Forensic typing of autosomal SNPs with a 29 SNP-multiplex—Results of a collaborative EDNAP exercise J.J. Sanchez a,m , C. Børsting a , K. Balogh d , B. Berger e , M. Bogus d , J.M. Butler c , A. Carracedo f , D. Syndercombe Court h , L.A. Dixon b , B. Filipovic ´ l , M. Fondevila f , P. Gill b , C.D. Harrison h , C. Hohoff i , R. Huel l , B. Ludes g , W. Parson e , T.J. Parsons l , E. Petkovski g , C. Phillips f , H. Schmitter j , P.M. Schneider k , P.M. Vallone c , N. Morling a, * a Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V’s Vej, DK-2100 Copenhagen, Denmark b The Forensic Science Service, Research and Development, Trident Court, Birmingham, UK c National Institute of Standards and Technology, Gaithersburg, MD, USA d Institute of Legal Medicine, Johannes Gutenberg University, Mainz, Germany e Institute of Legal Medicine, Innsbruck Medical University, Austria f Institute of Legal Medicine, University of Santiago de Compostela, Spain g Institut de Me ´dicine Legale, Strasbourg, France h Centre for Haematology, Queen Mary’s School of Medicine and Dentistry, London, UK i Institut fu ¨r Rechtsmedizin, Universita ¨tsklinikum Mu ¨nster, Germany j Bundeskriminalamt, Wiesbaden, Germany k Institute of Legal Medicine, University of Cologne, Germany l International Commission on Missing Persons, Sarajevo, Bosnia and Herzegovina m National Institute of Toxicology and Forensic Sciences, Canary Islands Delegation, Spain Received 1 October 2007; accepted 5 December 2007 Abstract We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot kit, capillary electrophoresis and multicolour fluorescence detection. For practical reasons, only the 29 SBE multiplex reaction was carried out by the participating laboratories. A total of 11 bloodstains on FTA cards including a sample of poor quality and a negative control were sent to the laboratories together with the essential reagents for the initial multiplex PCR and the multiplex SBE reaction. The total SNP locus dropout rate was 2.8% and more than 50% of the dropouts were observed with the poor quality sample. The overall rate of discrepant SNP allele assignments was 2.0%. Two laboratories reported 60% of all the discrepancies. Two laboratories reported all 29 SNP alleles in all 10 positive samples correctly. The results of the collaborative exercise were surprisingly good and demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: Forensic genetics; Single nucleotide polymorphism; Multiplex PCR; Single base extension; Human identification; EDNAP exercise 1. Introduction Single nucleotide polymorphisms (SNPs) have a number of features that make them useful for forensic genetic investiga- tions. Firstly, they are abundant throughout the human genome [1]. Secondly, SNPs can be typed by automated, low-cost www.elsevier.com/locate/fsig Available online at www.sciencedirect.com Forensic Science International: Genetics 2 (2008) 176–183 Abbreviations: RFU, relative fluorescence unit; SBE, single base exten- sion; SNP, single nucleotide polymorphism. * Corresponding author. E-mail address: niels.morling@forensic.ku.dk (N. Morling). 1872-4973/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2007.12.002