; 6: E1000840
9. Huang Y, Temperley ND, Ren L, Smith J, Li N, Burt DW: Molecular evolution of the vertebrate TLR1 gene family - A complex history of gene duplication, gene conversion, positive selection and co-evolution. BMC Evol Biol 2011; 11: 149
10. Hawn TR, Misch EA, Dunstan SJ et al: A common human TLR1 polymorphism regulates the innate immune response to lipopeptides. Eur J Immunol 2007; 37: 2280-2289
11. Ranoa DR, Kelley SL, Tapping RI: Human lipopolysaccharide-binding protein (LBP) and CD14 independently deliver triacylated lipoproteins to Toll-like receptor 1 (TLR1) and TLR2 and enhance formation of the ternary signaling complex. J Biol Chem2013; 288: 9729-9741
12. Takeuchi O, Sato S, Horiuchi T et al: Cutting edge: Role of Toll-like receptor 1 in mediating immune response to microbial lipoproteins. J Immunol 2002; 169: 10-14
13. Uciechowski P, Imhoff H, Lange C et al: Susceptibility to tuberculosis is associated with TLR1 polymorphisms resulting in a lack of TLR1 cell surface expression. J Leukoc Biol 2011; 90: 377-388
14. Krutzik SR, Ochoa MT, Sieling PA et al: Activation and regulation of Toll-like receptors 2 and 1 in human leprosy. Nat Med 2003; 9: 525-532
15. Oosting M, Ter Hofstede H, Sturm P et al: TLR1/TLR2 heterodimers play an important role in the recognition of Borrelia spirochetes. PLoS One 2011; 6: E25998
16. Netea MG, Ferwerda G, van der Graaf CA, Van der Meer JW, Kullberg BJ: Recognition of fungal pathogens by toll-like receptors. Curr Pharm Des 2006; 12: 4195-4201
17. Bellocchio S, Montagnoli C, Bozza S et al: The contribution of the Toll-like/IL-1 receptor superfamily to innate and adaptive immunity to fungal pathogens in vivo. J Immunol 2004; 172: 3059-3069
18. Kesh S, Mensah NY, Peterlongo P et al: TLR1 and TLR6 polymorphisms are associated with susceptibility to invasive aspergillosis after allogeneic stem cell transplantation. Ann N Y Acad Sci 2005; 1062: 95-103
19. Wurfel MM, Gordon AC, Holden TD et al: Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis. Am J Respir Crit Care Med 2008; 178: 710-720
20. Pino-Yanes M, Corrales A, Casula M et al: Common variants of TLR1 associate with organ dysfunction and sustained pro-inflammatory responses during sepsis. PLoS One 2010; 5: E13759
21. Misch EA, Macdonald M, Ranjit C et al: Human TLR1 deficiency is associated with impaired mycobacterial signaling and protection from leprosy reversal reaction. PLoS Negl Trop Dis 2008; 2: E231
22. Schuring RP, Hamann L, Faber WR et al: Polymorphism N248S in the human Toll-like receptor 1 gene is related to leprosy and leprosy reactions. J Infect Dis 2009; 199: 1816-1819
23. Stevens VL, Hsing AW, Talbot JT et al: Genetic variation in the toll-like receptor gene cluster (TLR10-TLR1-TLR6) and prostate cancer risk. Int J Cancer 2008; 123: 2644-2650
24. Taylor BD, Darville T, Ferrell RE, Kammerer CM, Ness RB, Haggerty CL: Variants in toll-like receptor 1 and 4 genes are associated with Chlamydia trachomatis among women with pelvic inflammatory disease. J Infect Dis 2012; 205: 603-609
25. Wong SH, Gochhait S, Malhotra D et al: Leprosy and the adaptation of human toll-like receptor 1. PLoS Pathog 2010; 6: E1000979
26. Hart BE, Tapping RI: Genetic diversity of Toll-like receptors and immunity to M. leprae infection. J Trop Med 2012; 2012: 415057
27. Ma X, Liu Y, Gowen BB, Graviss EA, Clark AG, Musser JM: Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to tuberculosis disease. PLoS One 2007; 2: E1318
28. Johnson CM, Lyle EA, Omueti KO et al: Cutting edge: A common polymorphism impairs cell surface trafficking and functional responses of TLR1 but protects against leprosy. J Immunol 2007; 178: 7520-7524
29. Barreiro LB, Ben-Ali M, Quach H et al: Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet 2009; 5: E1000562
30. Omueti KO, Mazur DJ, Thompson KS, Lyle EA, Tapping RI: The polymorphism P315L of human toll-like receptor 1 impairs innate immune sensing of microbial cell wall components. J Immunol 2007; 178: 6387-6394
31. Hamann L, Bedu-Addo G, Eggelte TA, Schumann RR, Mockenhaupt FP: The toll-like receptor 1 variant S248N influences placental malaria. Infect Genet Evol 2010; 10: 785-789
32. Mikacenic C, Reiner AP, Holden TD, Nickerson DA, Wurfel MM: Variation in the TLR10/TLR1/TLR6 locus is the major genetic determinant of interindividual difference in TLR1/2-mediated responses. Genes Immun 2013; 14: 52-57
33. Sabeti PC, Reich DE, Higgins JM et al: Detecting recent positive selection in the human genome from haplotype structure. Nature 2002; 419: 832-837
34. Voight BF, Kudaravalli S, Wen X, Pritchard JK: A map of recent positive selection in the human genome. PLoS Biol 2006; 4: E72
35. Wright S: Genetical structure of populations. Nature 1950; 166: 247-249
36. Ng PC, Henikoff S: SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003; 31: 3812-3814
37. Grantham R: Amino acid difference formula to help explain protein evolution. Science 1974; 185: 862-864
38. Siepel A, Bejerano G, Pedersen JS et al: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005; 15: 1034-1050
39. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68: 978-989
40. Hawley ME, Kidd KK: HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 1995; 86: 409-411
41. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR: MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010; 34: 816-834
42. Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995; 29: 311-322
43. Gu S, Pakstis AJ, Kidd KK: HAPLOT: A graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations. Bioinformatics 2005; 21: 3938-3939
44. Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK: ALFRED: An allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Res 2000; 28: 361-363
45. Hudson RR: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002; 18: 337-338
46. Jensen-Seaman MI, Furey TS, Payseur BA et al: Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 2004; 14: 528-538
47. Kidd KK, Pakstis AJ, Speed WC, Kidd JR: Understanding human DNA sequence variation. J Hered 2004; 95: 406-420
48. Kent WJ, Sugnet CW, Furey TS et al: The human genome browser at UCSC. Genome Res 2002; 12: 996-1006
49. Grossman SR, Shlyakhter I, Karlsson EK et al: A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 2010; 327: 883-886
50. Lee JS, Park HK, Suh JS et al: Toll-like receptor 1 gene polymorphisms in childhood IgA nephropathy: A case-control study in the Korean population. Int J Immunogenet 2011; 38: 133-138
51. The International HapMap Project Consortiuum. The International HapMap Project. Nature 2003; 426: 789-796
52. Kimura M: Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 1977; 267: 275-276