Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2015, Article ID 693193, 15 pages
http://dx.doi.org/10.1155/2015/693193
Research Article

Genetic Geostatistical Framework for Spatial Analysis of Fine-Scale Genetic Heterogeneity in Modern Populations: Results from the KORA Study

1Institute for Medical Biometry, Informatics, and Epidemiology, University of Bonn, 53127 Bonn, Germany
2Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
3DNA Analysis Unit, Official College of Pharmacists and Biochemists, C1184ABA Buenos Aires, Argentina
4Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
5Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
6FBK, 38122 Trento, Italy
7Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria
8Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
9Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
10Institute of Medical Statistics and Epidemiology, Technical University Munich, 81675 Munich, Germany
11German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany

Received 1 January 2015; Revised 6 April 2015; Accepted 7 April 2015

Academic Editor: Ian Dunham

Copyright © 2015 A. N. Diaz-Lacava et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. J. Bamshad, S. Wooding, W. S. Watkins, C. T. Ostler, M. A. Batzer, and L. B. Jorde, “Human population genetic structure and inference of group membership,” American Journal of Human Genetics, vol. 72, no. 3, pp. 578–589, 2003. View at Publisher · View at Google Scholar · View at Scopus
  2. L. R. Cardon and L. J. Palmer, “Population stratification and spurious allelic association,” The Lancet, vol. 361, no. 9357, pp. 598–604, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. C. D. Sloan, E. J. Duell, X. Shi et al., “Ecogeographic genetic epidemiology,” Genetic Epidemiology, vol. 33, no. 4, pp. 281–289, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. M. L. Freedman, D. Reich, K. L. Penney et al., “Assessing the impact of population stratification on genetic association studies,” Nature Genetics, vol. 36, no. 4, pp. 388–393, 2004. View at Publisher · View at Google Scholar · View at Scopus
  5. J. Marchini, L. R. Cardon, M. S. Phillips, and P. Donnelly, “The effects of human population structure on large genetic association studies,” Nature Genetics, vol. 36, no. 5, pp. 512–517, 2004. View at Publisher · View at Google Scholar · View at Scopus
  6. M. D. Shriver, G. C. Kennedy, E. J. Parra et al., “The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs,” Human genomics, vol. 1, no. 4, pp. 274–286, 2004. View at Publisher · View at Google Scholar · View at Scopus
  7. R. Holle, M. Happich, H. Löwel, and H. E. Wichmann, “KORA—a research platform for population based health research,” Gesundheitswesen, vol. 67, supplement 1, pp. S19–S25, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. A. Lindenberg, J. Brinkmeyer, N. Dahmen et al., “The German multi-centre study on smoking-related behavior-description of a population-based case-control study,” Addiction Biology, vol. 16, no. 4, pp. 638–653, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. H.-E. Wichmann, C. Gieger, and T. Illig, “KORA-gen—resource for population genetics, controls and a broad spectrum of disease phenotypes,” Gesundheitswesen, vol. 67, supplement 1, pp. S26–S30, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. A. Helgason, B. Yngvadòttir, B. Hrafnkelsson, J. Gulcher, and K. Stefánsson, “An Icelandic example of the impact of population structure on association studies,” Nature Genetics, vol. 37, no. 1, pp. 90–95, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. B. K. Epperson, Geographical Genetics, Princeton University Press, Princeton, NJ, USA, 2003.
  12. H. Kaessmann, V. Wiebe, G. Weiss, and S. Pääbo, “Great ape DNA sequences reveal a reduced diversity and an expansion in humans,” Nature Genetics, vol. 27, no. 2, pp. 155–156, 2001. View at Publisher · View at Google Scholar · View at Scopus
  13. K. N. Laland, J. Odling-Smee, and S. Myles, “How culture shaped the human genome: bringing genetics and the human sciences together,” Nature Reviews Genetics, vol. 11, no. 2, pp. 137–148, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. M. Steffens, C. Lamina, T. Illig et al., “SNP-based analysis of genetic substructure in the German population,” Human Heredity, vol. 62, no. 1, pp. 20–29, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. S. Wright, Evolution and the Genetics of Populations, Vol. 2: Theory of Gene Frequencies, University of Chicago Press, Chicago, Ill, USA, 1969.
