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

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.

Development of a polymorphic short tandem repeat locus multiplex system for efficient human identification

“…Their study population demonstrated an excess of homozygotes at this locus when genotyped using AmpFlSTR Profiler Plus TM . Similar results were found by Budowle et al (2000) in the population of Chamorros and Filipinos on the Island of Guam, and by Vanderheyden et al (2007) in the population in Belga. The statistical parameters obtained showed high values (Table 2).…”

Development and validation for identity testing of I-DNADuo, a combination of I-DNA1 and a new multiplex system, I-DNA2

“…A concordance of 99.9% between the genetic profiles of the two components of the kit I-DNADuo was observed, a result similar to those of other concordance studies [8,9]. Previous studies have reported that these discordances were due to mutations which probably coincide with the 3′ end binding region of one of the primer pairs, so the combination of two kits with different primers is therefore of great interest in detecting and preventing allelic dropouts [10][11][12].…”

Population genetics data for 22 autosomal STR loci in European, South Asian and African populations using SureID® 23comp Human DNA Identification Kit

“…HDplex but 14, 16 on SureID® 23comp). Discordance between different STR kits have been reported previously [17][18][19][20], thus it is recommended that careful approach should be taken when comparing results or using population databases generated using other kits for SureID® 23comp kit profiles.…”