A variety of polymorphic genetic markers have been identified in the euchromatin portion of the Y-chromosome, including a number of STR (Short Tandem Repeats) and SNP (Single Nucleotide Polymorphism) loci and a single hypervariable minisatellite locus. A number of candidate Y-SNP loci have been identified, but they suffer from a limited discrimination potential, and their implementation in forensic casework is dependent upon the development of additional markers and appropriately validated detection technologies. The hypervariable minisatellite, MSY1, is the most polymorphic single locus system found on the Y-chromosome but difficulties with the required minisatellite variant repeat (MVR) technique have discouraged its operational use. Y-STR loci, on the other hand, offer a number of advantages, including good discrimination potential, ease of analysis, and a number of available candidate loci amenable to multiplex analysis.

Although more than three hundred STR loci have been described on the Y-chromosome, a much more limited number have been appropriately evaluated for forensic casework use and some of these have presented a particular challenge for assay design. The Y-STR loci comprise di-, tri-, tetra-, and penta-nucleotide repeats with the di-nucleotides exhibiting the most polymorphism but an excessively high level of stutter artifacts.¹⁵ Due to their evolutionary relatedness, many homologous sequences are found on both the X- and Y-chromosomes, which can confound the analysis of mixed male/female specimens. Additionally, some of the loci are bi-local in the sense that one or both of the primer sites and associated tandem repeats are duplicated upstream or downstream of the parent sequence. In these particular cases, two alleles are co-amplified, and there is some, but not complete, correlation between the alleles at both loci. Importantly, sample quantity limitations with forensic specimens require that candidate Y-STR loci be analyzed together in a parallel fashion by incorporating them into a multiplex PCR (Polymerase Chain Reaction) assay format, the design of which can be complicated by some of the aforementioned factors.

A major international multicenter study of 13 candidate Y-STR markers in 1997 resulted in recommendations for the use of nine core loci for standard forensic haplotyping (designated the minimal haplotype loci, MHL or minHt).¹⁶ The nine MHL loci include:

• DYS19
• DYS 385 (a)
• DYS 385 (b)
• DYS389 I
• DYS389 II
• DYS390
• DYS391
• DYS392
• DYS393

Subsequent to the development of the MHL loci, additional microsatellite loci were described that proved to have utility in forensic genetics. In January 2003 the Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended for US forensic casework use a set of eleven core loci that included the MHL loci plus DYS 438 and DYS 439.

Commercial kit vendors in the US have incorporated the SWGDAM core loci into their Y-STR multiplex systems (ABI, Promega and Reliagene), which comprise eleven (Reliagene's Y-PLEX-12TM), twelve (Promega's PowerPlex YTM) or seventeen (Applied Biosystems' Y-FilerTM ) Y-STR loci (see Table).  These kits have been fully validated for forensic use according to the SWGDAM developmental validation guidelines. The kits have been designed to perform with a high degree of specificity for Y-chromosome sequences in the presence of a vast excess of X-chromosomal DNA from a female, despite the previously described extensive sequence homology between both chromosomes.

Read the Revised Validation Guidelines by SWGDAM in July 2004.

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