Population genetic data and forensic parameters of the 27 Y-STR panel Yfiler® Plus in Russian population

International Journal of Legal Medicine - This is the first report of a nation-wide study of the 27-STR Yfiler® Plus panel in the population of the Russian Federation. A total of 691 unrelated...     

Evaluation of forensic genetic efficiency parameters of 22 autosomal STR markers (PowerPlex® Fusion system) in a population sample of Arab descent from Jordan

Jordan is a country located in the Middle East, on the East Bank of the Jordan River. In this study, the PowerPlex® Fusion (PPF) system was used to determine the allele frequencies and forensic efficiency parameters of 22 autosomal STR loci. Autosomal STR information was collected from the blood samples of 500 individuals belonging to the Jordanian population of Arab descent. The PPF system (Promega Corporation) was used to amplify the 22 autosomal STRs and the amplified samples were analysed on the 3130xl Genetic Analyser using GeneMapper ID-X 1.2 software (Applied Biosystems). All the autosomal STR loci met the requirements of the Hardy-Weinberg equilibrium after Bonferroni correction. This study revealed that the most informative locus among the 22 STR loci (excluding Amelogenin and DYS39) was Penta E locus (power of discrimination (PD) = 0.99), while the least informative locus was TPOX locus (PD = 0.834). The combined matching probability (MP) of the 22 loci was 1.9 × 10^?28. These forensic genetic parameters indicated the practicality of analysing these 22 STRs in forensic DNA identification and paternity testing among individuals from the Jordanian Arab population.     

Genetic data of 22 autosomal STR loci in Khyber-Pakhtunkhwa,Balochistan and Gilgit Baltistan population of Pakistan using PowerPlex® fusion system

In this study we have provided forensic genetic data of 22 autosomal STRs for Pakhtun, Balochi and Balti population of Pakistan in total of 601 samples. Among these loci, Penta E was found the most discriminatory in all groups and allele 15 was observed most frequent at D22S1045 in Balti whereas in other two populations allele 8 was more common at TPOX. The combined power of discrimination, combined power of exclusion and the combined matching probability was calculated as 0.999999999999999999999999998385, 0.999999988089728 and 1.615 × 10^-27 respectively. Based on population differentiation test, significant differences were observed when compared with other populations however, phylogenetic analysis revealed close genetic associations among Pakistani Populations.     

Phylogenetic and forensic studies of the Southeast Florida Hispanic population using the next-generation forensic PowerPlex® Y23 STR marker system

The purpose of this study is to examine the robustness and sensitivity of the newly available Y-STR multiplex kit, the PowerPlex® Y23 System, by comparing our data at the 23-loci level to the routinely used 17 loci provided by the AmpFlSTR® Yfiler® PCR Amplification kit. For the first time, allelic and genotypic frequencies for the 23 Y-STR loci included in the PowerPlex® Y23 System are provided for the Southeast Florida Hispanic (SFH) population. In addition, we have characterized the SFH population in terms of intra-population and inter-population parameters. We also compared these indices of forensic and population genetics interest in the SFH population to comparable data of previously published populations to assess their phylogenetic relationships. Our 23-loci data was shown to provide more discriminatory values as compared to the data when using only 17 loci. Also, the R_ST distance values demonstrate the superior capacity of the PowerPlex® Y23 system to discriminate among populations.     

Evaluation of genetic parameters of 22 autosomal STR loci (PowerPlex® Fusion System) in a population sample from Northern Italy

The PowerPlex® Fusion System (Promega, Madison, WI) is a short tandem repeat (STR) multiplex that allows co-amplification of 22 autosomal STRs, including the CODIS core and the European Standard Set loci, plus amelogenin for gender determination and DYS391 male specific marker included in order to avoid errors in gender assignment when null Y-alleles or deletions of the Y-chromosome short arm involve the amelogenin locus. Allele frequencies and forensic efficiency parameters were estimated in a population sample of 303 unrelated healthy individuals living in Northern Italy. No significant deviations from Hardy–Weinberg expectations were observed after applying Bonferroni’s correction for multiple testing. The combined power of discrimination was 0.999999999999 and the combined power of exclusion was 0.9999956. A rare 28 allele at locus D12S391 was observed, while one tri-allelic pattern at Penta E locus was detected. Population differentiation test revealed significant genetic diversity between our population sample and other European populations considered. The results showed that the PowerPlex® Fusion System is one of the most informative kit available in forensic genetics and may prove useful in both human identification and kinship analysis.     

