Population data of the AmpFlSTR® NGM™ loci in South Portuguese population

Allele frequencies and other relevant forensic parameters for 15 loci studied with AmpFlSTR(R) NGM™ kit were calculated in a population of individuals residing in the south of Portugal. Blood stain samples were obtained from a total of 452 unrelated individuals involved in paternity testing casework. The kit has five loci – D10S1248, D22S1045, D2S441, D1S1656 and D12S391 not present in any other kit used in our laboratory (Powerplex 16 System and Identifiler Plus). In our laboratory, this new kit is used as a screening tool to solve deficient cases as fatherless paternity test, and to help in paternity investigations with only one genetic incompatibility after the use of routine seventeen loci. Furthermore, this five loci included in the European Standard Set are also recommended by the European Network of Forensic Science Institutes “ENFSI” and the European DNA Profiling group “EDNAP”. These studies are necessary to calculate statistical forensic parameters such as power of discrimination, power of exclusion, minimum allele frequency. Statistical parameters such as heterozigoty, homozigoty and combined power of exclusion were determinated. This kind of study is part of the Quality Program for Certificated Forensic Laboratories.     

Korean population genetic data and concordance for the PowerPlex® ESX 17, AmpFlSTR Identifiler®, and PowerPlex® 16 systems

In case of paternity or maternity investigations with short tandem repeat (STR) analysis, deficient cases, missing person, or mutations are encountered and common STRs cannot provide sufficient forensic parameters. Thus, it is recommended that additional STRs are needed to complement conventional analysis for more reliable forensic information. We analyzed variation of 23 STRs contained in the new PowerPlex^® ESX 17 kit (Promega) and two conventional kits of the AmpFlSTR Identifiler^® (Applied Biosystems) and PowerPlex^® 16 systems (Promega) in 452 randomly chosen individuals from Korea to provide an expanded and reliable Korean database. Allele frequencies and forensic parameters were used to evaluate suitability and robustness of the new kit for forensic genetic analysis as well as in concordance studies. The combined probability of match for the 16 loci in the PowerPlex^® ESX 17 system was 2.76 × 10⁻²⁰. One genotyping discrepancy due to a null allele was observed at the D18S51 locus (the concordant rate = 99.99%), showing a primer-binding site mutation in the sequence of the locus (G-to-A substitution at position 146 of Genbank accession number JX018211). Thus, the new kit is a valuable forensic tool and is suitable to extend the Korean population genetic data obtained with well-established polymerase chain reaction multiplex-kits of the AmpFlSTR Identifiler^® and PowerPlex^® 16 systems.     

Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR® Y-filer™) in Casablanca resident population

Allele frequencies and population data for 17 Y-STR loci included in the AmpFlSTR? Y-filer? PCR amplification kit (Applied Biosystems, Foster City, USA), that permit the simultaneous amplification of all the markers included in the actually used European "extended haplotype", DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 166 healthy unrelated males resident in Casablanca (from Morocco). A total of 166 haplotypes were identified, of which 142 were unique. The overall haplotype diversity for the 17 Y-STR loci reached 0.9974, and a discrimination capacity was 0.855. We report some non-standard situations, including duplications and microvariant alleles.     

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.     

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...     

Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens

Though the utility of next-generation sequencing (NGS) technologies for forensic short tandem repeat (STR) typing has been evident for several years, commercially available assays and software solutions developed specifically to meet forensic needs have only recently become available. One of these, the ForenSeq™ DNA Signature Prep Kit (Illumina, Inc.) sequences 27 autosomal STR (aSTR) and 24 Y chromosome STR (Y-STR) loci (concurrent with additional nuclear markers) per multiplexed sample, with automated secondary and tertiary analyses of the data accomplished via the associated ForenSeq™ Universal Analysis Software (UAS). In this study we investigated the performance of the ForenSeq system for aSTR and Y-STR typing by examination of 151 sample libraries developed from high quality DNAs amplified at the target 1 ng template. Utilizing PCR Primer Mix B, greater than 99.5% of aSTR loci and 97.0% of Y-STR loci were recovered when 42 or fewer sample libraries were pooled for sequencing. A direct comparison of UAS developed fragment length results to capillary electrophoresis (CE) based data identified only two allele call discrepancies when no UAS quality flag was triggered. Review of the ForenSeq data indicated that most samples with total sequence read counts exceeding 40,000 could be interpreted to develop nearly complete aSTR genotypes or Y-STR haplotypes. However, markers D22S1045 and DYS392 produced poor or inconsistent results even when sample read counts were greater than 85,000. Excluding these two loci, analyst-interpreted aSTR and Y-STR ForenSeq profiles were 99.96% and 100% concordant, respectively, with CE data. In addition to demonstrating concordance on par with other CE kit to kit comparisons, the results from this study will assist laboratories seeking to develop workflows for high volume processing and analysis of aSTRs and Y-STRs from reference-type specimens using the ForenSeq system.     

