Differential DNA extraction of challenging simulated sexual-assault samples: a Swiss collaborative study

When analyzing samples from sexual-assault cases, such as gynecological swabs, forensic-genetics laboratories aim to establish the autosomal DNA profile of the male contributor to help identify its source. The success of these analyses depends upon several factors: the circumstances of the case (number of aggressors, presence/absence of ejaculation, etc.), the aggressor's semen characteristics, time elapsed between the aggression and the collection of gynecological swabs [1-3], and the sampling and storage conditions. Another important factor, which is seldom assessed, is the analytical process itself. Indeed, experimental studies have shown that protocol variation can influence the success of DNA analysis [4-6].Samples from sexual-assault cases are often characterized by imbalanced mixtures of epithelial cells and sperm, with an excess of the victim's material, resulting in an unfavorable ratio of male to female DNA. According to several studies [7,8] and our own internal validations, the male autosomal DNA component of the mixture is too low to be detected beyond a ratio of 1:10 to 1:20 of male:female DNA. This is essentially due to competition for the primers during PCR amplification, which leads to preferential amplification of the major component of the mixture. In such cases, the use of Y-chromosome genetic markers, such as short tandem repeats (STRs), may allow the amplification of low quantities of male DNA independently of the victim's DNA background [7-10]. However, a Y-STR profile is not as informative as an autosomal STR profile. First, paternally related males cannot be discriminated. Second, the frequency of a Y-STR profile in the population can be relatively high [11], impeding the discrimination of some unrelated males. Third, Y-STR profiles are often not included in national DNA databases. Therefore, the acquired Y-STR profile can generally only be compared with the Y-STR profile of known suspects.Hence, forensic-genetics laboratories try to separat