A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes

American Journal of Human Genetics

Volumn 77, Issue 5, 2005, Pages 781-794

  Fearnhead, Paul ^a   Smith, Nick G C ^a  

^a LANCASTER UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; HAPLOTYPE; HUMAN; MAXIMUM LIKELIHOOD METHOD; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

EID: 27244445943     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/497579     Document Type: Article

References (24)

1. Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, Nickerson DA, Stephens M (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet 36:700-706
2. Fearnhead P, Donnelly P (2001) Estimating recombination rates from population genetic data. Genetics 159:1299-1318
3. Fearnhead P, Donnelly P (2002) Approximate likelihood methods for estimating local recombination rates (with discussion) J Roy Stat Soc B 64:657-680
4. Fearnhead P, Harding RM, Schneider JA, Myers S, Donnelly P (2004) Application of coalescent methods to reveal fine-scale rate variation and recombination hotspots. Genetics 167:2067-2081
5. Hellmann I, Ebersberger I, Ptak SE, Pääbo S, Przeworski M (2003) A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet 72:1527-1535
6. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338
7. Hudson RR, Slatkin M, Maddison WP (1992) Estimation of levels of gene flow from DNA-sequence data. Genetics 132:583-589
8. Jeffreys AJ, Kauppi L, Neumann R (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29:217-222
9. Jeffreys AJ, Neumann R (2002) Reciprocal crossover asymmetry and meiotic drive in a human recombination hotspot. Nat Genet 31:267-271
10. Jeffreys AJ, Neumann R, Panayi M, Myers S, Donnelly P (2005) Human recombination hotspots hidden within regions of strong marker association. Nat Genet 37:601-606
11. Kong A, Gubdjartsson DF, Sainz J, Jonsdottir GM, Gudjonson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K (2002) A high-resolution recombination map of the human genome. Nat Genet 31:241-247
12. Li N, Stephens M (2003) Modelling LD, and identifying recombination hotspots from SNP data. Genetics 165:2213-2233
13. Marais G (2003) Biased gene conversion: implications for genome and sex evolution. Trends Genet 19:330-338
14. McVean GAT, Awadalla P, Fearnhead P (2002) A coalescent method for detecting recombination from gene sequences. Genetics 160:1231-1241
15. McVean GAT, Myers SR, Hunt S, Deloukas P, Bentley DR, Donnelly P (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304:581-584
16. Ptak SE, Hinds DA, Koehler K, Nickel B, Patil N, Ballinger DG, Przeworski M, Frazer KA, Pääbo S (2005) Fine-scale recombination patterns differ between chimpanzees and humans. Nat Genet 37:429-434
17. Rambaut A, Grassly NC (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 13:235-238
18. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Res (in press)
19. Smith NGC, Fearnhead P (2005) A comparison of three estimators of the population-scaled recombination rate: accuracy and robustness. Genetics (electronically published June 14, 2005; accessed September 7, 2005)
20. Stephens M, Donnelly P (2000) Inference in molecular population genetics (with discussion). J Roy Stat Soc B 62:605-635
21. - (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162-1169
22. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989
23. Webster MT, Smith NGC (2004) Fixation biases affecting human SNPs. Trends Genet 20:122-126
24. Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean G. AT, Gabriel SB, Reich D, Donnelly P, Altshuler D (2005) Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308:107-111