Genetic analysis of 15 STR loci in the population of Zhejiang Province (Southeast China)

Fifteen autosomal STR loci were analyzed from a population sample of 598 unrelated individuals residing in Zhejiang Province. We report allele frequencies distribution and statistical parameters for all 15 STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA. Allele frequencies, the observed heterozygosity (Ho), the polymorphic information content (PIC), and the probability of paternity exclusion (PE) were calculated. All loci were in accordance with Hardy–Weinberg equilibrium (P > 0.05). Our studied population data were compared with the previously published population data of other ethnic groups or areas in China. Our results of present study were valuable for human identification and paternity tests in Zhejiang Province.     

A genomic exploration of 15 autosomal STR loci for establishment of a DNA profile database of the population of Himachal Pradesh

In order to create an autosomal STR loci population database for Himachal Pradesh, 259 blood samples were taken from people residing in various regions of the state and AmpFlSTR® Identifiler® Plus PCR amplification kit was used for evaluation of 15 autosomal STR markers. A total of 149 alleles were investigated in this study with a mean allele number of 9.933 per locus. The locus D2S1338 was most informative in our data, as it had the highest discrimination power (PD-0.967) and the highest polymorphic information content (PIC-0.86). The matching probability and typical paternity index for all the studied loci were observed as 2.9x10^-18 and 4.7x10⁵, respectively. Discrimination power (CPD) and exclusion power (CPE) for all the studied loci were observed as 1 and 0.999998.     

Genetic polymorphisms of 20 autosomal STR loci in the Vietnamese population from Yunnan Province,Southwest China

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated in 522 healthy unrelated Vietnamese from Yunnan, China. All of the loci reached the Hardy–Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999999999999999999999991 26 and 0.999999975, respectively. Results suggested that the 20 STR loci are highly polymorphic, which is suitable for forensic personal identification and paternity testing.

     

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.     

Allele frequency data for 17 short tandem repeats in a Czech population sample

Allele frequencies for 17 short tandem repeats (STRs) autosomal loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, PentaD, PentaE, TH01, TPOX, vWA) were studied in an extensive sample (max. N = 1411) of unrelated individuals originating from the Czech Republic. Population and forensic parameters were estimated. Except for FGA and Penta E loci, no deviations from the Hardy–Weinberg equilibrium were detected. A comparative analysis with published data revealed significant differences in allele frequencies for some loci from the Polish population and three Hungarian populations (Ashkenazim population and Romany populations from Debrecen and Baranya County, respectively). A combination of these 17 STR loci provides a powerful tool for forensic identification in the native Czech population.     

Genetic variation of 15 autosomal STR loci in a population sample from Poland

Fifteen autosomal STR loci included in AmpF?STR® NGM? kit were analyzed in 154 unrelated individuals from Poland. This multiplex kit enables simultaneous amplification of 10 standard STR loci included in AmpF?STR® SGM Plus® kit (D3S1358, vWA, D16S539, D2S1338, D8S1179, D19S433, TH01, FGA, D21S11 and D18S51) and five new mini- and midi-STR loci (D10S1248, D22S1045, D2S441, D1S1656 and D12S391). Population study was conducted to evaluate usefulness of the loci (especially the five new microsatellite systems) in forensic genetic identification examinations. All 15 markers were found to be in Hardy–Weinberg equilibrium. The combined probability of match for the 15 studied STR loci was 3.998 × 10^?19. The same parameter calculated for five new microsatellite loci equaled 8.83 × 10^?7. Discrimination power was particularly high in case of D1S1656 (0.975) and D12S391 (0.972) STR loci.     

