Even small SNP clusters are non-randomly distributed: Is this evidence of mutational non-independence?

Proceedings of the Royal Society B: Biological Sciences

Volumn 277, Issue 1686, 2010, Pages 1443-1449

  Amos, William ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Heterozygote instability; Human; Mismatch repair; Mutation hotspot; SNP clusters

Indexed keywords

CHROMOSOME; GENOME; HUMAN EVOLUTION; HYPOTHESIS TESTING; MUTATION; NATURAL SELECTION; POLYMORPHISM; YEAST;

EID: 77952258116     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2009.1757     Document Type: Article

References (36)

1. Akey, J. M., Zhang, K., Xiong, M. & Jin, L. 2003 The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol. Biol. Evol. 20, 232-242. (doi:10.1093/molbev/ msg032) (Pubitemid 36237381)
2. Amos, W. 2010 Heterozygosity and mutation rate: evidence for an interaction and its implications. BioEssays 32, 82-90.
3. Amos, W., Flint, J. & Xu, X. 2008 Heterozygosity increases microsatellite mutation rate, linking it to demographic history. BMC Genet. 9, 72. (doi:10.1186/1471-2156-9-72)
4. Baker, S. M. et al. 1995 Male mice defective in the DNA mismatch repair gene PMS2 exhibit abnormal chromosome synapsis in meiosis. Cell 82, 309-319. (doi:10. 1016/0092-8674(95)90318-6)
5. Borts, R. H. & Haber, J. E. 1989 Length and distribution of meiotic gene conversion tracts and crossovers in Saccharomyces cerevisiae. Genetics 123, 69-80.
6. Borts, R. H., Leung, W.-Y., Kramer, W., Kramer, B., Williamson, M., Fogel, S. & Haber, J. E. 1990 Mismatch repair-induced meiotic recombination requires the PMS1 gene product. Genetics 124, 573-584. (Pubitemid 20106330)
7. Bubb, K. L. et al. 2006 Scan of human genome reveals no new loci under ancient balancing selection. Genetics 173, 2165-2177. (doi: 10.1534/genetics. 106.055715)
8. Charlesworth, B., Nordberg, M. & Charlesworth, D. 1997 The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet. Res. Comb. 70, 155-174. (doi:10.1017/S0016672397002954) (Pubitemid 28021578)
9. Chen, J.-Q., Wu, Y., Yang, H., Bergelson, J., Kreitman, M. & Tian, D. 2009 Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol. Biol. Evol. 26, 1523-1531. (doi:10.1093/ molbev/msp063)
10. Clark, A. G., Hubisz, M. J., Bustamante, C. D., Williamson, S. H. & Nielsen, R. 2005 Ascertainment bias in studies of human genome-wide polymorphism. Genome Res. 15, 1496-1502. (doi:10.1101/gr.4107905) (Pubitemid 41545003)
11. Collins, I. & Newton, C. S. 1994 Meiosis-specific formation of joint DNA molecules containing sequences from homologous chromosomes. Cell 76, 65-75. (doi:10. 1016/0092-8674(94)90173-2) (Pubitemid 24035282)
12. Eriksson, A., Haubold, B. & Mehlig, B. 2002 Clustering of SNPs along a chromosome: can the neutral model be rejected? (http://arxiv.org/abs/physics/ 0207024)
13. Giver, C. R. & Grosovsky, A. J. 1997 Single and coincident intragenic mutations attributable to gene conversion in a human cell line. Genetics 146, 1429-1439.
14. Hartl, D. L. 1988 A primer of population genetics. Sunderland, MA: Sinauer.
15. Hellmann, I., Prüfer, K., Ji, H., Zody, M. C., Pääbo, S. & Ptak, S. 2005 Why do human diversity levels vary at a megabase scale? Genome Res. 15, 1222-1231. (doi:10. 1101/gr.3461105) (Pubitemid 41247912)
16. Hudson, R. R. & Kaplan, N. L. 1995 The coalescent process and background selection. Phil. Trans. R. Soc. Lond. B 349, 19-23. (doi:10.1098/rstb.l995.0086)
17. Jeffreys, A. J. & May, C. A. 2004 Intense and highly localized gene conversion activity in human meiotic crossover hotspots. Nat. Genet. 36, 151-156. (doi:10.1038/ng1287)
