Evidence for substantial fine-scale variation in recombination rates across the human genome

Nature Genetics

Volumn 36, Issue 7, 2004, Pages 700-706

  Crawford, Dana C ^a   Bhangale, Tushar ^a   Li, Na ^a,b   Hellenthal, Garrett ^a   Rieder, Mark J ^a   Nickerson, Deborah A ^a   Stephens, Matthew ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; CLINICAL ARTICLE; DNA BASE COMPOSITION; EUROPEAN AMERICAN; GENE CLUSTER; GENETIC RECOMBINATION; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; SPERM;

GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 3042700117     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1376     Document Type: Article

References (30)

1. de Massy, B. Distribution of meiotic recombination sites. Trends Genet. 19, 514-522 (2003).
2. Pritchard, J.K. & Przeworski, M. Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69, 1-14 (2001).
3. Clark, A.G. et al. Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am. J. Hum. Genet. 73, 285-300 (2003).
4. Jeffreys, A.J., Ritchie, A. & Neumann, R. High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Hum. Mol. Genet. 9, 725-733 (2000).
5. Jeffreys, A.J., Kauppi, L. & Neumann, R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29, 217-222 (2001).
6. Schneider, J.A., Peto, T.E., Boone, R.A., Boyce, A.J. & Clegg, J.B. Direct measurement of the male recombination fraction in the human beta-globin hot spot. Hum. Mol. Genet. 207-215 (2002).
7. Arnheim, N., Calabrese, P. & Nordborg, M. Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved. Am. J. Hum. Genet. 73, 5-16 (2003).
8. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J. & Lander, E.S. High-resolution haplotype structure in the human genome. Nat. Genet. 29, 229-232 (2001).
9. Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719-1723 (2001).
10. Gabriel, S.B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225-2229 (2002).
11. Wang, N., Akey, J.M., Zhang, K., Chakraborty, R. & Jin, L. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am. J. Hum. Genet. 71, 1227-1234 (2002).
12. Phillips, M.S. et al, Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33, 382-387 (2003).
13. Wall, J.D. & Pritchard, J.K. Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73, 502-515 (2003).
14. Chakravarti, A. et al. Nonuniform recombination within the human beta-globin gene cluster. Am. J. Hum. Genet. 36, 1239-1258 (1984).
15. Li, N. & Stephens, M. A new multilocus model for linkage disequilibrium, with applicationto exploring variations in recombination rate. Genetics 165, 2213-2233 (2003).
16. Li, N. Modeling and inference for linkage disequilibrium and recombination. (PhD Thesis, Department of Biostatistics, University of Washington, 2003)
17. Gerton, J.L. et al. Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97, 11383-11390 (2000).
18. Kong, A. et al. A high-resolution recombination map of the human genome. Nat. Genet. 31, 241-247 (2002).
19. Cullen, M., Perfetto, S.P., Klitz, W., Nelson, G.W. & Carrington, M. High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am. J. Hum. Genet. 71, 759-776 (2002).
20. Wall, J.D., Frisse, L.A., Hudson, R.R. & Di Rienzo, A. Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates. Am. J. Hum. Genet. 73, 1330-1340 (2003).
21. Ptak, S.E. et al. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol. (in the press).
22. Nachman, M.W., Bauer, V.L., Crowell, S.L. & Aquadro, C.F. DNA variability and recombination rates at X-linked loci in humans. Genetics 150, 1133-1141 (1998).
23. Ptak, S.E., Voelpel, K. & Przeworski, M. Contrasting large-scale and local recombination rates in humans. Genetics (in the press).
24. Fullerton, S.M., Carvalho, A.B. & Clark, A.G. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18, 1139-1142 (2001).
25. Petes, T.D. Meiotic recombination hot spots and cold spots. Nat. Rev. Genet. 2, 360-369 (2001).
26. Fullerton, S.M. et al. Polymorphism and divergence in the beta-globin replication origin initiation region. Mol. Biol. Evol. 17, 179-188 (2000).
27. Stephens, M., Smith, N.J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978-989 (2001).
28. Stephens, M. & Donnelly, P. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73, 1162-1169 (2003).
29. Hudson, R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338 (2002).
30. Frisse, L. et al. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69, 83-843 (2001).