Sibling assessment based on likelihood ratio and total number of shared alleles using 21 short tandem repeat loci included in the GlobalFiler™ kit

Sibling assessment using the 15 autosomal short tandem repeat (STR) loci included in the Identifiler® kit can be difficult when comparing an unidentified party to an alleged sibling. Therefore, we investigated the likelihood ratio (LR) and the total number of shared alleles (TNSA) for sibship determination using the 21 autosomal STR loci included in the GlobalFiler™ kit.We computationally generated the genotypes of 10,000 sibling pairs and 10,000 unrelated pairs based on previously reported allele frequencies of the 15 Identifiler loci and the remaining 6 GlobalFiler loci. The LR and the TNSA were then calculated in each pair using the 15 and 21 loci. Next, these calculations were applied to 22 actual sibling pairs.LR values ⩾10,000 were observed in 48% of the sibling pairs using the 15 loci and in 80% of the sibling pairs using the 21 loci. The TNSA distribution between siblings and unrelated pairs was more divergent in GlobalFiler than in Identifiler. TNSA values ⩾20 were found only in true siblings in Identifiler, while TNSA values ⩾24 in GlobalFiler. In Identifiler, all pairs with TNSA ⩾24 had LR values ⩾10,000 and the same was true in GlobalFiler for TNSA ⩾29. Therefore, increasing the number of loci is very efficient for sibship determination.The LR is most reliable for determining sibship. However, TNSA values may be useful for the preliminary method of LR values because LR value demonstrated a significantly positive correlation with TNSA value in both Identifiler and GlobalFiler.     

Genetic structure and forensic parameters of 38 Indels for human identification purposes in eight Mexican populations

Insertion–deletions for human identification purposes (HID-Indels) offer advantages to solve particular forensic situations and complex paternity cases. In Mexico, admixed population known as Mestizos is the largest (∼90%), plus a number of Amerindian groups (∼10%), which have not been studied with HID-Indels. For this reason, allele frequencies and forensic parameters for 38 HID-Indels were estimated in 531 unrelated individuals from one Amerindian (Purépecha) and seven Mestizo populations from different regions of the country. Genotype distribution was in agreement with Hardy–Weinberg expectations in almost all loci/populations. The linkage disequilibrium (LD) test did not reveal possible associations between loci pairs in all eight Mexican populations. The combined power of discrimination was high in all populations (PD >99.99999999998%). However, the power of exclusion of the 38 HID-Indel system (PE >99.6863%) was reduced regarding most of autosomal STR kits. The assessment of genetic structure (AMOVA) and relationships between populations (F_ST) demonstrated significant differences among Mexican populations, mainly of the Purépecha Amerindian group. Among Mexican-Mestizos, three population clusters consistent with geography were defined: (i) North-West region: Chihuahua, Sinaloa, and Jalisco; (ii) Central-Southern region: Mexico City, Veracruz and Yucatan; (iii) South region: Chiapas. In brief, this report validates the inclusion of the 38 HID-Indel system in forensic casework and paternity cases in seven Mexican-Mestizo populations from different regions, and in one Mexican Amerindian group.     

Comparison of southern Chinese Han and Brazilian Caucasian mutation rates at autosomal short tandem repeat loci used in human forensic genetics

The short tandem repeat (STR) loci used in human genetic studies are characterized by having relatively high mutation rates. In particular, to ensure an appropriate evaluation of genetic evidence in parentage and forensic analyses, it is essential to have accurate estimates of the mutation rates associated with the commonly used autosomal and sex chromosome STR loci. Differences in STR mutation rates between different ethnic groups should also be determined. Mutation data from two laboratories working with different ethnic groups were extracted from many meiotic transmissions ascertained for 15 autosomal STR loci currently used in forensic routine. Forty-five thousand and eighty-five trios were checked for the biological consistency of maternity and paternity through the analysis of a minimum of 15 loci. Mutations were scored as paternal, maternal, or ambiguous according to the most parsimonious explanation for the inconsistency, using always the least requiring hypothesis in terms of number of repeat differences. The main findings are: (a) the overall mutation rate across the 15 loci was 9.78?×?10^?4 per gamete per generation (95 % CI?=?9.30?×?10^?4–1.03?×?10^?3), and with just 48 (out of 1,587) exceptions, all of the mutations were single-step; (b) repeat gains were more frequent than losses; (c) longer alleles were found to be more mutable; and (d) the mutation rates differ at some loci between the two ethnic groups. Large worldwide meiotic transmission datasets are still needed to measure allele-specific mutation rates at the STR loci consensually used in forensic genetics.     

