Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system M.E. D’Amato a, *, V.B. Bajic b,c , S. Davison a a Forensic DNA Lab, University of the Western Cape, Biotechnology Department, Private Bag X17, 7535 Bellville, Cape Town, South Africa b SANBI (South African National Bioinformatics Institute), University of the Western Cape, South Africa c Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia 1. Introduction The success in the resolution of forensic cases is dependent upon an efficient recovery of DNA from the crime scene and the utilization of an efficient and discriminatory method of genetic profiling. Short Tandem Repeats on the Y-chromosome (Y-STRs) are highly valuable in forensics for their applicability to the study of sexual assault cases. In this context, the male biological material is usually recovered in a mixture with great excess of female’s cells or fluids, what makes the identification of somatic male markers virtually impossible. Therefore, targeting of male-specific DNA is the only experimental approach that would allow for the identification of the perpetrator. To enhance the recovery of information from such a crime scene, several differential DNA extraction protocols have been reported that favor the separation of semen from the victim’s epithelial cells (reviewed in [1]). In cases where the recovery of DNA applying differential extraction is hampered by degradation or sperm lyses, the identification of a male genetic profile is still possible, provided that the male DNA concentration is not too low. The application of Y-chromosome markers in forensics is then limited only when DNA mixtures contain DNA of related males, as only one genetic profile would be detected, and when male DNA quantities are below the level of detection for specific PCR conditions (reviewed in [2]). South Africa has one the highest incidence of rape in the world, with nearly 54,000 cases being reported yearly to the South African Police. Given the known utility of Y-STR markers for their application in sexual assault casework, we conducted preliminary surveys of the genetic diversity in the local metropolitan populations. The metropolitan area of Cape Town hosts approxi- mately three million inhabitants, with a complex composition of native population groups (mainly Xhosa, 31%), the descendants of Europe immigrants, mainly from English and Dutch origin (19%), India (0.5%), SE Asia (now admixed), and the admixed group resulting from the partial integration of these communities, named ‘‘coloured’’ (48%). Our studies of minimal haplotype (MH) loci showed low genetic diversity and poor haplotype resolution in the native group [3,4]. This observation encouraged further studies to identify loci with high informative value, and we extended the study to nearly 300 individuals of Xhosa, European and Indian ancestry to a total of 45 Y-STRs, including the MH loci, the additional loci incorporated in PowerPlex1Y System (Promega) [5] and AmpF‘STR1Y-filer TM (Applied Biosystems) [6], and additional non-core loci [7–9 and D’Amato et al., unpublished data). The minimal number of Y-STR loci that achieved the highest haplotype resolution (DYS710, DYS385ab, DYS447, DYS504, Forensic Science International: Genetics 5 (2011) 122–125 ARTICLE INFO Keywords: Y-STRs Multiplex Developmental validation Forensic genetics ABSTRACT The Y-chromosome STRs (short tandem repeat) markers are routinely utilized in the resolution of forensic casework related to sexual assault. For this, the forensic community has adopted a set of eleven (core) Y-STR that is incorporated in all commercial diagnostic systems. Our previous studies of Y-STR polymorphisms in the South African population identified low levels of diversity and discrimination capacity for many commercial marker sets, determining a limited applicability of these systems to the local population groups. To overcome this shortcoming, we designed a Y-STR 10-plex system that shows higher discriminatory capacity (DC) than available commercial systems. The markers were selected from a population group of 283 individuals with African, European and Asian ancestry genotyped at 45 Y-STRs, applying an optimization based selection procedure to achieve the highest possible DC with the minimal number of markers. The 10-plex was satisfactorily subjected to developmental validation tests following the SWGDAM guidelines and shows potential for its application to genealogical and evolutionary studies. ß 2010 Elsevier Ireland Ltd. All rights reserved. * Corresponding author. Tel.: +27 21 959 3372/2065; fax: +27 21 959 3505. E-mail address: medamato@uwc.ac.za (M.E. D’Amato). Contents lists available at ScienceDirect Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig 1872-4973/$ – see front matter ß 2010 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2010.08.015