Allele frequencies of 31 autosomal short tandem repeat (auSTR) loci obtained using the Precision ID GlobalFiler™ NGS STR Panel v2 in 322 individuals from the Japanese population

In human identification methods that target short tandem repeats (STRs), massively parallel sequencing (MPS) technology has made it possible to genotype at the level of the specific sequence itself. This allows for the detection of repeat unit variants and single nucleotide polymorphisms (SNPs) adjacent to the STRs. Using the GlobalFiler™ NGS STR Panel v2, Ion S5, and Converge software, this study constructed a Japanese database of 31 autosomal STRs (auSTRs) and two sex markers from 322 individuals. After excluding some sequence errors and stutters, a total of 31 novel alleles were identified. Additionally, using the allele frequencies of 31 auSTR loci, the match probabilities for the length-based and sequence-based data were calculated to be 1.433 × 10⁻³⁴ and 9.163 × 10⁻³⁸, respectively. These values are at least nine orders of magnitude higher than that obtained from 21 auSTR loci in the Japanese population using the conventional capillary electrophoresis method. The database generated in this study is expected to be implemented in forensic practice and used to solve difficult casework.     

Hungarian population data on the loci HLA-DQα, LDLR,GYPA, HBGG,D7S8 and GC

Population data studies for HLA-DQa and PM loci (LDLR, GYPA, HBGG, D7S8, GC) were carried out on a Hungarian Caucasian population sample of 163 unrelated individuals. Whereas the observed PM allele frequencies were similar to those reported for Caucasians, significant differences were found for HLA-DQa between the Hungarian and some Caucasian population data. All six loci meet Hardy-Weinberg expectations and there is no evidence for association between any pairs of loci.     

Developmental validation of STRmix™ NGS,a probabilistic genotyping tool for the interpretation of autosomal STRs from forensic profiles generated using NGS

We describe the developmental validation of the probabilistic genotyping software – STRmix™ NGS – developed for the interpretation of forensic DNA profiles containing autosomal STRs generated using next generation sequencing (NGS) also known as massively parallel sequencing (MPS) technologies. Developmental validation was carried out in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) Guidelines for the Validation of Probabilistic Genotyping Systems and the International Society for Forensic Genetics (ISFG) recommendations and included sensitivity and specificity testing, accuracy, precision, and the interpretation of case-types samples. The results of developmental validation demonstrate the appropriateness of the software for the interpretation of profiles developed using NGS technology.     

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.     

Population data and genetic characteristics of 12 X-STR loci using the Investigator® Argus X-12 Quality Sensor kit for the Kedayan population of Borneo in Malaysia

International Journal of Legal Medicine - DNA profiling of X-chromosomal short tandem repeats (X-STR) has exceptional value in criminal investigations, especially for complex kinship and incest...     

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.     