18. Jeffreys, A. J. & Neumann, R. 2009 The rise and fall of a human recombination hotspot. Nat. Genet. 41, 625-629. (doi:10.1038/ng.346)
19. Kayser, M., Vowles, E. J., Kappei, D. & Amos, W. 2006 Microsatellite length differences between humans and chimpanzees at autosomal but not Y-chromosomal loci. Genetics 173, 2179-2186. (doi:10.1534/genetics.106. 055632)
20. Kühner, M. K., Beerli, P., Yamato, J. & Felsenstein, J. 2000 Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156, 439-447.
21. Lercher, M. J. & Hurst, L. D. 2002 Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18, 337-340. (doi: 10.1016/S01689525(02)02669-0)
22. Lindblad-Toh, K. et al. 2000 Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat. Genet. 24, 381-386. (doi:10.1038/ 74215)
23. Myers, S., Freeman, C., Auton, A., Donnelly, P. & McVean, G. 2008 A common sequence motif associated with recombination hot spots and genome instability in humans. Nat. Genet. 40, 1124-1129. (doi:10.1038/ng. 213)
24. Nielsen, R. 2000 Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154, 931-942. (Pubitemid 30096611)
25. Oleksyk, T. K., Zhao, K., de la Vega, F. M., Gilbert, D. A., O'Brien, S. J. & Smith, M. W. 2008 Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. PLoS ONE 3, e1712. (doi:10.1371/journal.pone. 0001712)
26. Ptak, S., Hinds, D. A., Koehler, K., Nickel, B., Patil, N., Ballinger, D. G., Przeworski, M., Frazer, K. A. & Pääbo, S. 2005 Fine-scale recombination patterns differ between chimpanzees and humans. Nat. Genet. 37, 429-434. (doi:10.1038/ng1529) (Pubitemid 40490495)
27. Ramirez-Soriano, A. & Nielsen, R. 2009 Correcting estimators of t and Tajima's D for ascertainment biases caused by single-nucleotide polymorphism discovery process. Genetics 181, 701-710. (doi:10.1534/genetics.108. 094060)
28. Rogozin, I. B. & Pavlov, Y. I. 2003 Theoretical analysis of mutation hotspots and their sequence context specificity. Mut. Res. 544, 65-85. (doi:10.1016/S1383-5742(03) 00032-2)
29. Soldevila, M. F., Calafell, F., Helgason, A., Stefansson, K. & Bertranpetit, J. 2005 Assessing the signature of selection in PRNP from polymorphism data: results support Kreitman and Di Rienzo's opinion. Trends Genet. 21, 389-391. (doi:10.1016/j.tig.2005.05.001) (Pubitemid 40835724)
30. Tenaillon, M. I., Austerlitz, F. & Tenaillon, O. 2008 Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck. J. Evol. Biol. 21, 541-550. (doi: 10.1111/j.1420-9101.2007. 01490.x) (Pubitemid 351208138)
31. Tian, D. et al. 2008 Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455, 105-109. (doi:10.1038/ nature07175)
32. Vallente, R. U., Cheng, E. Y. & Hassold, T. J. 2006 The synaptonemal complex and meiotic recombination in humans: new approaches to old questions. Chromosoma 115, 241-249. (doi:10.1007/s00412-0060058-4)
33. Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. 2006 A map of recent positive selection in the human genome. PLoS Biol. 4, e72. (doi:10.1371/journal.pbio. 0040072)
34. Wakeley, J., Nielsen, R., Liu-Cordero, S. N. & Ardlie, K. 2001 The discovery of single-nucleotide polymorphisms-and inferences about human demographic history. Am. J. Hum. Genet. 69, 1332-1347. (doi:10.1086/ 324521)
35. Wang, E., Kodama, G., Balbi, P. & Moyzis, R. K. 2006 Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl Acad. Sci. USA 103, 135-140. (doi:10.1073/pnas.0509691102) (Pubitemid 43076117)
36. Winckler, W. et al. 2005 Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308, 107-111. (doi:10.1126/science.1105322) (Pubitemid 40471008)