  16. J. K. Pritchard, M. Stephens, and P. Donnelly, “Inference of population structure using multilocus genotype data,” Genetics, vol. 155, no. 2, pp. 945–959, 2000. View at Google Scholar · View at Scopus
  17. S. Wright, “The genetical structure of populations,” Annals of Eugenics, vol. 15, pp. 323–354, 1951. View at Google Scholar · View at MathSciNet
  18. G. R. Abecasis, S. S. Cherny, W. O. C. Cookson, and L. R. Cardon, “GRR: graphical representation of relationship errors,” Bioinformatics, vol. 17, no. 8, pp. 742–743, 2001. View at Publisher · View at Google Scholar · View at Scopus
  19. B. Devlin and K. Roeder, “Genomic control for association studies,” Biometrics, vol. 55, no. 4, pp. 997–1004, 1999. View at Publisher · View at Google Scholar · View at Zentralblatt MATH · View at Scopus
  20. G. Guillot, A. Estoup, F. Mortier, and J. F. Cosson, “A spatial statistical model for landscape genetics,” Genetics, vol. 170, no. 3, pp. 1261–1280, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Nei and A. K. Roychoudhury, “Sampling variances of heterozygosity and genetic distance,” Genetics, vol. 76, no. 2, pp. 379–390, 1974. View at Google Scholar · View at MathSciNet
  22. M. Nei, “Analysis of gene diversity in subdivided populations,” Proceedings of the National Academy of Sciences, vol. 70, no. 12, pp. 3321–3323, 1973. View at Publisher · View at Google Scholar
  23. S. Wright, “Isolation by distance,” Genetics, vol. 28, pp. 114–138, 1943. View at Google Scholar
  24. S. Wright, “Isolation by distance under diverse systems of mating,” Genetics, vol. 31, pp. 39–59, 1946. View at Google Scholar · View at Scopus
  25. G. Guillot, F. Santos, and A. Estoup, “Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface,” Bioinformatics, vol. 24, no. 11, pp. 1406–1407, 2008. View at Publisher · View at Google Scholar · View at Scopus
  26. N. Patterson, A. L. Price, and D. Reich, “Population structure and eigenanalysis,” PLoS Genetics, vol. 2, p. e190, 2006. View at Publisher · View at Google Scholar
  27. A. L. Price, N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick, and D. Reich, “Principal components analysis corrects for stratification in genome-wide association studies,” Nature Genetics, vol. 38, no. 8, pp. 904–909, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. S. Purcell, B. Neale, K. Todd-Brown et al., “PLINK: a tool set for whole-genome association and population-based linkage analyses,” American Journal of Human Genetics, vol. 81, no. 3, pp. 559–575, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. O. J. Hardy and X. Vekemans, “SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels,” Molecular Ecology Notes, vol. 2, no. 4, pp. 618–620, 2002. View at Publisher · View at Google Scholar · View at Scopus
  30. M. Neteler and H. Mitasova, Open Source GIS: A GRASS GIS Approach, Kluwer Academic, Boston, Mass, USA, 2004.
  31. H. Mitášová and L. Mitáš, “Interpolation by regularized spline with tension: I. Theory and implementation,” Mathematical Geology, vol. 25, no. 6, pp. 641–655, 1993. View at Publisher · View at Google Scholar · View at Scopus
  32. R. Bivand, spdep: Spatial Dependence: Weighting Schemes, Statistics and Models, R package version 0.5-21, 2010, http://cran.r-project.org/web/packages/spdep/index.html.
  33. R. S. Bivand, E. J. Pebesma, and V. Gomez-Rubio, Applied Spatial Data Analysis with R, Springer, New York, NY, USA, 2008.
  34. V. Vitart, A. D. Carothers, C. Hayward et al., “Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design,” American Journal of Human Genetics, vol. 76, no. 5, pp. 763–772, 2005. View at Publisher · View at Google Scholar · View at Scopus
  35. N. Liu, L. Chen, S. Wang, C. Oh, and H. Zhao, “Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure,” BMC Genetics, vol. 6, supplement 1, article S26, 2005. View at Publisher · View at Google Scholar · View at Scopus
  36. N. A. Rosenberg, L. M. Li, R. Ward, and J. K. Pritchard, “Informativeness of genetic markers for inference of ancestry,” American Journal of Human Genetics, vol. 73, no. 6, pp. 1402–1422, 2003. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Manel, F. Berthoud, E. Bellemain et al., “A new individual-based spatial approach for identifying genetic discontinuities in natural populations,” Molecular Ecology, vol. 16, no. 10, pp. 2031–2043, 2007. View at Publisher · View at Google Scholar