Patterns of Population Differentiation and Natural Selection on the Celiac Disease Background Risk Network

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Sams, Aaron ^a,b   Hawks, John ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Program on Infrastructure Policy   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELIAC DISEASE; DNA FLANKING REGION; EUROPE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GEOGRAPHIC DISTRIBUTION; HETEROZYGOSITY; HOLOCENE; HUMAN; HUMAN GENOME; NATURAL SELECTION; POPULATION DIFFERENTIATION; SINGLE NUCLEOTIDE POLYMORPHISM;

CELIAC DISEASE; EUROPE; EVOLUTION, MOLECULAR; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HUMANS; IMMUNITY; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; SELECTION, GENETIC;

EID: 84881139332     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070564     Document Type: Article

References (37)

1. Nistico L, (2006) Concordance, disease progression, and heritability of coeliac disease in Italian twins. Gut 55: 803-808 doi:10.1136/gut.2005.083964.
2. Sollid LM, (2000) Molecular basis of celiac disease. Annual Review of Immunology 18: 53-81.
3. Wolters VM, Wijmenga C, (2008) Genetic Background of Celiac Disease and Its Clinical Implications. The American Journal of Gastroenterology 103: 190-195 doi:-10.1111/j.1572-0241.2007.01471.x.
4. Kagnoff MF, (2007) Celiac disease: pathogenesis of a model immunogenetic disease. Journal of Clinical Investigation 117: 41-49 doi:10.1172/JCI30253.
5. Zhernakova A, Elbers CC, Ferwerda B, Romanos J, Trynka G, et al. (2010) Evolutionary and Functional Analysis of Celiac Risk Loci Reveals SH2B3 as a Protective Factor against Bacterial Infection. The American Journal of Human Genetics 86: 970-977 doi:10.1016/j.ajhg.2010.05.004.
6. Zhernakova A, Stahl EA, Trynka G, Raychaudhuri S, Festen EA, et al. (2011) Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci. PLoS Genetics 7: e1002004 doi:10.1371/journal.pgen.1002004.t004.
7. Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, et al. (2011) Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nature Genetics 43: 1193-1201.
8. Hunt KA, Zhernakova A, Turner G, Heap GAR, Franke L, et al. (2008) Newly identified genetic risk variants for celiac disease related to the immune response. Nature Genetics 40: 395-402 doi:10.1038/ng.102.
9. Dubois PCA, Trynka G, Franke L, Hunt KA, Romanos J, et al. (2010) Multiple common variants for celiac disease influencing immune gene expression. Nature Genetics 42: 295-302 doi:10.1038/ng.543.
10. Van Heel DA, Franke L, Hunt KA, Gwilliam R, Zhernakova A, et al. (2007) A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nature Genetics 39: 827-829 doi:10.1038/ng2058.
11. Larsen CS, (2006) The agricultural revolution as environmental catastrophe: Implications for health and lifestyle in the Holocene. Quaternary International 150: 12-20 doi:10.1016/j.quaint.2006.01.004.
12. Armelagos GJ, Harper KN, (2005) Genomics at the origins of agriculture, part two. Evol Anthropol 14: 109-121 doi:10.1002/evan.20048.
13. Hawks J, Wang ET, Cochran GM, Harpending HC, Moyzis RK, (2007) Recent acceleration of human adaptive evolution. Proceedings of the National Academy of Sciences 104: 20753-20758 doi:10.1073/pnas.0707650104.
14. Barker J, Liu E, (2008) Celiac Disease: Pathophysiology, Clinical Manifestations, and Associated Autoimmune Conditions. Advances in pediatrics 55: 349-365 doi:10.1016/j.yapd.2008.07.001.
15. Soni S, Badawy S (2010) Celiac disease and its effect on human reproduction. The Journal of Reproductive Medicine 55.
16. Gasbarrini G, Rickards O, Martínez-Labarga C, (2012) Origin of celiac disease: How old are predisposing haplotypes? World Journal of Gastroenterology 18: 5300-5304.
17. Albrechtsen A, Moltke I, Nielsen R, (2010) Natural Selection and the Distribution of Identity-by-Descent in the Human Genome. Genetics 186: 295-308 doi:10.1534/genetics.110.113977.
18. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837 doi:10.1038/nature01140.
19. Voight BF, Kudaravalli S, Wen X, Pritchard JK, (2006) A map of recent positive selection in the human genome. Plos Biol 4: e72 doi:10.1371/journal.pbio.0040072.st004.
20. Hancock AM, Alkorta-Aranburu G, Witonsky DB, Di Rienzo A, (2010) Adaptations to new environments in humans: the role of subtle allele frequency shifts. Philosophical Transactions of the Royal Society B: Biological Sciences 365: 2459-2468 doi:10.1098/rstb.2010.0032.
21. Barreiro LB, Quintana-Murci LIS, (2010) From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet 11: 17-30 doi:10.1038/nrg2698.
22. Abadie V, Sollid LM, Barreiro LB, Jabri B, (2011) Integration of Genetic and Immunological Insights into a Model of Celiac Disease Pathogenesis. Annual Review of Immunology 29: 493-525 doi:10.1146/annurev-immunol-040210-092915.
23. Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, et al. (2009) A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nature Genetics 41: 1182-1190.
24. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, et al. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Comms 3: 698 doi:10.1038/ncomms1701.
25. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li J, et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research 19(5): 826-837.
26. Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, et al. (2011) Pervasive sharing of genetic effects in autoimmune disease. PLoS Genetics 7(8): e1002254.
27. Skoglund P, Malmström H, Raghavan M, Storå J, Hall P, et al. (2012) Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science 336: 466-469 doi:10.1126/science.1218389.
28. Fu Q, Rudan P, Pääbo S, Krause J, (2012) Complete Mitochondrial Genomes Reveal Neolithic Expansion into Europe. PLoS ONE 7: e32473.
29. Sánchez-Quinto F, Schroeder H, Ramirez O, Avila-Arcos MC, Pybus M, et al. (2012) Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Current Biology 22: R631-R633 doi:10.1016/j.cub.2012.06.005.
30. Durbin RM, Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073 doi:10.1038/nature09534.
31. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America 106: 9362-9367.
32. Akey JM, (2002) Interrogating a High-Density SNP Map for Signatures of Natural Selection. Genome Research 12: 1805-1814 doi:10.1101/gr.631202.
33. Pagani L, Ayub Q, Macarthur DG, Xue Y, Baillie JK, et al. (2011) High altitude adaptation in Daghestani populations from the Caucasus. Hum Genet 131: 423-433 doi:10.1007/s00439-011-1084-8.
34. Yu F, Keinan A, Chen H, Ferland RJ, Hill RS, et al. (2009) Detecting natural selection by empirical comparison to random regions of the genome. Human Molecular Genetics 18: 4853-4867 doi:10.1093/hmg/ddp457.
35. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science 328(5979): 710-722.
36. Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.
37. Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, et al. (2012) Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 150(3): 457-469.