Forensic DNA specimens often possess low levels of DNA. When amplifying very low levels of DNA template, a phenomenon known as stochastic fluctuation can occur. Stochastic effects, which are an unequal sampling of the two alleles present from a heterozygous individual, result when only a few DNA molecules are used to initiate PCR (Walsh et al. 1992). PCR reactions involving DNA template levels below approximately 100 pg of DNA, or about 17 diploid copies of genomic DNA, have been shown to exhibit allele dropout (Fregeau et al. 1993, Kimpton et al. 1994, Gill et al. 2000). False homozygosity results if one of the alleles fails to be detected. The problem of stochastic effects can be avoided by adjusting the cycle number of the PCR reaction such that approximately 20 or more copies of target DNA are required to yield a successful typing result (Walsh et al. 1992). However, efforts have been made to obtain results with low-copy number (LCN) DNA testing (Gill et al. 2000, Gill 2002). The challenges of LCN work and trying to interpret data obtained with less than 100pg of DNA template will be addressed in Chapter 7. Whole genome amplification prior to PCR and locus-specific amplification also have the same issues in terms of stochastic fluctuations with low levels of DNA (Schneider et al. 2004; D.N.A. Box 4.1).
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