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

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

Research output: Contribution to journalArticle

19 Citations (Scopus)

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 250-500 pg 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, 500 pg 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 500 pg 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 500 pg 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.

Original languageEnglish
Pages (from-to)369-375
Number of pages7
JournalForensic Science International: Genetics
Volume5
Issue number5
DOIs
StatePublished - 1 Nov 2011

Fingerprint

Single Nucleotide Polymorphism
DNA
Amelogenin

Keywords

  • Autosomal SNPs
  • Degraded DNA
  • Forensic science
  • GenPlex™ HID

Cite this

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. / Autosomal SNP typing of forensic samples with the GenPlex™ HID System : Results of a collaborative study. In: Forensic Science International: Genetics. 2011 ; Vol. 5, No. 5. pp. 369-375.
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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 250-500 pg 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, 500 pg 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 500 pg 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 500 pg 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.",
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Tomas, C, Axler-Diperte, G, Budimlija, ZM, Børsting, C, Coble, MD, Decker, AE, Eisenberg, A, Fang, R, Fondevila, M, Frisk Fredslund, S, Gonzalez, S, Hansen, AJ, Hoff-Olsen, P, Haas, C, Kohler, P, Kriegel, AK, Lindblom, B, Manohar, F, Maroñas, O, Mogensen, HS, Neureuther, K, Nilsson, H, Scheible, MK, Schneider, PM, Sonntag, ML, Stangegaard, M, Syndercombe-Court, D, Thacker, CR, Vallone, PM, Westen, AA & Morling, N 2011, 'Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study', Forensic Science International: Genetics, vol. 5, no. 5, pp. 369-375. https://doi.org/10.1016/j.fsigen.2010.06.007

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.

In: Forensic Science International: Genetics, Vol. 5, No. 5, 01.11.2011, p. 369-375.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Autosomal SNP typing of forensic samples with the GenPlex™ HID System

T2 - Results of a collaborative study

AU - Tomas, C.

AU - Axler-Diperte, G.

AU - Budimlija, Z. M.

AU - Børsting, C.

AU - Coble, M. D.

AU - Decker, A. E.

AU - Eisenberg, A.

AU - Fang, R.

AU - Fondevila, M.

AU - Frisk Fredslund, S.

AU - Gonzalez, S.

AU - Hansen, A. J.

AU - Hoff-Olsen, P.

AU - Haas, C.

AU - Kohler, P.

AU - Kriegel, A. K.

AU - Lindblom, B.

AU - Manohar, F.

AU - Maroñas, O.

AU - Mogensen, H. S.

AU - Neureuther, K.

AU - Nilsson, H.

AU - Scheible, M. K.

AU - Schneider, P. M.

AU - Sonntag, M. L.

AU - Stangegaard, M.

AU - Syndercombe-Court, D.

AU - Thacker, C. R.

AU - Vallone, P. M.

AU - Westen, A. A.

AU - Morling, N.

PY - 2011/11/1

Y1 - 2011/11/1

N2 - 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 250-500 pg 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, 500 pg 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 500 pg 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 500 pg 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.

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KW - Autosomal SNPs

KW - Degraded DNA

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