Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data

Genetics

Volumn 168, Issue 4, 2004, Pages 2373-2382

  Nielsen, Rasmus ^a,b,c   Hubisz, Melissa J ^a   Clark, Andrew G ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c Center for Bioinformatics   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC LINKAGE; GENOTYPE; MATHEMATICAL ANALYSIS; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; DATA INTERPRETATION, STATISTICAL; GENE FREQUENCY; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 11244313872     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.031039     Document Type: Article

References (21)

1. AKEY, J. M., G. ZHANG, K. ZHANG, L. JIN and M. D. SHRIVER, 2002 Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12: 1805-1814.
2. AKEY, J. M., K. ZHANG, M. XIONG and L. JIN, 2003 The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol. Biol. Evol. 20: 232-242.
3. ALTSHULER, D., V. J. POLLAR, C. R. COWLES, W. J. VAN ETTEN, J. BALDWIN et al., 2000 A SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.
4. CASELLA, G., and R. L. BERGER, 1990 Statistical Inference. Duxbury Press, Belmont, CA.
5. CAVALLI-SFORZA, L. L., and M. W. FELDMAN, 2003 The application of molecular genetic approaches to the study of human evolution. Nat. Genet. 33: 266-275.
6. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
7. KINGMAN, J. F. C., 1982 The coalescent. Stoch. Proc. Appl. 13: 235-248.
8. KUHNER, M. K., P. BEERLI, J. YAMAMOTO and J. FELSENSTEIN, 2000 Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156: 439-447.
9. MATISE, T. C., R. SACHIDANANDAM, A. G. CLARK, L. KRUGLYAK, E. WIJSMAN et al., 2003 A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am. J. Hum. Genet. 73: 271-284.
10. NlELSEN, R., 2000 Estimation of population parameters and recombination rates using single nucleotide polymorphisms. Genetics 154: 931-942.
11. NIELSEN, R., and J. SIGNOROVITCH, 2003 Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol. 63: 245-255.
12. PICOULT-NEWBERG, L., T. E. IDEKER, M. G. POHL, S. L. TAYLOR, M. A. DONALDSON et al., 1999 Mining SNPs from EST databases. Genome Res. 9: 167-174.
13. POLANSKI, A., and M. KIMMEL, 2003 New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics 165: 427-436.
14. PRESS, W. H., S. A. TEUKOLSKY, W. T. VETTERLING and B. P. FLANNERY, 1992 Numerical Recipes in C. Cambridge University Press, Cambridge, UK.
15. SABETI, P. C., D. E. REICH, J. M. HIGGINS, H. Z. P. LEVINE, D. J. RICHTER et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
16. STEPHENS, J. C., J. A. SCHNEIDER, D. A. TANGUAY, J. CHOI, T. ACHARYA et al., 2001 Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
17. SUNYAEV, S. R., W. C. LATHE, III, V. E. RAMENSKY and P. BORK, 2000 SNP frequencies in human genes: an excess of rare alleles and differing modes of selection. Trends Genet. 16: 335-337.
18. TAILLON-MILLER, P., Z. Gu, Q. Li, L. HILLIER and P. Y. KWOK, 1998 Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. 8: 748-754.
19. THORISSON, G. A., and L. D. STEIN, 2003 The SNP Consortium website: past, present and future. Nucleic Acids Res. 31: 124-127.
20. WAKELEY, J., R. NIELSEN, S. N. LIU-CORDERO and K. ARDLIE, 2001 The discovery of single-nucleotide polymorphisms-and inferences about human demographic history. Am. J. Hum. Genet. 69: 1332-1347.
21. WANG, D. G., J. B. FAN, C. J. SIAO, A. BERNO, P. YOUNG et al., 1998 Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280: 1077-1082.