Minimum Allele Frequency

In order to make a reliable estimation of an allele frequency, it is important to collect more than one data point for that allele. Recall that in Table 20.2 we only observed a single allele 15. As noted by Chakraborty (1992), a conservative minimum allele frequency is used to insure that an allele has been sampled sufficiently to be used reliably in statistical tests. Furthermore, the National Research Council report (1996) states that an estimate of an allele frequency can be very inaccurate if the allele is so rare that it is represented only once or a few times in a database; and some rare alleles might not be represented at all (NRC II, p. 148). Thus, it is recommended that each allele should be observed at least five times to be included in reliable statistical calculations. The minimum allele frequency is therefore 5/2N, where N is the number of individuals sampled from a population and 2N is the number of chromosomes counted because autosomes are in pairs due to inheritance of one allele from one's mother and one from one's father.

Going back to the example of allele 15 in Table 20.2, we find that the minimum allele frequency is 5/2N or 5/604, which equals 0.00828. Therefore, 0.00828 should be used in calculations involving a D13S317 allele 15 rather than the empirically observed 0.00166. In other words, because allele 15 was not observed enough times to reliably estimate its true value in the population, its frequency is inflated to five times its observed value in order to be conservative. The impact of database size on minimum allele frequency can be seen in Table 20.3.

A conservative minimum allele frequency is used to insure that an allele has been sampled sufficiently to be used reliably in statistical tests. On the basis of these criteria, usually 100-150 DNA samples from unrelated individuals is sufficient for STR loci that possess between five and 15 alleles (Chakraborty 1992).

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