DNA analysis of root canal-filled teeth

Teeth are markedly useful as samples for DNA analysis; however, intact teeth are not always available. This study examined the possibility of identifying autosomal and Y-chromosome short tandem repeat (STR) types in samples from 34 teeth (15 intact and 19 root canal filled) that had been preserved for 10–33 years after dental extraction. The aim was to explore the feasibility of individual identification by DNA analysis of samples obtained from highly decomposed and skeletonized corpses. Only one out of 24 autosomal STR loci was not identified in two of the 15 intact teeth, whereas all 23 loci of the Y chromosome STR were detected. One or two autosomal STR loci remained unidentified in eight of the 19 root-filled teeth, and four or five of the 23 Y STR loci were undetected in three cases. However, the types were identified in about 20 loci in all samples, and the composition of the root canal filling material did not appear to interfere with the PCR. This study demonstrates that the storage period of the teeth had no influence on our results indicating that root canal filled teeth can be used for DNA analysis.     

Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province,Southwest China

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex^® 21 kit were evaluated from 748 unrelated healthy individuals of the Miao ethnic minority living in the Yunnan province in southwestern China. All of the loci reached Hardy–Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationship between the Miao population and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999 999 999 999 999 999 999 991 26 and 0.999 999 975, respectively. The results suggested that the 20 STR loci were highly polymorphic, which makes them suitable for forensic personal identification and paternity testing.     

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.     

Efficiency analysis of VersaPlex™ 27PY system in Central Indian Population: First report from Indian population

In the current scenario, DNA typing is the need of forensic science field due to its ability to provide results in much shorter time. In view of advancement of forensic DNA typing and incensement in the number of STRs markers, Promega offered a new VersaPlex™ 27PY system with 27 loci (23 autosomal STR loci, Amelogenin, DYS391 and two rapidly mutating Y-STR loci (DYS570 and DYS576)). In this study, the efficacy of “23 autosomal STR loci” for paternity testing and personal identification was demonstrated in Indian population. For this, 217 central Indians were tested and all the statistical parameters of forensic and population genetic interest were calculated. In addition, sensitivity of the kit was also tested for forensic casework. During investigation with VersaPlex™ 27PY system, allele 11 at locus TPOX was observed to be most frequent with the highest allelic frequency 0.432. Studied 23 loci showed valuable together with highest value of combined power of discrimination (CPD = 1), combined power of exclusion (CPI = 0.9999999989) and lowest value of combined matching probability (CPM = 7.92x10^-28).     

Genetic variation of 15 autosomal short tandem repeat (STR) loci in the Palestinian population of Gaza Strip

Fifteen autosomal STR loci included in the PowerPlex^®16 System were typed in a population sample of 125 unrelated individuals from Palestinian population of Gaza Strip. Allele frequencies, Hardy–Weinberg equilibrium and forensic parameters were determined for the following loci: Penta E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, vWA, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818.     

Applications of 1993 single nucleotide polymorphism loci in forensic pairwise kinship identifications and inferences

Kinship testing plays critical roles in criminal investigations, missing person searches, civil disputes, as well as identifying disaster victims. The existing commonly used short tandem repeat (STR) loci have limited effectiveness in the identification of second-degree and more distant kinships. In this study, a total of 1993 SNP loci of 119 Chinese Han individuals from eight families were sequenced on the MGISEQ-2000RS platform. The system powers of this panel for kinship identifications were evaluated based on both the likelihood ratio (LR) and identical by state (IBS) methods. The results indicated that this panel could be used as an effective tool to kinship analyses including paternity testing, full sibling testing, second-degree kinships, and first cousin kinship analyses. Both the LR and IBS methods could be applied in distinguishing first-degree and second-degree pairs from unrelated individuals. Based on the 1993 SNP loci, LR>1000 and LR<0.001 are recommended as the thresholds of identifying first-cousin kinships from unrelated individuals, and the system power of such thresholds was 0.9470. Besides, kinship coefficients for different kinship pairs were estimated and then were used to predict the kinships for pairwise individuals. This panel performs an effective kinship inference power for the predictions of first-degree, second-degree kinships and unrelated individual pairs, while presenting low sensitivity in the prediction of first-cousin kinships.     

