International Journal of Legal Medicine

, Volume 121, Issue 4, pp 297–301

Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus™ and PowerPlex® 16

  • Nancy Vanderheyden
  • Ahnly Mai
  • Anja Gilissen
  • Jean-Jacques Cassiman
  • Ronny Decorte
Original Article

DOI: 10.1007/s00414-007-0167-5

Cite this article as:
Vanderheyden, N., Mai, A., Gilissen, A. et al. Int J Legal Med (2007) 121: 297. doi:10.1007/s00414-007-0167-5

Abstract

During duplicate analysis of buccal swabs from 1,377 individuals with 2 commercial short tandem repeat (STR) kits, we observed 8 discordant phenotypes with SGM Plus™ (SGM, second generation multiplex) for the STRs THO1 (2), vWA (4) and D18S51 (2), and 1 discrepancy with PowerPlex® 16 for D18S51. One individual even showed two discrepancies (vWA and THO1) for SGM Plus™. In each case, the difference observed was due to the non-amplification or allele dropout of the second allele in a heterozygous genotype. Sequence analysis revealed each time the presence of a mutation that probably coincided with the primer-binding site. Primer-binding site mutations for vWA and D18S51 have been reported previously, while the mutation for THO1 (C-to-T substitution at position 1286 of GenBank sequence D00269) is reported here for the first time. While the frequency of these silent alleles remains low (0.58% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.

Keywords

SGM Plus™PowerPlex® 16Allele dropoutSilent allelePrimer-binding site mutation

Supplementary material

414_2007_167_MOESM1_ESM.doc (28 kb)
Table S1Primers used for PCR and cloning (DOC 29 kb)
414_2007_167_MOESM2_ESM.pdf (63 kb)
Figure S1a GeneMapper ID analysis of AmpFlSTR® SGM Plus™ result for Individual 4 with 2 silent alleles (vWA and THO1) b GeneMapper ID analysis of PowerPlex® 16 result for Individual 4 showing 2 with alleles (vWA and THO1). Allele dropout in vWA and THO1 (PDF 64 kb)
414_2007_167_MOESM3_ESM.pdf (47 kb)
Figure S2Aligned sequence of the observed mutation (A1631T) at the vWA locus in Individual 4. Upper panel shows a partial sequence of allele 18 with the mutation (A>T; GenBank accession number EF421234) and the lower panel shows a partial sequence of allele 14 with the wild type. The position of the mutation (gray background) in the sequence is indicated with a vertical arrow, the position of the PowerPlex® 16 primer with a horizontal arrow, and the tandem repeat sequence with a horizontal black bar. Sequence of A1631T mutation in vWA (PDF 48 kb)
414_2007_167_MOESM4_ESM.pdf (46 kb)
Figure S3Aligned sequence of the observed mutation (C1286T) at the THO1 locus in Individual 4. Upper panel shows a partial sequence of allele 9 with the wild type and the lower panel shows a partial sequence of allele 7 with the mutation (C>T; GenBank accession number EF421230). The position of the mutation (gray background) in the sequence is indicated with a vertical arrow and the position of the PowerPlex® 16 primer with a horizontal arrow. Sequence of C1286T mutation in THO1 (PDF 47 kb)
414_2007_167_MOESM5_ESM.pdf (46 kb)
Figure S4Aligned sequence of the observed mutation (G453A) at the D18S51 locus in Individual 7. Lower panel shows a partial sequence of allele 19 with the mutation (G>A; GenBank accession number EF421233) and the upper panel shows a partial sequence of allele 14 with the wild type. The position of the mutation (gray background) in the sequence is indicated with a vertical arrow and the position of the PowerPlex® 16 primer with a horizontal arrow. Sequence of G453A mutation in D18S51 (PDF 47 kb)
414_2007_167_MOESM6_ESM.pdf (47 kb)
Figure S5Sequence analysis of the observed mutation (G152A) at the D18S51 locus in Individual 8. Upper panel shows a partial sequence of allele 14 with the mutation (G>A; GenBank accession number EF421232) and the lower panel shows a partial sequence of allele 20 with the wild type. The position of the mutation (gray background) in the sequence is indicated with a vertical arrow and the position of the PowerPlex® 16 primer with a horizontal arrow. Sequence of G152A mutation in D18S51 (PDF 48 kb)

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Nancy Vanderheyden
    • 1
  • Ahnly Mai
    • 1
  • Anja Gilissen
    • 1
  • Jean-Jacques Cassiman
    • 1
  • Ronny Decorte
    • 1
  1. 1.Laboratory of Forensic Genetics and Molecular ArchaeologyK.U. Leuven, Campus Gasthuisberg O&NLeuvenBelgium