Genetic diversity study on 12 X-STR loci of investigator® Argus X STR kit in Bangladeshi population

The X-chromosome short tandem repeat (STR) loci are of particular interest for solving complex kinship and paternity cases. Here, we report the genetic data from 209 unrelated Bangladeshi individuals (102 males and 107 females) that were genotyped using the 12 X-chromosomal STR markers included in the Investigator® Argus X-12 kit (Qiagen). The 12 X-STR markers are located in four linkage groups (linkage group I: DXS10135, DXS10148, and DXS8378; linkage group II: DXS7132, DXS10079, and DXS10074; linkage group III: DXS10103, HPRTB, and DXS10101; and linkage group IV: DXS10146, DXS10134, and DXS7423). Allelic frequencies of the 12 X-STR loci and haplotype frequencies of the four linkage groups were investigated. No significant difference was observed in the allele frequencies of males and females. Distributions of heterozygosity were observed from 64.5 to 92.5% among the studied 12 X STR loci. DXS10135 and DXS10101 loci were found to be most polymorphic. For all the four linkage groups, the haplotype diversity was found to be greater than 0.986. A total of 95, 73, 66, and 74 haplotypes were observed in linkage groups I, II, III, and IV, respectively. Hardy–Weinberg equilibrium tests showed no significant deviation from expected values for all 12 loci (p > 0.05). The exact test for pairwise linkage disequilibrium for the 12 loci in the male samples did not show any significant linkage disequilibrium except the DXS10103 and DXS10101 loci after the p values were corrected by Bonferroni’s correction for multiple testing (p > 0.05/66). A combined power of discrimination in male and female individuals were 0.999999998159791 and 0.999999999999993, respectively. The combined mean exclusion chance were 0.999997635 in deficiency cases, 0.999999996 in normal trio cases, and 0.999999178 in duo cases. The currently investigated Bangladeshi population showed significant differences when compared with previously reported X-STR data from other 12 populations. The results of the data analysis indicated that all the loci in the Investigator® Argus X 12 kit were fairly informative and might be useful in forensic application and kinship analysis in Bangladeshi population.

     

Genetic data for PowerPlex 21™ autosomal and PowerPlex 23 Y-STR™ loci from population of the state of Uttar Pradesh,India

International Journal of Legal Medicine - In the present study, the statistical forensic parameters were evaluated for the loci present in PowerPlex 21 autosomal and PowerPlex 23 Y-STR multiplex...     

Evaluation of forensic genetic parameters of 12 STR loci in the Korean population using the InvestigatorⓇ HDplex kit

We genotyped and calculated the forensic parameters of 10 non-CODIS loci and 2 CODIS loci of 990 Korean individuals using the Investigator^Ⓡ HDplex kit. No significant deviations from Hardy–Weinberg equilibrium (after Bonferroni correction for multiple testing) or genetic linkage disequilibrium were observed. The calculated matching probability and power of discrimination ranged from 0.0080 to 0.2014, and 0.7986 to 0.9920, respectively. We conclude that the markers of the kit are highly informative corroborative tools for forensic DNA analysis.

     

Population genetic data of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS STR loci in four Canadian populations

Allele frequencies and forensically relevant population statistics were estimated for the short tandem repeat (STR) loci of the AmpF?STR® Identifiler® Plus and PowerPlex® 16 HS amplification kits, including D2S1338, D19S433, Penta D, and Penta E, for three First Nations Aboriginal populations and for Caucasians in Canada. The cumulative power of discrimination was ≥0.999999999999984 and the cumulative power of exclusion was ≥0.999929363 for both amplification systems in all populations. No significant departure from Hardy–Weinberg equilibrium was detected for D2S1338, D19S433, Penta D, and Penta E or the 13 Combined DNA Index System core STR loci after correction for multiple testing. Significant genetic diversity was observed between these four populations. Comparison with published frequency data for other populations is also presented.     

Genetic polymorphism investigation of the Chinese Yi minority using PowerPlex® Y23 STR amplification system

International Journal of Legal Medicine - Twenty-three Y-STR loci (DYS576, DYS389I, DYS389 II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392,...     

Performance of two 17 locus forensic identification STR kits-Applied Biosystems's AmpFℓSTR® NGMSElect™ and Promega's PowerPlex® ESI17 kits

We compared the performance of two recently released 17 loci STR multiplexes for human identification: Applied Biosystems's AmpF?STR^® NGMSElect? and Promega's PowerPlex^® ESI17. The comparative parameters were chosen by their relevance in forensic identification and particularly in crime cases. The comparative analyses encompass: amplification ability, heterozygote balance, allelic drop-out, drop-in, stutter analysis and inter-locus balance.Four DNA profiles were analysed in various concentrations in a serial dilution experiment. The amounts of DNA in the PCR ranged from 3 pg to 420 pg and were analysed in triplicate using 28, 29 and 30 PCR cycles. In order to compare the kits, aliquots from each sample were analysed with both kits under identical conditions. Furthermore, DNA profiles from 200 reference profiles were analysed using both kits.The results from the statistical analyses did not indicate any substantial differences of practical relevance between the kits for forensic case work. For all parameters included in this comparative study, the two kits showed no departure from previously observed patterns relative to e.g. the amounts of DNA or amplicon lengths. Based on our analyses, both kits are considered applicable for forensic crime case work.     

Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex® ESI 17 and AmpFℓSTR® NGM SElect™ in Somalis,Danes and Greenlanders

A concordance study of the results of PowerPlex^® ESI 17 and AmpFℓSTR^® NGM SElect™ kits obtained from 591 individuals from Somalia (N = 198), Denmark (N = 199) and Greenland (N = 194) was performed. Among 9456 STR types, seven discordant results were found with the two kits: one observed in the D19S433 system in an individual from Denmark and six in the SE33 system in six individuals from Somalia. Sequencing of SE33 in the six samples with discordant results showed G > A transition 15 bp downstream of the repeat unit in three of the individuals, and G > A transition 68 bp downstream of the repeat unit in the other three individuals. Population data for 16 autosomal STR systems analyzed in 989 individuals from Somalia, Denmark and Greenland are also presented. The highest mean heterozygosity was observed in Danes (82.5%). With the exception of D8S1179 in Danes, no significant deviations from Hardy–Weinberg expectations were observed. Only one pair of systems (D12S391 and D18S51) showed significant allelic association in Greenlanders (after Holm-Šidák correction). A MDS plot drawn from pairwise F_ST values calculated between 21 populations showed a clear displacement of the Greenlandic population versus the other ones included in the analyses. The highest combined chance of exclusion and power of discrimination was observed for Danes reaching values of 99.9999987% and 1 in 1.8 × 10²¹, respectively.     

Genetic variation analysis of 15 autosomal STR loci of AmpFℓSTR® Sinofiler™ PCR Amplification Kit in Henan (central China) Han population

AmpF?STR® Sinofiler? PCR Amplification Kit is specially developed for Chinese forensic laboratories, but there are little population-genetic indices about this kit as a whole. This kit contains 15 STR loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, D13S317, D16S539, D2S1338, D19S433, vWA, D18S51, D6S1043, D12S391, D5S818 and FGA. In order to evaluate this kit and to get basic population-genetic indices for its use in forensic practice in Chinese Han population, the DNA of 231 unrelated Han individuals from Henan (central China) were typed using the Kit. The most discriminating locus was D6S1043 while the least was D3S1358. The combined match probability was 9.81 × 10^?19 and the combined power of exclusion was 0.99999974. Statistical analysis of the generated data indicated no departure from expectation of Hardy–Weinberg Equilibrium (HWE) in all loci but D6S1043 and no linkage disequilibrium in all pairs of loci. The observed and expected heterozygosity, power of discrimination, polymorphic information content, the other population-genetic indices were calculated.     

Recognizing the advantage of employing the PowerPlex® ESI and PowerPlex® ESX complementary kits for purposes of clarification in routine casework

In an effort to promote European cross-border cooperation in fighting crime and international terrorism the Treaty of Prüm was drafted and accepted within the European forensic community. This move led to the commercial development of new multiplex kits which introduced five new STR loci and promised better performance. Recently the Israel Police DNA Casework and Database laboratories adopted the PowerPlex^® ESI kit for routine use in our laboratories. Presented in this paper are examples of three types of ambiguous results encountered during the implementation of the PowerPlex^® ESI kit into routine work. These ambiguous products presented themselves in the form of (1) extreme variants outside of loci borders, (2) failure to amplify sister allele pairs or expression of null alleles and (3) episodes of loss of separation of adjacent microvariants primarily in mixture samples. The re-analysis of all these samples using the PowerPlex^® ESX kit successfully and rapidly clarified all three categories of anomalies.Spotlighting such events to the forensic community, especially regarding the novel loci introduced in these next generation kits, can aid in raising the analyst's awareness to their future appearances and prevent possible erroneous conclusions. In addition, providing timely DNA results to investigating teams is of great importance and operational forensic laboratories do not have at their immediate disposal methods such as sequencing to elucidate such manifestations. We suggest that the complementary use of the PowerPlex^® ESI and PowerPlex^® ESX can provide a benefit for clarification purposes in routine casework.     

Evaluation of InnoTyper® 21 in a sample of Rio de Janeiro population as an alternative forensic panel

International Journal of Legal Medicine - The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of...     

Forensic evaluation of STR data for the PowerPlex™ 16 System loci in a Bangladeshi population

Allele frequencies of 15 autosomal STR loci included in PowerPlex™ 16 System were determined from a sample of 148 unrelated Bangladeshi individuals. Forensic efficiency parameters such as, the power of discrimination (PD), observed and expected heterozygosity (H), polymorphism information content (PIC), probability of match (PM), power of exclusion (PE), and typical paternity index were calculated for the loci. These parameters indicated the usefulness of the loci in paternity testing and personal identification in the Bangladeshi population.     

Development and evaluation of a rapid PCR method for the PowerPlex®S5 system for forensic DNA profiling

Forensic DNA profiling is a multi-step process taking approximately 10 h to complete. A reduction in the amount of time required for the amplification step would allow for faster human identification and increase laboratory throughput. The goal of this work was to optimize and evaluate a rapid PCR method for the PowerPlex®S5 system for forensic DNA profiling. By pairing fast chemistries with a fast thermal cycler, we were able to reduce the amplification time by 70% (1 h). Sensitivity and heterozygous peak height ratios were comparable between the fast and standard protocols. However, there was a notable decrease (5%) in peak height ratio at the D18S51 locus with the fast cycling method. An increase in average mean stutter for combined loci of 2.6% was observed in profiles amplified using the fast protocol compared to the standard system. Our results suggest that with further optimization and validation the fast protocol can be used to replace the standard amplification conditions.