Bi-parentally inherited short tandem repeat polymorphisms have been routinely used in human identity testing for about 25 years. More recently, the analysis of uni-parentally inherited markers from the human Y chromosome and mitochondrial DNA was introduced for special applications of DNA-based human identification. This article provides a brief perspective on uni-parental markers in human identity testing including forensic DNA analysis.

Characteristics and Applications

A selected and standardized set of bi-parentally inherited autosomal markers, so called short tandem repeats (STRs) or microsatellites, has become the Golden Standard in human identity testing, including forensic DNA analysis (1). Compound STR genotypes are collected as repeat number codes (“DNA profiles”) in criminal DNA databases in many countries, providing powerful tools for more effective law enforcement. The uni-parentally inherited markers are usually applied to cases where autosomal STR profiles cannot be obtained because of technical constraints or do not provide unequivocal answers (for example, when profiles overlap in mixed stain analysis). They are sex-specific inherited markers; that is, those from the nonrecombining part of the human Y chromosome (NRY) transferred through the male germline (females do not normally carry Y chromosomes) and markers from the human mitochondrial genome transferred through the female germline (human sperm cells do not normally transmit mitochondrial DNA). Both parts of our genome are inherited in the absence of homologous recombination and thus are unchanged from one male (NRY-DNA) or female (mtDNA) generation to the next, as illustrated in (Figure 1), unless mutations occur.

Figure 1.

The recombination-free inheritance of uni-parental markers provides advantages as well as disadvantages in their applications to human identification testing including forensic analysis. A clear advantage of NRY markers is their male-specificity. DNA analysis of material from cases of sexual assault is often complicated by mixed stains that contain high ratios of female victim DNA but low ratios of male perpetrator DNA, resulting in the problem of preferential amplification of the excess female DNA during PCR and potential profile overlap when using autosomal STRs. Both problems can in principle be overcome by specifically analyzing the male DNA component with NRY markers ((Figure 2)). The suitability of NRY markers for male identification in rape cases has been demonstrated in numerous cases (2,3), including those with low or no sperm count due to the NRY detection from male epithelial cells (4). Autosomal STR analysis can be especially problematic in sexual assault cases with multiple male perpetrators, but those cases can be solved using NRY markers that can differentiate between male lineages. Clearly, the presence of any NRY marker in a DNA sample indicates the male sex of the sample donor. However, since the absence of NRY markers does not necessarily mean that the donor is a female, because of potential experimental failure, a DNA-based sex test was developed that includes markers from the amelogenin gene (5). The human amelogenin gene exists in two copies on the NRY and the X chromosome with a clearly detectable length difference (5), and is part of most commercially available kits for human identification. Unfortunately, the amelogenin test is not error-free: in those Y-chromosomal deletions that include the amelogenin gene, such males wrongly appear as females in the outcomes of such DNA tests (6). Though such deletions appear to be rare (7), they do exist in increased frequency in certain populations (8,9).

Figure 2.

Advantages of both types of uni-parental markers are also found in family testing for solving deficiency cases where putative fathers or mothers are not available for DNA analysis; the unavailable male or female can be replaced by any male or female relative in the analysis of NRY or mtDNA markers, respectively. Such applications can also include historic cases, as long as living paternal or maternal descendents are available. Prominent examples are the identification of the skeletons of Czar Nicholas II of Russia and his family using (in part) mtDNA (10,11), and the likely paternity of Thomas Jefferson of Eston Hemmings Jefferson, son of Jefferson's slave Sally Hemmings, using NRY markers (12). In the same way that uni-parental markers are used for family testing, they can be applied to identify missing persons using putative paternal or maternal relatives as reference samples (see also below) (13).