ABSTRACT
By virtue of its nonrecombining status, haploid nature, and strong linkage to certain cultural practices, the genetic diversity of the major part of the human Y chromosome (nonrecombining part of the Y-chromosome, NRY) has been a useful tool to trace population history and movements, link paternally related males to each other, and dierentiate between unrelated male lineages (Coble et al. 2009; Kayser 2003; Kayser et al. 2001, 2005, 2007; King and Jobling 2009; Roewer 2009; Shi et al. 2010). Furthermore, the Y-chromosome provides the ability for DNA-based sex testing, particularly when combined with X-chromosomal analysis examining X-Y homologues that display length or sequence dierences between both chromosomes suitable for DNA-based sex determination (Santos et al. 1998; Sullivan et al. 1993). Forensic geneticists have utilized X-Y homologous genes, Y-chromosomal short tandem repeats (Y-STRs), and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) for these purposes. e most common application of Y-STRs is in sexual assault cases, where the female component can greatly overshadow the male component, making autosomal STR typing dicult or impossible (Corach et al. 2001; Henke et al. 2001; Prinz et al. 2001; Prinz and Sansone 2001; Tsuji et al. 2001). Current autosomal STR kits have a routine mixture detection limit of 1:10, whereas Y-STRs (only detected in male DNA) have been shown to be able to detect the male component in a malefemale mixture ratio of up to 1:2,000 (Prinz et al. 1997). is is particularly relevant in the investigation of sexual assault cases, where dierential DNA extractions (attempting to extract sperm DNA separately from the DNA of other cells in vaginal swab material) cannot be used to separate the male-derived nonsperm cells from the more numerous female cells, especially in cases involving azoospermic males or nonintimate samples (Shewale et al. 2003; Sibille et al. 2002). Furthermore, mixtures with multiple male contributors can be extremely dicult, if not impossible, to resolve with autosomal STR proling, while haploid Y-STRs are commonly able to resolve mixtures produced from two or three unrelated males (Cerri et al. 2003; Parson et al. 2001; Prinz et al. 1997). Additionally, in paternity or familial testing Y-STRs can be highly useful, particularly for deciency cases involving male ospring where the alleged father is not available for genetic testing and none of the male relatives are potential fathers. In such cases, autosomal STRs may not be informative unless both parents of the diseased alleged father are available for testing. In contrast, when using Y-STRs any of the available paternal relatives can be used to replace the deceased father in the analysis as paternal relatives usually share the same Y-STR haplotype (Kayser et al. 2000b; Kayser and Sajantila 2001; Rolf et al. 2001). For missing persons or disaster victim identication, Y-STR proling of male relatives can be useful when antemortem reference samples are unavailable (Alonso et al. 2005; Bradford et al. 2011).
