False homozygosities at various loci revealed by discrepancies between commercial kits: implications for genetic databases

Delamoye, Magali; Duverneuil, Charlotte; Riva, Katia; Leterreux, Michel; Taieb, Stéphane; Mazancourt, Philippe de

doi:10.1016/j.forsciint.2004.02.001

Cited by 44 publications

(38 citation statements)

References 10 publications

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“…S5). Delamoye et al [11] reported previously the G152A mutation that is localized within the forward primer for D18S51 in PowerPlex® 16 (Fig. 1).…”

Section: Resultsmentioning

confidence: 89%

“…The impact of these mutations on the binding capacity of the Applied Biosystems primers is difficult to assess, as the primer sequences have not been published in contrast to those from the PowerPlex® 16 kit [18]. However, the mutation at vWA has been previously reported with a population frequency of up to 0.46% for several STR kits from Applied Biosystems [11,[19][20][21], and it has been confirmed that the mutation is localized at the second position from the 3′ end of the vWA forward primer in the kits from Applied Biosystems (Margaret Kline, personal communication) [22]. Although several reports have been published about allele dropout at THO1, none have provided data for the molecular basis of these discrepancies [10,21].…”

Section: Resultsmentioning

confidence: 99%

“…This problem becomes more acute with an increased exchange and comparison of DNA profiles or DNA databases from different European countries (e.g., Interpol DNA database, the Prüm Treaty). To overcome these potential false exclusions, it is necessary to implement appropriate database search algorithms so that differences of one allele are not classified as exclusion [11,22]. In addition, a record of the used primer set or commercial kit for the establishment of each DNA profile should be retained to clarify differences of one allele due to possible allele dropout [11].…”

Section: Resultsmentioning

confidence: 99%

“…Each kit uses locusspecific primers that are designed to bind to conserved flanking sequences of the STR locus. However, variations in the nucleotide sequence of the flanking sequences have been described, which may interfere with the binding of the primers [4][5][6][7][8][9][10][11][12][13][14]. As a result, false homozygosity could be observed due to an allele dropout.…”

Section: Introductionmentioning

confidence: 99%

“…As a result, false homozygosity could be observed due to an allele dropout. These primer-binding site mutations or silent alleles can be detected either by the use of different primer sets [5,11] or when deviation from Mendelian inheritance is observed in a family [10]. In the latter case, the parent and the offspring appear homozygous for different alleles at the same locus.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2007

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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.

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“…S5). Delamoye et al [11] reported previously the G152A mutation that is localized within the forward primer for D18S51 in PowerPlex® 16 (Fig. 1).…”

Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2007

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Variants in linkage status at D5S818 detected by multiple STR kits comparison and Sanger sequencing

Shao

Pan³

et al. 2021

Molec Gen & Gen Med

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Background D5S818 discrepancies have been reported in forensic parental testing due to null alleles. However, more cases may be ignored since proportional null alleles were missed without detection of heredity discrepancy between parents and offspring. Results In this study, null allele 12 at D5S818 was detected by the PowerPlex® 21 System with a higher occurrence rate on the basis of review on 2824 samples from the 1282 routine cases in Chinese Han population. Sequencing results revealed novel variant of guanine (G) into adenine (A) in the 7th [AGAT] repeats in the core repeat region accompanied by rs1187948322 in the samples with null allele 12. Conclusions Forensic STR typing may benefit from this discovery: (1) primer design of CE profiling system could be improved for sensitive population and (2) polymorphic information could be enriched for the accuracy and precision of NGS genotyping system. Peak area of D5S818 was also analyzed through different commercial STR kits. It is suggested that more attention should be paid on observed homozygosity with reduced peak area, especially for the samples from Chinese Han population.

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The new guidelines for paternity analysis in Germany—how many STR loci are necessary when investigating duo cases?

Poetsch

Preusse-Prange²,

Schwark³

et al. 2013

Int J Legal Med

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The requirements in the new German guidelines for paternity analysis have not only changed according to the so-called Gendiagnostikgesetz, the new German law regulating human genetic as well as paternity analyses, but also regarding the minimal number of short tandem repeats (STRs) which should be investigated (15 STRs) and the minimal required average exclusion chance (99.999 %). Even in paternity analyses involving only two people (e.g., father and child or mother and child), this exclusion chance is mandatory. A retrospective analysis of 330 father-child cases from our routine investigations showed in 142 cases (43 %) an individual exclusion chance below 99.999 % when using 15 STRs as required, in our routine work provided by the Powerplex® 16 kit which is reported to have an average exclusion chance of 99.988 %. Therefore, these same 330 father-child pairs were additionally analysed using the Powerplex® 21 kit and 120 of these duos were additionally analysed using the Powerplex® ESX17 kit enabling the analysis of 20 or 16 loci respectively. Now, an individual exclusion chance of more than 99.999 % could be achieved in 95.5 % (Powerplex® 21; calculation without the results of D6S1043), 98.8 % (Powerplex® 21; calculation with the results of D6S1043, using allele frequencies established in this study for a German and a West African population) and 98.3 % (Powerplex® ESX17). These data clearly demonstrate that in duo cases, more than the required 15 STR loci have to be investigated to obtain sufficient results.

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False homozygosities at various loci revealed by discrepancies between commercial kits: implications for genetic databases

Cited by 44 publications

References 10 publications

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

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

Variants in linkage status at D5S818 detected by multiple STR kits comparison and Sanger sequencing

The new guidelines for paternity analysis in Germany—how many STR loci are necessary when investigating duo cases?

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