Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 Systems

doi:10.1016/j.fsigen.2010.03.014

Forensic Science International: Genetics

Volume 5, Issue 4, August 2011, Pages 269-275

https://doi.org/10.1016/j.fsigen.2010.03.014 Get rights and content

Abstract

The PowerPlex^® ESX 17 and ESI 17 Systems for short tandem repeat (STR) amplification were developed by the Promega Corporation to meet the European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling (EDNAP) Group recommendations for increasing the number of STR loci included in the European Standard Set (ESS). The PowerPlex ESX 17 and ESI 17 Systems utilize different PCR primer combinations to co-amplify the following 17 loci: D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, vWA, SE33, and the sex-typing locus amelogenin. A total of 1443 U.S. population samples were evaluated with pre-commercialization versions of both kits. Stutter and heterozygote peak height ratios have been used to characterize kit performance. Typing results have been used to estimate the match probabilities provided by the chosen loci as well as in concordance studies. Full concordance between the typing results for the two kits was observed in 99.994% (49,055 out of 49,062) STR allele calls compared. All genotyping discrepancies were confirmed by DNA sequence analysis. As a result of these comparisons, a second forward primer for the D22S1045 locus has been added to the PowerPlex ESX 17 System to address a primer binding site mutation and the D1S1656 locus reverse primer in the PowerPlex ESI 17 System was modified to eliminate an amplification-efficiency reducing primer dimer.

Introduction

As many national DNA databases are growing at a rapid rate, concern for the potential of false matches with a large number of comparisons being made within and between databases has prompted the desire to add additional loci [1], [2], [3]. This is particularly important in Europe where cross-border criminal investigations need to be able to compare DNA data between countries [3], [4]. The original European Standard Set (ESS) includes only seven loci: D3S1358, D8S1179, D18S51, D21S11, FGA, TH01, and vWA [3]. In 2006, the European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling (EDNAP) groups published recommendations to extend the ESS loci [5], [6] by adopting three miniSTR loci [7]: D2S441, D10S1248, and D22S1045, as well as two additional polymorphic loci [8]: D1S1656 and D12S391.

The recently released PowerPlex^® European Systems from the Promega Corporation (Madison, WI) were created to include these extra loci and meet the ENFSI and EDNAP 2006 requests [9]. The PowerPlex ESX 17 (PP-ESX17) and PowerPlex ESI 17 (PP-ESI17) Systems allow co-amplification of 17 STR loci with different size range and dye label configurations as shown in Fig. 1 [10], [11]. The PowerPlex ESX 16 (PP-ESX16) and PowerPlex ESI 16 (PP-ESI16) Systems are the same as the PP-ESX17 and -ESI17 Systems with the exception that they do not co-amplify the SE33 locus.

While the PP-ESX17 and PP-ESI17 Systems amplify the same STR loci, different polymerase chain reaction (PCR) primer sequences are utilized for 13 of the 16 STR loci (including SE33) enabling cross-checking for potential primer binding site mutations when the same DNA samples are examined with both kits [12], [13]. In order to assess the frequency of allele dropout due to primer binding site mutations, concordance studies were performed between the two new kits as well as other widely used kits [14], [15]. In addition, heterozygote peak height ratios and stutter percentages were evaluated as part of characterizing kit performance [16]. Population variation for the 16 STR loci in U.S. Caucasian, African American, Hispanic, and Asian groups are also reported [17].

Section snippets

DNA samples

Anonymous liquid blood samples with self-identified ethnicities were purchased from Interstate Blood Bank (Memphis, TN) and Millennium Biotech, Inc. (Ft. Lauderdale, FL) and extracted, quantified, and previously typed with the Identifiler^® kit (Applied Biosystems, Foster City, CA) [18], the PowerPlex^® 16 (PP16) System (Promega, Madison, WI) (data not published), MiniFiler^® kit (Applied Biosystems) [19], and the three in-house assays: NIST-23plex, -NC01 and -NC02 [20]. A set of father and son

Amplicon size differences between STR kits

The amplicon size differences in base pairs (bp) for each locus in the PowerPlex European Systems were determined for PP-ESI17, PP16, and Identifiler relative to the PP-ESX17 System. The size differences are summarized in Table 3. Several of the primer sets that were used in the new European kits are the same as in PP16. Many of the loci that are smallest in size for PP-ESX17 (<200 bp) were designed to be larger in the PP-ESI17 kit (>200 bp). Since some loci are not present in one or both of the

Conclusions

The new PP-ESX17 and -ESI17 Systems produce well-balanced PCR products across all loci tested and offer high powers of discrimination with the extended European Standard Set. Both kits have high concordance rates across all NIST samples tested and enable robust comparisons to current commercial multiplex kits including Identifiler and PP16.

While these kits offer high powers of discrimination as compared to the other PCR amplification kits, two of the loci (vWA and D12S391) included in both kits

Acknowledgements

The authors express appreciation for the technical assistance of Jan Redman and Richard Schoske in the initial preparation and quantitation of the NIST U.S. population samples used in this study and to Tom Reid for supplying the DNA Diagnostics Center (DDC) father/son samples. This work was funded in part by the National Institute of Justice (NIJ) through an interagency agreement 2008-DN-R-121 with the NIST Office of Law Enforcement Standards. Points of view in this document are those of the

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Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 Systems

Abstract

Introduction

Section snippets

DNA samples

Amplicon size differences between STR kits

Conclusions

Acknowledgements

Forensic Sci. Int.

Forensic Sci. Int.

Forensic Sci. Int.: Genet. Suppl. Ser.

Forensic Sci. Int.: Genet.

Forensic Sci. Int.: Genet. Suppl. Ser.

Matching and partially-matching DNA profiles

J. Forensic Sci.

The rarity of DNA profiles

Ann. Appl. Stat.

Expansion of the European Standard Set of DNA database loci—the current situation

Profiles DNA

Characterization of new miniSTR loci to aid analysis of degraded DNA

J. Forensic Sci.

Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex^® ESX 17 and ESI 17 Systems