Allele 6 amplicon has 'dropped out'

Figure 6.9

Impact of a sequence polymorphism in the primer binding site illustrated with a hypothetical heterozygous individual. Heterozygous allele peaks may be well-balanced (a), imbalanced (b), or exhibit allele dropout (c).

To overcome this potential problem, the matching criteria in database searches can be made less stringent when searching a crime stain sample against the DNA database of convicted offender profiles (see Chapter 18). That is, the database search might be programmed to return any profiles with a match at 25 out of 26 alleles instead of 26 out of 26.

When primers are selected for amplification of STR loci, candidate primers are evaluated carefully to avoid primer binding site mutations (Schumm et al. 1996, Wallin et al. 2002). Sequence analysis of multiple alleles is performed, family inheritance studies are conducted, within-locus peak signal ratios for heterozygous samples are examined, apparent homozygous samples are re-amplified with lower annealing temperatures, and statistical analysis of observed versus expected homozygosity is performed on population databases (Walsh 1998). It is truly a challenge to design multiplex STR primer sets in which primer binding sites are located in sequence regions that are as highly conserved as possible and yet do not interfere with primers amplifying other loci.

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