The effect of genomic inversions on estimation of population genetic parameters from SNP data

Genetics

Volumn 193, Issue 1, 2013, Pages 243-253

  Seich al Basatena, Nafisa Katrin ^a   Hoggart, Clive J ^a   Coin, Lachlan J ^a   O'Reilly, Paul F ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 8P; COMPUTER PROGRAM; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOMICS; HAPLOTYPE; HUMAN; INVERSION POLYMORPHISM; NONHUMAN; PHENOTYPE; POPULATION GENETIC PARAMETERS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; RISK FACTOR; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

GENETICS, POPULATION; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84871777927     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.145599     Document Type: Article

References (53)

1. Akey, J. M., 2009 Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Res. 19: 711-722.
2. Antonacci, F., J. M. Kidd, T. Marques-Bonet, M. Ventura, P. Siswara et al., 2009 Characterization of six human disease-associated inversion polymorphisms. Hum. Mol. Genet. 18: 2555-2566
3. Astle, W., and D. J. Balding, 2009 Population structure and cryptic relatedness in genetic association studies. Stat. Sci. 24: 451-471.
4. Bansal, V., A. Bashir, and V. Bafna, 2007 Evidence for large in-version polymorphisms in the human genome from HapMap data. Genome Res. 17: 219-230.
5. Boettger, L. M., R. E. Handsaker, M. C. Zody, and S. A. McCarroll, 2012 Structural haplotypes and recent evolution of the human 17q21.31 region. Nat. Genet. 44: 881-885.
6. Deng, L., Y. Zhang, J. Kang, T. Liu, H. Zhao et al., 2008 An un-usual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism. Hum. Mutat. 29: 1209-1216.
7. Frazer, K. A., D. G. Ballinger, D. R. Cox, D. A. Hinds, L. L. Stuve et al., 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
8. Hoggart, C. J., M. Chadeau-Hyam, T. G. Clark, R. Lampariello, J. C. Whittaker et al., 2007 Sequence-level population simulations over large genomic regions. Genetics 177: 1725-1731.
9. Hudson, R. R., 1983 Testing the constant-rate neutral allele model with protein sequence data. Evolution 37: 203-217
10. Jakkula, E., K. Rehnström, T. Varilo, O. P. H. Pietiläinen, T. Paunio et al., 2008 The Genome-wide patterns of variation expose significant substructure in a founder population. Am. J. Hum. Genet. 83: 787-794.
11. Jeffreys, A. J., L. Kauppi, and R. Neumann, 2001 Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29: 217-222.
12. Jolliffe, I., 2002 Principal Component Analysis. Springer-Verlag, New York.
13. Kelley, J. M., L. B. Hughes, R. Feng, N. Liu, M. A. Padilla et al., 2008 Evaluating linkage disequilibrium and recombination provides a haplotype-tagging SNP panel of the major histocompatibility complex in African Americans. Genes Immun. 9: 271-273.
14. Kidd, J. M., G. M. Cooper, W. F. Donahue, H. S. Hayden, N. Sampas et al., 2008 Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
15. Kimura, M., 1985 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge/London/New York.
16. Kong, A., G. Thorleifsson, D. F. Gudbjartsson, G. Masson, A. Sigurdsson et al., 2010 Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-1103.
17. Koolen, D. A., L. E. L. M. Vissers, R. Pfundt, N. de Leeuw, S. J. L. Knight et al., 2006 A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat. Genet. 38: 999-1001.
18. Lakich, D., H. H. Kazazian, S. E. Antonarakis, and J. Gitschier, 1993 Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nat. Genet. 5: 236-241.
19. Lencz, T., C. Lambert, P. DeRosse, K. E. Burdick, T. V. Morgan et al., 2007 Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc. Natl. Acad. Sci. USA 104: 19942-19947.
20. Li, Y., H. Zheng, R. Luo, H. Wu, H. Zhu et al., 2011 Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat. Biotechnol. 29: 723-730.
21. Marchini, J., B. Howie, S. Myers, G. McVean, and P. Donnelly, 2007 A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39: 906-913.
22. Matise, T. C., F. Chen, W. Chen, F. M. De La Vega, M. Hansen et al., 2007 A second-generation combined linkage physical map of the human genome. Genome Res. 17: 1783-1786.
23. McVean, G. A. T., S. R. Myers, S. Hunt, P. Deloukas, D. R. Bentley et al., 2004 The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584.
24. Munté, A., J. Rozas, M. Aguadé, and C. Segarra, 2005 Chromosomal inversion polymorphism leads to extensive genetic structure: a multilocus survey in Drosophila subobscura. Genetics 169: 1573-1581.
