The unique biology of the Y chromosome has led to the widespread use in forensic and evolutionary studies of genetic markers thereon in determining patrilineal relationships within and between population groups 
. A subset of these markers, minisatellites or short tandem repeats (Y-STRs), are now used routinely in certain forensic casework situations 
. Their intended use is not to supplant the current battery of autosomal STR loci but to apply them to certain defined casework situations whereby the traditional autosomal loci would not be expected to yield sufficient probative information. Y-STRs are particularly beneficial for the analysis of the male donor in a male/female DNA admixture when the female DNA component is present in vast excess (e.g. ≥100×) and when traditional autosomal STR analysis fails or is not possible 
Autosomal STR analysis may not be possible if the sample contains an admixture of body fluids other than semen, such as in saliva/saliva mixtures, saliva/vaginal secretion mixtures, or fingernail scrapings comprising cells from the (female) victim and cells from the perpetrator. In these types of samples a differential extraction to separate the male and female cells is not possible with current technology and the male component is often not detectable with the autosomal STR multiplex systems routinely used due to a titration of critical PCR reagents by the major contributor in the sample 
. Autosomal STR analysis may also fail with some semen containing samples in which the sperm are present in very low copy number, or are present in an extremely fragile state, such as in extended interval (i.e. >48 h) post-coital samples. Differential extraction of these particular samples may yield no profile from the male donor due to a combination of premature lysis of the sperm's cellular constituents into the non-sperm fraction and to sperm loss during the physical manipulations required of the DNA isolation process. Therefore, the use of Y-STRs, which target only the male fraction, eliminate the need for a differential extraction process and lessen the potential to lose the trace amounts of male DNA that may be present.
There are several additional benefits of Y-STR analysis in forensic casework. Y-STR analysis allows for the facile determination of the number of male contributors in mixtures. Y-STR profiles are hemizygous in nature, with one allele being found at most loci (the exception being a small number of multi-copy loci). Multiple alleles at single copy loci give a clear indication of the number of male contributors 
. Y-STR analysis can also aid in the identification of haplotypes of missing persons. While the X and Y chromosomes exhibit a degree of homology, they do not undergo genetic recombination during meiosis (except for the pseudoautosomal regions at the chromosome tip) 
. As a result, most of the Y chromosome is inherited paternally as a block of linked haplotype markers from generation to generation. Thus, males in the same lineage will possess identical Y-STR haplotypes allowing for the determination of a missing person's male haplotype by typing male relatives. Finally, Y-STR analysis can provide additional discriminatory power when combined with (often partial) autosomal STR profile results 
A set of nine Y-STR loci, commonly referred to as the “minimal haplotype loci” set (MHL), have been recommended for use in the forensic community 
. Subsequently, several additional loci were reported that, in conjunction with the MHL loci, proffered increased discriminatory capacity 
. A number of casework-validated commercial Y-STR kits are available and most incorporate 12–17 markers into single multiplex analysis systems 
. These commercial kits incorporate all twelve of the Y-STR ‘core’ markers that were recommended for forensic use by the US Scientific Working Group on DNA Analysis Methods (SWGDAM) 
. Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants.
A large number of Y-STR loci (>400) have been identified by various groups and deposited into public databases such as the GDB Human Genome Database (www.gdb.org
). A comprehensive annotated STR physical map of the human Y chromosome details the precise location of each locus along the chromosome 
. Despite the identification and positioning of hundreds of currently known Y-STR loci, a majority of these markers have not been fully characterized with respect to their utility in forensic casework.
A small number of studies have been published involving an in-depth evaluation of a significant numbers of these novel markers 
. A seminal study by Kayser and co-workers describes an extensive survey of human Y-chromosome microsatellites 
. While providing an extensive overview, less detail is provided on specific loci, with a small number of loci being identified as the “most variable”. However the gene diversity values used in classifying these loci as variable are based on a population size of only eight male samples. Current forensic literature is replete with small population data studies involving a few novel markers 
. However, simply describing individual allele frequencies in numerous populations is not sufficient to determine if a novel Y-STR could be used in forensic casework. While some of these markers may exhibit individually high gene diversity values, few studies have demonstrated the ability of these markers to aid in resolving coincidental matches.
Only a few novel non-‘core’ markers have been incorporated into multiplex PCR systems that have undergone the extensive developmental validation studies 
required, for example, by US national standards 
. Without such developmental validation studies it is not possible to evaluate whether the loci are sufficiently robust for use with degraded and limiting quantities of sample in a multiplex analysis format, or can provide sufficient additional discrimination potential when used in combination with other core Y-STR markers.
We have extensively evaluated one hundred and thirty three Y-STR loci (33% of all known loci) for possible use in forensic casework 
. Twenty five of these loci were rejected due to poor diversity values or amplification inefficiencies. The remaining one hundred and eight loci have been incorporated into ten multiplex systems that have undergone full developmental validations as required by industry standards (
, unpublished data). However, due to the limited amount of sample and limited resources of operational crime laboratories, it is unlikely that all ten multiplexes would be employed simultaneously to produce 108-locus profiles. Additionally, not every locus included in these multiplex systems would be beneficial in helping to distinguish between male individuals. Therefore in the present work, attempts were made to construct a non-core loci containing Y-STR multiplex system that, based upon empirical data, offered an extremely high discrimination potential and was robust enough for forensic use.
The result of these efforts was the development of an ultra-high discrimination (UHD) multiplex system incorporating fourteen novel Y-STR loci with a discriminatory capacity greater than that achieved with any commercial kit.