Announcement of Population Data A study of East Timor variability using the SNPforID 52-plex SNP panel C. Santos a,b , C. Phillips a, *, M. Fondevila a , L. Porras-Hurtado a,c ,A ´ . Carracedo a , L. Souto b , M.V. Lareu a a Forensic Genetics Department, Genomic Medicine Group, University of Santiago de Compostela and Centro Nacional de Genotipado (CeGen), Genomic Medicine Group, Hospital Clı´nico Universitario, Galicia, Spain b Departamento de Biologia, Universidade de Aveiro, 3810-193 Aveiro, Portugal c Medical Genetic Laboratory, Universidad Tecnolo ´gica de Pereira, Colombia Population: Forty-six unrelated individuals from the East Timor population, including the regions of the Oecussi-Ambeno enclave and Atau ´ ro Island. Samples from volunteers were collected with informed consent. This study followed the guidelines for publication of forensic population data [1]. Samples and DNA extraction: Blood samples were preserved on FTA cards (Whatman, Florham Park, USA). DNA was extracted by standard phenol/chloroform methods. SNP genotyping assay: We used the 52-plex assay developed by Sanchez et al. [2]. The assay is based on a single 52-plex PCR amplification followed by two multiplexed single base extension (SBE) reactions of 23 and 29 SNPs using the SNaPshot TM primer extension kit (Applied Biosystems: AB, Foster City, CA, USA). PCR amplification conditions: 1–10 ng of DNA was amplified in a 15 ml total reaction volume containing 0.83 Â PCR buffer (without MgCl 2 ), 0.83 Â BSA, 5.42 mM MgCl 2 , 580 mM of each dNTP, 0.008–0.136 mM of each primer and 1 U AmpliTaq TM Gold DNA polymerase (AB) (adapted from [2]). The amplification was performed in a GeneAmp 1 PCR System 9700 (AB) according the following cycling program: denaturation at 95 8C for 10 min, 35 cycles of 95 8C for 30 s, 60 8C for 50 s and 65 8C for 40 s, followed by a final elongation step at 65 8C for 6 min. Successful amplification was verified by electrophoresis of products in a T 9 C 5 acrylamide gel. Then 2.5 ml of PCR product was purified with 1 ml of ExoSAP-IT (GE Healthcare, Amersham, UK) by incubation at 37 8C for 45 min followed by 85 8C for 15 min [2]. SBE reaction conditions: Single base extension was performed in a total volume of 6 ml containing 2 ml of purified PCR product, 2.5 ml of SNaPshot Ready Reaction mix (AB) and 1.5 ml of SBE primer mix. The extension was performed on a GeneAmp 9700 with 35 cycles at 96 8C for 10 s, 55 8C for 5 s and 60 8C for 30 s. The SBE products were then purified using 1 U of SAP (1 U/ml) with incubation at 37 8C for 80 min and 85 8C for 15 min [2]. Electrophoresis: 3 ml of purified SBE product was mixed with 10 ml of Hi-Di formamide (AB) and 0.3 ml of 120-LIZ TM internal size standard (AB). Capillary electrophoresis was performed with an AB Prism 3130 Genetic Analyzer using 50 cm capillary arrays with POP-6 polymer and analyzed with GeneMapper TM 3.2 [2]. Data and statistical analysis: Data completeness was 99.4% (10 SNPs with single genotype gaps and 2 SNPs with two gaps). Allele frequencies, observed and expected heterozygosity, Hardy–Wein- berg (HW) equilibrium analysis and pairwise population F ST values were calculated using Arlequin 3.11 computer software. For the HW test the significance level was corrected by the Bonferroni method and P-values <0.00096 were considered statistically significant [3,4]. Forensic and paternity parameters (random match prob- ability and discrimination power, plus exclusion power and typical paternity index, respectively) were calculated using Promega Forensic Science International: Genetics 5 (2011) e25–e26 ARTICLE INFO Article history: Received 2 August 2009 Received in revised form 15 March 2010 Accepted 15 March 2010 Keywords: East Timor 52-Plex assay Autosomal SNPs SNPforID Human identification ABSTRACT A set of 52 autosomal single nucleotide polymorphism (SNP) loci was analyzed in 46 unrelated individuals from the East Timor population using the forensic assay previously described by Sanchez et al. (2006) [J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe Court, PM. Schneider, A ´ . Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713–1724]. Allele frequencies are presented for the 52 SNPs with all loci in Hardy–Weinberg equilibrium for the study population. Comparison with African, European, East Asian and Oceanian populations of the CEPH human genome diversity panel (CEPH-HGDP) revealed significant differences in allele frequency distributions between East Timor and each of the above population groups. Statistical parameters measuring forensic informativeness were also calculated and the values obtained reached comparable levels to those previously described for the other global population groups. This is the first study of variability in these SNPs in an Oceanian population outside of the CEPH-HGDP. ß 2010 Elsevier Ireland Ltd. All rights reserved. * Corresponding author. Tel.: +34 981 582 327; fax: +34 981 580 336. E-mail address: c.phillips@mac.com (C. Phillips). 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.2010.03.006