Population data and mutation rates of 19 STR loci in seven provinces from China based on Goldeneye™ DNA ID System 20A

Short tandem repeat (STR) analysis is a primary tool in forensic casework. Population data and mutation rates of STRs are very important for paternity testing and forensic genetics. However, the population data and mutation rates of STRs in Han nationality based on large samples have still not been fully described in China. In this study, the allelic frequencies, forensic parameters, and mutation rate of 19 STR loci (D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSFIPO, PentaD, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, and FGA) based on the Goldeneye™ DNA ID System 20A in Southern China Han nationality among seven provinces were investigated. Furthermore, population stratification of Southern China Han nationality among seven provinces was established. The multidimensional scaling (MDS) plot based on genetic distances (Fst) showed that the studied populations can be clustered into two major groups. However, relationships among populations were weak (Fst < 0.0043). A total of 376 cases of mutation were detected from the 19 selected loci in 15,396 meioses. The average mutation rate for the 19 loci was estimated to be 1.3 × 10⁻³ per meiosis. The mutation was mainly single step; the paternal mutation rate was higher than the maternal; and paternal mutation rate increases with paternal age.

     

Validation and assessment of the Investigator® 24plex QS kit for forensic casework application: Comparison with the PowerPlex® fusion system and GlobalFiler™ PCR amplification kits

Casework evidence samples are likely to be placed under diverse and harsh environments as compared to quantified DNA samples including serial-diluted standard DNA samples. Internal validation of a novel STR kit using casework evidence sample, which is conducted according to various conditions such as DNA contamination and degradation, is crucial before being used as a forensic application. Therefore, this study aimed to elucidate the reliability of the Investigator® 24plex QS kit through DNA derived from casework evidence and to assess whether it is applicable to STR analysis together with PowerPlex® Fusion System and GlobalFiler™ PCR Amplification Kit. DNA was extracted from 189 casework evidence samples in a total of 77 cases. The mismatch of the allelic size of this kit through allelic sizing precision test, was suitable according to ENFSI guidelines. All heterozygous balance of the three kits were above 0.6 recommended value of ENFSI guideline. The number of allele drop-in was most frequent in the GlobalFiler™ PCR Amplification Kit. In addition, the number of allele drop-out was most frequent in the Investigator® 24plex QS kit. The cutoff concentration of DNA detected in three kits of one complete STR was approximately 45 pg/μL on average. Despite of several limitations, the Investigator® 24plex QS kit is considered to have the capability to be used for STR analysis of casework evidence samples.     

Population data and mutation rate of nine Y-STRs in a mestizo Mexican population from Guadalajara, Jalisco, México

Nine Y-STR (DYS19, DYS390, DYS391, DYS392, DYS446, DYS447, DYS448, DYS456 and DYS458) were analyzed in a male sample of 285 unrelated individuals from Guadalajara, Jalisco, México. The haplotype diversity (0.996) and discrimination capacity (0.986) were calculated. A family study of around 200 father/son pairs and among 1828 meiosis showed five mutational events. All mutations were single step. The overall mutation rate estimated across the nine Y-STRs was 2.7 x 10(-3) (95% CI 1.2-6.4 x 10(-3))/locus/meiosis. The results indicate that these nine loci are useful Y-linked markers for forensic applications.     

Genetic population analysis of 17 Y-chromosomal STRs in three states (Valle del Cauca,Cauca and Nariño) from Southwestern Colombia

Seventeen Y-chromosomal (DYS19, DYS389 I/II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATA-H4 and DYS385a/b) short tandem repeat (STR) polymorphic systems were typed in three South West Colombian populations: Valle (short term for Valle del Cauca), Cauca and Nariño. DYS385a/b showed the highest gene diversity in the three populations. A total of 287 different Y-chromosome haplotypes were observed in the 308 males analyzed, and the haplotype diversity among populations was 0.9977. The most frequent haplotype was observed only three times and only nineteen others were observed two times. The highest gene diversity was found in Valle and the lowest in Cauca. Analysis of molecular variance (AMOVA) revealed that variation is mainly within populations (99.1%) in agreement with previous results in European populations. In conclusion, these populations could be pooled together in order to create one “Colombian-Mestizo” database for forensic use.     

Comparison between MACSprep™ forensic sperm microbead kit and Erase Sperm Isolation kit for the enrichment of sperm fractions recovered from sexual assault samples

International Journal of Legal Medicine - Sexual assault samples often contain mixtures of cells coming from at least two donors. Ideally, one would need to separate the cells into two cellular...