25. Myers, S., L. Bottolo, C. Freeman, G. McVean, and P. Donnelly, 2005 A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-324.
26. Navarro, A., E. Betrán, A. Barbadilla, and A. Ruiz, 1997 Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes. Genetics 146: 695-709.
27. Navarro, A., A. Barbadilla, and A. Ruiz, 2000 Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila. Genetics 155: 685-698.
28. Newton-Cheh, C., T. Johnson, V. Gateva, M. D. Tobin, M. Bochud et al., 2009 Genome-wide association study identifies eight loci associated with blood pressure. Nat. Genet. 41: 666-676.
29. Novembre, J., T. Johnson, K. Bryc, Z. Kutalik, A. R. Boyko et al., 2008 Genes mirror geography within Europe. Nature 456: 98-101.
30. O'Reilly, P. F., E. Birney, and D. J. Balding, 2008 Confounding between recombination and selection, and the Ped/Pop method for detecting selection. Genome Res. 18: 1304-1313.
31. O'Reilly, P. F., L. J. M. Coin, and C. J. Hoggart, 2010 invertFREGENE: software for simulating inversions in population genetic data. Bioinformatics 26: 838-840.
32. Osborne, L. R., M. Li, B. Pober, D. Chitayat, J. Bodurtha et al., 2001 A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nat. Genet. 29: 321-325.
33. Padhukasahasram, B., P. Marjoram, and M. Nordborg, 2004 Estimating the rate of gene conversion on human chromosome 21. Am. J. Hum. Genet. 75: 386-397.
34. Price, A. L., N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick et al., 2006 Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38: 904-909.
35. Price, A. L., M. E. Weale, N. Patterson, S. R. Myers, A. C. Need et al., 2008 Long-range LD can confound genome scans in admixed populations. Am. J. Hum. Genet. 83: 132-135; author reply 135-139.
36. Price, A. L., A. Tandon, N. Patterson, K. C. Barnes, N. Rafaels et al., 2009 Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5: e1000519.
37. Redon, R., S. Ishikawa, K. R. Fitch, L. Feuk, G. H. Perry et al., 2006 Global variation in copy number in the human genome. Nature 444: 444-454.
38. Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. P. Levine, D. J. Richter et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
39. Sabeti, P. C., P. Varilly, B. Fry, J. Lohmueller, E. Hostetter et al., 2007 Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
40. Schaffner, S. F., C. Foo, S. Gabriel, D. Reich, M. J. Daly et al., 2005 Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15: 1576-1583.
41. Schaeffer, S. W., M. P. Goetting-Minesky, M. Kovacevic, J. R. Peoples, J. L. Graybill et al., 2003 Evolutionary genomics of inversions in Drosophila pseudoobscura: evidence for epistasis. Proc. Natl. Acad. Sci. USA 100: 8319-8324.
42. Sindi, S. S., and B. J. Raphael, 2010 Identification and frequency estimation of inversion polymorphisms from haplotype data. J. Comput. Biol. 17: 517-531.
43. Spencer, C. C. A., and G. Coop, 2004 SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 20: 3673-3675.
44. Stefansson, H., A. Helgason, G. Thorleifsson, V. Steinthorsdottir, G. Masson et al., 2005 A common inversion under selection in Europeans. Nat. Genet. 37: 129-137.
45. Steinberg, K. M., F. Antonacci, P. H. Sudmant, J. M. Kidd, C. D. Campbell et al., 2012 Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat. Genet. 44: 872-880.
46. Stumpf, M. P. H., and G. A. T. McVean, 2003 Estimating recombination rates from population-genetic data. Nat. Rev. Genet. 4: 959-968.
47. Tantisira, K. G., R. Lazarus, A. A. Litonjua, B. Klanderman, and S. T. Weiss, 2008 Chromosome 17: association of a large inversion polymorphism with corticosteroid response in asthma. Pharmacogenet. Genomics 18: 733-737.
48. Voight, B. F., S. Kudaravalli, X. Wen, and J. K. Pritchard, 2006 A map of recent positive selection in the human genome. PLoS Biol. 4: e72.
49. Wegmann, D., D. E. Kessner, K. R. Veeramah, R. A. Mathias, D. L. Nicolae et al., 2011 Recombination rates in admixed individuals identified by ancestry-based inference. Nat. Genet. 43: 847-853.
50. Weir, B. S., L. R. Cardon, A. D. Anderson, D. M. Nielsen, and W. G. Hill, 2005 Measures of human population structure show heterogeneity among genomic regions. Genome Res. 15: 1468-1476.
51. Winckler, W., S. R. Myers, D. J. Richter, R. C. Onofrio, G. J. McDonald et al., 2005 Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308: 107-111.
52. WTCCC, 2007 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
53. Yu, H. X., J.-M. Chia, G. Bourque, M. V. Wong, S. H. Chan et al., 2005 A population-based LD map of the human chromosome 6p. Immunogenetics 57: 559-565.