Correcting for ascertainment biases when analyzing SNP data: Applications to the estimation of linkage disequilibrium

Theoretical Population Biology

Volumn 63, Issue 3, 2003, Pages 245-255

  Nielsen, Rasmus ^a   Signorovitch, James ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE; POLYMORPHISM; POPULATION GENETICS;

ARTICLE; EPIDEMIOLOGY; GENE LINKAGE DISEQUILIBRIUM; GENETICS; HUMAN; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS; UNITED STATES;

BIAS (EPIDEMIOLOGY); GENETICS, POPULATION; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; UNITED STATES;

EID: 0042991419     PISSN: 00405809     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0040-5809(03)00005-4     Document Type: Article

References (28)

1. Ardlie K., Liu-Cordero S.N., Eberle M.A., Daly M., Barrett J., Winchester E., Lander E.S., Kruglyak L. Linkage disequilibrium and gene conversion. Am. J. Hum. Genet. 69:2001;582-589.
2. Ewens W.J. The sampling theory of selectively neutral alleles. Theor. Pop. Biol. 3:1972;87-112.
3. Ewens W.J., Speilman R.S., Harris H. Estimation of genetic variation at the DNA level from restriction endonuclease data. Proc. Natl. Acad. Sci. USA. 78:1981;3748-3750.
4. Fearnhead, P., Donnelly, P., 2001. Estimating recombination rates from population genetic data. Technical report available from http://www.stats.ox.ac. uk/~fhead/.
5. Griffiths R.C., Marjoram P. Ancestral inference from samples of DNA sequences with recombination. J. Comp. Biol. 3:1996;479-502.
6. Griffiths R.C., Marjoram P. An ancestral recombination graph. Tavare S., Donnelly P. Progress in Population Genetics and Human Evolution, IMA Volumes in Mathematics and its Applications. 1997;257-270 Spriger, Berlin.
7. Griffiths R.C., Tavaré S. Simulating probability distributions in the coalescent. Theor. Popul. Biol. 46:1994;131-159.
8. Griffiths R.C., Tavaré S. Ancestral inference in population genetics. Stat. Sci. 9:1994;307-319.
9. Griffiths R.C., Tavaré S. The age of a mutation in a general coalescent tree. Stochastic Models. 14:1998;273-295.
10. Harding R.M., Fullerton S.M., Griffiths R.C., Bond J., Cox M.J., Schneider J.A., Moulin D.S., Clegg J.B. Archaic African and Asian lineages in the genetic ancestry of modern humans. Am. J. Hum. Genet. 60:1997;772-789.
11. Hudson R.R. Properties of the neutral allele model with intergenic recombination. Theor. Pop. Biol. 23:1983;183-201.
12. Hudson R.R. The sampling distribution of linkage disequilibrium under an infinite alleles model without selection. Genetics. 109:1985;566-631.
13. Hudson R.R. Two-locus sampling distributions and their application. Genetics. 159:2001;1805-1817.
14. Kingman J.F.C. The coalescent. Stochastic Proc. Appl. 13:1982;235-248.
15. Kuhner M.K., Yamato J., Felsenstein J. Estimating effective population size and mutation rate from sequence data using metropolis-hastings sampling. Genetics. 140:1995;1421-1430.
16. Kuhner M.K., Beerli P., Yamato J., Felsenstein J. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics. 156:2000;439-447.
17. Kuhner M.K., Yamato J., Felsenstein J. Maximum likelihood estimation of recombination rates from population data. Genetics. 156:2000;1393-1401.
18. Lange K. Numerical Analysis for Statisticians, Springer Series in Statistics and Computing. 2000;Springer, Berlin.
19. Nielsen R. Estimation of population parameters and recombination rates using single nucleotide polymorphisms. Genetics. 154:2000;931-942.
20. Picoult-Newberg L., Ideker T.E., Pohl M.G., Taylor S.L., Donaldson M.A., Nickerson D.A., Boyce-Jacino M. Mining SNPs from EST databases. Genome Res. 9:1999;167-174.
21. Pritchard J.K., Przeworski M. Linkage disequilibrium in humans. models and data Am. J. Hum. Genet. 69:2001;1-14.
22. Stephens M., Donnelly P. Inference in molecular population genetics. J. Roy. Statist. Soc. Ser. B. 62:2000;605-655.
23. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:1989;585-595.
24. Templeton A.R., Clark A.G., Weiss K.M., Nickerson D.A., Boerwinkle E., Sing C.F. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66:2000;69-83.
25. Thompson E.A. Evolutionary Trees. 1975;Cambridge University Press, Cambridge, UK.
26. Wakeley, J., Nielsen, R., Ardlie, K., Liu-Cordero, S.N., 2001. The discovery of single nucleotide polymorphisms and inferences about human demographic history. Am. J. Hum. Genet., in review.
27. Wang D.G., Fan J.B., Siao C.J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J., Kruglyak L., Stein L., Hsie L., Topaloglou T., Hubbell E., Robinson E., Mittmann M., Morris M.S., Shen N., Kilburn D., Rioux J., Nusbaum C., Rozen S., Hudson T.J., Lander E.S.et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 280:1998;1077-1082.
28. Zhao Z., Jin L., Fu Y.-X., Ramsay M., Jenkins T., Leskinen E., Pamilo P., Trexler M., Patthy L., Jorde L.B., Ramos-Onsins S., Yu N., Li W-H. Worldwide dna sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. USA. 97:2000;11354-11358.