Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study

Tomas, C.; Axler-DiPerte, G.; Budimlija, Z.M.; Børsting, C.; Coble, M.D.; Decker, A.E.; Eisenberg, A.; Fang, R.; Fondevila, M.; Frisk Fredslund, S.; Gonzalez, S.; Hansen, A.J.; Hoff-Olsen, P.; Haas, C.; Kohler, P.; Kriegel, A.K.; Lindblom, B.; Manohar, F.; Maroñas, O.; Mogensen, H.S.; Neureuther, K.; Nilsson, H.; Scheible, M.K.; Schneider, P.M.; Sonntag, M.L.; Stangegaard, M.; Syndercombe-Court, D.; Thacker, C.R.; Vallone, P.M.; Westen, A.A.; Morling, N.

doi:10.1016/j.fsigen.2010.06.007

« Previous Next »Forensic Science International: Genetics
Volume 5, Issue 5 , Pages 369-375, November 2011

Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study

C. Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹
- Corresponding author. Tel.: +45 35326283; fax: +45 35326270.
G. Axler-DiPerte
- New York City Office of Chief Medical Examiner, Department of Forensic Biology New York, NY, USA
Z.M. Budimlija
- New York City Office of Chief Medical Examiner, Department of Forensic Biology New York, NY, USA
C. Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹
M.D. Coble
- Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, Rockville, MD, USA
A.E. Decker
- U.S. National Institute of Standards and Technology, Biochemical Science Division, Gaithersburg, MD, USA
A. Eisenberg
- University of North Texas Health Science Center, Institute of Investigative Genetics, University of North Texas for Human Identification, Fort Worth, TX, USA
R. Fang
- Applied Biosystems/Life Technologies, Foster City, CA, USA
M. Fondevila
- Institute of Legal Medicine, Genomic Medicine Group, University of Santiago de Compostela, Spain
S. Frisk Fredslund
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹
S. Gonzalez
- University of North Texas Health Science Center, Institute of Investigative Genetics, University of North Texas for Human Identification, Fort Worth, TX, USA
A.J. Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹
P. Hoff-Olsen
- Institute of Forensic Medicine, University of Oslo, Rikshospitalet, Norway
C. Haas
- Institute of Legal Medicine, University of Zurich, Switzerland
P. Kohler
- Institute of Forensic Medicine, University of Oslo, Rikshospitalet, Norway
A.K. Kriegel
- Institute of Legal Medicine, University Hospital, Cologne, Germany
B. Lindblom
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
F. Manohar
- Applied Biosystems/Life Technologies, Foster City, CA, USA
O. Maroñas
- Institute of Legal Medicine, Genomic Medicine Group, University of Santiago de Compostela, Spain
H.S. Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹
K. Neureuther
- Federal Criminal Police Office, Wiesbaden, Germany
H. Nilsson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
M.K. Scheible
- Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, Rockville, MD, USA
P.M. Schneider
- Institute of Legal Medicine, University Hospital, Cologne, Germany
M.L. Sonntag
- Federal Criminal Police Office, Wiesbaden, Germany
M. Stangegaard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹
D. Syndercombe-Court
- Academic Haematology Unit, BICMS Pathology Group, Barts and The London School of Medicine and Dentistry, London, UK
C.R. Thacker
- Academic Haematology Unit, BICMS Pathology Group, Barts and The London School of Medicine and Dentistry, London, UK
P.M. Vallone
- U.S. National Institute of Standards and Technology, Biochemical Science Division, Gaithersburg, MD, USA
A.A. Westen
- Department of Human Biological Traces (R&D), Netherlands Forensic Institute, The Hague, The Netherlands
N. Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark¹

Received 17 May 2010; received in revised form 24 June 2010; accepted 24 June 2010. published online 23 July 2010.

Abstract

The GenPlex™ HID System (Applied Biosystems – AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex™ HID System using 250–500pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex™ HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the GenPlex™ HID System with the most commonly used STR kits, 500pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two thirds of the locus dropouts. The median percentage of discrepant results was 0.2% with 500pg degraded DNA. An increasing percentage of locus dropouts and discrepant results were observed when lower amounts of DNA were used. Different success rates were observed for the various SNPs. The rs763869 SNP was the least successful. With the exception of the MiniFiler™ kit (AB), GenPlex™ HID performed better than five other tested STR kits. When partly degraded DNA was analyzed, GenPlex™ HID showed a very low mean mach probability, while all STR kits except MiniFiler™ had very limited discriminatory power.