Forensic value of 14 novel STRs on the human Y chromosome

Abstract

We identified and characterized 14 novel short-tandem-repeats (STRs) on the Y chromosome and typed them in two samples, a globally diverse panel of 73 cell lines, and 148 individuals from a European–American population. These Y-STRs include eight tetranucleotide repeats (DYS449, DYS453, DYS454, DYS455, DYS456, DYS458, DYS459, and DYS464), five pentanucleotide repeats (DYS446, DYS447, DYS450, DYS452, and DYS463), and one hexanucleotide repeat (DYS448). Sequence data were obtained to designate a repeat number nomenclature. The gene diversities of an additional 22 Y-STRs, including the most commonly used in forensic databases, were directly compared in the cell line DNAs. Six of the 10 most polymorphic markers include the newly identified Y-STRs. Furthermore, these novel Y-STRs greatly improved the resolution of paternal lineages, above the level obtained with commonly used Y-STRs, in the European–American population.

Introduction

Short-tandem-repeats (STRs) markers on the Y chromosome are valuable tools in sexual assault cases. Sex crime evidence is often made up of sample mixtures of semen from the assailant and cells from the victim. Conventional techniques can separate sperm from the female components, however, complete separation is not always achieved. In addition, sample mixtures that derive from vasectomized or azoospermic males preclude sperm-based separations. Moreover, sample mixtures that are analyzed with autosomal markers via PCR can suffer from competition between a relatively small male DNA component and a large female DNA component. Targeting male-specific polymorphisms on the non-recombining portion of the Y-chromosome (NRY) does not require the separation of sperm from female cells, and thus it improves the likelihood of obtaining male-specific DNA profiles in mixed samples. Y-STR typing will be especially useful in sample mixtures involving: (1) one or more male semen donors, (2) vasectomized or azoospermic men, and (3) the presence of other body–fluid mixtures (e.g. saliva–skin, skin–sweat) from victims and suspects of different sex [1], [2], [3], [4]. The primary limitation of Y-STRs in forensic applications is the lack of independence of these markers on the NRY, that is, the absence of recombination. Y-STRs commonly differentiate unrelated Y chromosomes (i.e. paternal Y lineages), while autosomal STRs can differentiate any two individuals with high statistical confidence. Nonetheless, Y-STRs provide a valuable addition to the forensic scientist’s tool kit. As more variable Y-STRs are discovered the potential to distinguish paternal lineages increases.

Approximately 35 Y-STRs have been described to date [1], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15]. In total, these Y-STRs include: four dinucleotide (YCAI, YCAII, YCAII, and DYS288) six trinucleotide (DYF371, DYS388, DYS392, DYS425, DYS426, DYS436), 23 tetranucleotide (DYS19, DYS385, DYS389I, DYS389AB, DYS390, DYS391, DYS393, DYS434, DYS435, DY437, DYS439, DYS441, DYS442, DYS443, DYS444, DYS445, DYS460, DYS461, DYS462, G10123, A10, C4, and H4), and two pentanucleotide repeats (DXYS156Y, and DYS438). Most of the Y-STR primer pairs amplify one PCR product, while some Y-STR primer pairs amplify two or more PCR products (YCAI, YCAII, YCAIII, DYF371, DYS385, G10123). We refer to the former Y-STRs as single-copy, and to the latter as multi-copy because they are present in more than one copy on the NRY.

With the exception of one multicenter-study using 13 Y-STRs [1], global population screens using the majority of the published Y-STRs have not been performed. One recent study [15] compared a collection of 19 Y-STRs in a large sample of individuals from the Iberian Peninsula. Much progress has been made in establishing a large database of many European populations using the following Y-STRs: DYS19, DYS385, DYS389I, DYS389II-I, DYS390, DYS391, DYS392, and DYS393. These Y-STRs define the “minimal haplotype”, while the addition of YCAII to the these Y-STRs has been termed the “extended haplotype” [1], [16], [17] (Y-STR Haplotype Reference Database http://www.ystr.charite.de/index_gr.html).

The identification of additional Y-STRs is warranted for several reasons. First and foremost, increasing the number of highly polymorphic markers will improve the ability to distinguish paternal lineages. There are shared Y-STR haplotypes in populations because either males share identity by descent or because a particular set of Y-STRs does not distinguish closely related, but different, paternal lineages. In a sample of 41 European populations the discrimination capacities were 52% (n=4688 individuals) and 71% (n=1957 individuals) using the minimal and extended sets of Y-STRs, respectively [17]. The discrimination capacity in the Iberian Peninsula study [15] was 83% using 19 Y-STRs. The sharing of paternal lineages is likely to be more common in isolated populations where there is a higher degree of genetic drift, such as Native American populations. Second, there is a need to identify more Y-STRs that have longer repeats units. For example, YCAII is a polymorphic dinucleotide marker that suffers from “stutter” products during the PCR process due to polymerase slippage [18]. Stutter products are pronounced in dinucleotide repeats. Stutter bands are often reduced in longer repeat motif STRs, these loci can provide additional resolution in sample mixtures of multiple-male DNA profiles [19]. Third, a large pool of Y-STRs will provide a diverse sample of markers from which one can select tailored sets of STRs with distinct characteristics for multiplex design for particular applications. A small multiplex of the most informative Y-STRs could more efficiently distinguish Y-chromosome lineages than a set of a dozen or more less informative Y-STRs. Finally, increasing the number of Y-STRs will improve the estimation of the time to the most recent common ancestor (TMRCA). The TMRCA between two Y-STR haplotypes provides a natural metric to describe the relatedness between two individuals and could be used to make exclusions in forensics [20]. By including more Y-STRs, estimates of the TMRCA become more precise [21], [20]and the ability to exclude paternal relatives increases.

Here we describe variation among 14 novel Y-STRs and make comparisons with 22 previously identified Y-STRs. This is accomplished by comparing the gene diversities of these 36 Y-STRs in the same panel of 73 cell line DNAs. In addition, we demonstrate the forensic value of the new Y-STRs in a European–American population from South Dakota.