Discovery Of Null Alleles

Null alleles have been 'discovered' by the observation of different typing results when utilizing independent STR primer sets. During a comparison of STR typing results on 600 population samples at the VWA locus, one sample typed 16,19 with Promega's PowerPlex kit and 16,16 with Applied Biosystem's AmpFlSTR® Blue kit (Kline et al. 1998). In this case, VWA allele 19 dropped out with the AmpFlSTR® VWA primer set due to a sequence polymorphism near the 3'-end of the forward primer (Walsh 1998).

Allele dropout may occur due to mutations (variants) at or near the 3'-end of a primer and thus produce little or no extension during PCR. In this case, the VWA allele 19 was present in the sample but failed to be amplified by one of the primer sets. It was later reported that the null allele resulted from a rare A—T nucleotide change in the DNA template at the second base from the 3'-end of the AmpFlSTR® VWA forward primer (Walsh 1998).

Potential null alleles resulting from allele dropout can be predicted by statistical analysis of the STR typing data. The observed number of homozygotes can be compared to the expected number of homozygotes based on Hardy-Weinberg equilibrium (Chakraborty et al. 1992). An abnormally high level of homozygotes would indicate the possible presence of null alleles. Thus, each set of population data should be carefully examined when new STR markers are being tested in a forensic DNA laboratory (see Chapter 20).

A number of primer concordance studies have been conducted in the past few years as use of various STR kits has become more prevalent. An examination of over 2000 samples comparing the PowerPlex® 16 kit to the Profiler Plus™ and COfiler™ kit results found 22 examples of allele dropout due to a primer mismatch at seven of the 13 core STR loci: CSF1PO, D8S1179, D16S539, D21S11, FGA, TH01, and VWA (Budowle et al. 2001, Budowle and Sprecher 2001). Table 6.2 contains a summary of findings from some concordance studies that identified allele dropout with a particular primer pair.

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Stammering Its Cause and Its Cure

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