Geodesic
Sampling Properties of Estimators of Nucleotide Diversity at Discovered snp Sites
International Journal of Applied Mathematics and Computer Science, Tome 13 (2003) no. 3, pp. 385-394.

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SNP sites are generally discovered by sequencing regions of the human genome in a limited number of individuals. This may leave SNP sites present in the region, but containing rare mutant nucleotides, undetected. Consequently, estimates of nucleotide diversity obtained from assays of detected SNP sites are biased. In this research we present a statistical model of the SNP discovery process, which is used to evaluate the extent of this bias. This model involves the symmetric Beta distribution of variant frequencies at SNP sites, with an additional probability that there is no SNP at any given site. Under this model of allele frequency distributions at SNP sites, we show that nucleotide diversity is always underestimated. However, the extent of bias does not seem to exceed 10-15
Keywords: single nucleotide polymorphisms, ascertainment bias, nucleotide diversity, molecular evolution
Mots-clés : genetyka, statystyka 
@article{IJAMCS_2003_13_3_a10,
     author = {Renwick, A. and Bonnen, P. E. and Trikka, D. and Nelson, D. L. and Chakraborty, R. and Kimmel, M.},
     title = {Sampling {Properties} of {Estimators} of {Nucleotide} {Diversity} at {Discovered} snp {Sites}},
     journal = {International Journal of Applied Mathematics and Computer Science},
     pages = {385--394},
     publisher = {mathdoc},
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     number = {3},
     year = {2003},
     language = {en},
     url = {http://geodesic.mathdoc.fr/item/IJAMCS_2003_13_3_a10/}
}
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Renwick, A.; Bonnen, P. E.; Trikka, D.; Nelson, D. L.; Chakraborty, R.; Kimmel, M. Sampling Properties of Estimators of Nucleotide Diversity at Discovered snp Sites. International Journal of Applied Mathematics and Computer Science, Tome 13 (2003) no. 3, pp. 385-394. http://geodesic.mathdoc.fr/item/IJAMCS_2003_13_3_a10/