Estimating the rate of gene conversion on human chromosome 21

American Journal of Human Genetics

Volumn 75, Issue 3, 2004, Pages 386-397

  Padhukasahasram, Badri ^a,b   Marjoram, Paul ^a   Nordborg, Magnus ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CHROMOSOME 21; CPG ISLAND; CROSSING OVER; GENE CONVERSION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MUTATION; GENETIC POLYMORPHISM; GENOME; HUMAN; HUMAN GENOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 4143054668     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/423451     Document Type: Article

References (28)

1. Andolfatto P, Nordborg M (1998) The effect of gene conversion on intralocus associations. Genetics 148:1397-1399
2. Ardlie K, Liu-Cordero SN, Eberle MA, Daly M, Barrett J, Winchester E, Lander ES, Kruglyak L (2001) Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. Am J Hum Genet 69:582-589
3. Carpenter ATC (1984) Meiotic roles of crossing-over and of gene conversion. Cold Spring Harbor Symp Quant Biol 49: 23-26
4. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, Princeton
5. Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E (2003) Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet 73:285-300
6. Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, et al (1999) The DNA sequence of human chromosome 22. Nature 402:489-495
7. Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A (2001) Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet 69:831-843
8. Fullerton SM, Harding RM, Boyce AJ, Clegg JB (1994) Molecular and population genetic analysis of allelic sequence diversity at the human β-globin locus. Proc Natl Acad Sci USA 91:1805-1809
9. Holliday R (1964) A mechanism for gene conversion in fungi. Genet Res 5:282-287
10. Hudson RR (2001) Two-locus sampling distributions and their applications. Genetics 159:1805-1817
11. Hudson RR, Kaplan NL (1985) Properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164
12. Innan H, Padhukasahasram B, Nordborg M (2003) The pattern of polymorphism on human chromosome 21. Genome Res 13:1158-1168
13. Jeffreys AJ, Kauppi L, Neumann R (2001) Intensely punctuate meiotic recombination in the class II region of the major histocompatibilty complex. Nat Genet 29:217-222
14. Jeffreys AJ, May CA (2004) Intense and highly localized gene conversion activity in human meiotic crossover hotspots. Nat Genet 36:151-156
15. Kingman JFC (1982) The coalescent. Stochast Proc Appl 13: 235-248
16. Kuhner M, Yamato KJ, Felsenstein J (2000) Maximum likelihood estimation of recombination rates from population genetic data. Genetics 156:1393-1401
17. Marjoram P, Molitor J, Plagnol V, Tavare S (2003) Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 100:15324-15328
18. Nielsen R (2000) Estimation of population parameters and recombination rates from single-nucleotide polymorphisms. Genetics 154:931-942
19. Nordborg M (2001) Coalescent theory. In: Balding DJ, Bishop M, Cannings C (eds) Handbook of statistical genetics. John Wiley, Chichester, United Kingdom, pp 213-238
20. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR (2001) Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science 294:1719-1723
21. Przeworski M, Wall JD (2001) Why is there so little intragenic linkage disequilibrium in humans? Genet Res 77:143-151
22. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF (2000) Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet 66:69-83
23. Wall JD (2000) A comparison of estimators of the population recombination rates. Mol Biol Evol 17:156-163
24. Wall JD, Pritchard JK (2003) Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet 73:502-515
25. Weiss G, von Haeseler A (1998) Inference of population history using a likelihood approach. Genetics 149:1539-1546
26. Wiehe T, Mountain J, Parham P, Slatkin M (2000) Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns. Genet Res 75:61-73
27. Wiuf C, Hein J (2000) The coalescent with gene conversion. Genetics 155:451-462
28. Zangenberg G, Huang MM, Arnheim N, Erlich H (1995) New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm. Nat Genet 10:407-444