Sex Chromosome Haplotyping

Chromosomes X and Y have been true homologues and have evolved differently over the years. The Y chromosome has shrunk to about 60 Mb in size as a result of deletions throughout time. Still there is a lot of sequence homology with the X chromosome. The Y chromosome is made up primarily of heterochromatin and has the fewest genes of any chromosome. When it comes to sexual development, the genes on the Y chromosome are crucial (sex-determining region on the Y gene, SRY, which only determines male sex) (Skaletsky et al. Nature 423:825–837, 2003). Two pseudoautosomal areas on the Y chromosome can potentially recombine with the X chromosome during spermatogenesis. These regions are located at both ends of the chromosome. Ninety-five percent of the Y-chromosome contains functional genes and transcription-inert heterochromatin region which contributes to formation of the non-recombining area. This is only found in males and is passed down intact from father to son and is abundant in micro- and minisatellite DNA as well as polymorphic repetitive elements. The Y chromosome’s non-recombining region contains short tandem repeat (STR) loci, which are inherited as a block of linked haplotypes. The identification of unknown people, the determination of a person’s paternity, the detection of the male DNA profile in mixtures and azoospermic people, and the confirmation of amelogenin-deficient males are all forensic applications that greatly benefit from Y-STR haplotyping (Quintana-Murci and Fellous J Biomed Biotechnol 1:18, 2001). The use of X-chromosomal markers is also numerous in forensic contexts. More than 30 STRs have been recognized as forensic markers. Joint typing of STRs that are extremely closely connected produces stable haplotypes that can be utilized to determine the relationship between distant relatives and have been very beneficial in kindship testing (Kauppi et al. Ann N Y Acad Sci 1267:18, 2012).