Population data for 12 STR loci in Hong Kong Chinese

The allele distributions at the 12 short tandem repeat (STR) loci D3S1358, HUMvWA, HUMFIBRA/FGA, HUMTHO1, HUMTPOX, HUMCSF1P0, D5S818, D13S317, D7S820, D8S1179, D21S11 and D18S51 have been determined for 284 unrelated Chinese in Hong Kong. The combined probability of identity for the 12 STR loci was about 4.1 × 10^–14 and the overall probability of excluding paternity 0.999978. None of the 12 loci were found to deviate from Hardy-Weinberg expectations according to the results of the exact test. There was also little evidence for association of alleles between loci. The results demonstrate that the loci are useful for forensic human identification and parentage testing for the Chinese population in Hong Kong. Received: 2 December 1999 / Accepted: 12 April 2000     

Population genetic data for 17 STR markers from Lebanon

Seventeen autosomal STRs were analyzed (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, Penta D, and Penta E) in the Lebanese population. A total of 192 unrelated individuals were genotyped for the 15 autosomal STRs in the Promega PowerPlex 16 STR kit. An additional 275 unrelated individuals were genotyped for the Applied Biosystems AmpFlSTR Identifiler and SGM + STR kits. Allele frequencies for the shared CODIS 13 loci among the three STR kits tested were not significantly different among individuals within the Lebanese population. Forensic and population genetic parameters for the 17 loci were calculated. We also compared the allele frequencies from this population with other populations in the same geographic vicinity.     

An integrated system of ABO typing and multiplex STR testing for forensic DNA analysis

A new amplification system for ABO and STR genotyping in a single reaction has been successfully developed. Two types of information can be obtained from a biological sample at one time. One is the classical information of ABO blood group typing for screening suspects and the other is STR information for individual identification. The system allows for the simultaneous detection of 15 autosomal STR loci (containing all CODIS STR loci as well as Penta D and Penta E), six ABO genotypes (O/O, B/B, A/A, A/O, A/B, and B/O) and the gender-determining locus Amelogenin. Primers are designed so that the amplicons are distributed ranging from 75 bp to 500 bp within a four-dye fluorescent design, leaving a fourth dye for the internal size standard. With 30 cycles, the results showed that the optimal amount of DNA template for this multiplex ranges from 250 pg to 2 ng and the lowest detection threshold is 125 pg (as low as 63pg for ABO loci). For the DNA template outside the optimal detection range, we could adjust the number of cycles to obtain the robust profiles. Mixture studies showed that over 83% of minor alleles were detected at 1:9 ratios. The full profiles were still observed when 4 ng of degraded DNA was digested by DNase I and 1 ng undegraded DNA was added to 40 μM haematin. Polymerase chain reaction (PCR)-based conditions including the concentrations of primers, magnesium and the Taq polymerase as well as volume, cycle numbers and annealing temperature were examined and optimised. In addition, the system was validated by 364 bloodstain samples and 32 common casework samples. According to the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, our system demonstrates good detection performance and is an ideal tool for forensic DNA typing with potential application.     

Population structure of Han nationality in Central-Southern China

Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a F_st value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing.     

Fourteen non-CODIS autosomal short tandem repeat loci multiplex data from Taiwanese

Interest in the development of polymorphic short tandem repeat (STR) markers unlinked to the CODIS loci is growing among forensic practitioners. We developed a multiplex system in which14 autosomal STR (D3S1744, D4S2366, D8S1110, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 572 unrelated Taiwanese Han subjects were analyzed using this 14 STR multiplex system. Thirty parent–child pairs of parentage testing cases with a combined paternity index (CPI) below 1,000 and 32 parent–child pairs with single-step mutations found in AmpFℓSTR Identifiler loci were also recruited for validation of the newly developed system. DNA sequencing was performed for novel STRs and novel alleles found in these subjects. The distributions of allelic frequencies for these autosomal STRs and sequence data, allele nomenclature for the STRs, and forensic parameters are presented. The discrimination power in our multiplex loci ranged from 0.6858 (D18S536) to 0.9168 (Penta E), with a combined discrimination power of 0.999999999. It provides additional power to distinguish the possible single-step mutations in parent–child pairs and improves the ability to prove parentage by increasing the CPI. The combined power of exclusion of these 14 loci in Taiwanese Han in this study was 0.9999995913. In conclusion, this 14-autosomal STRs multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing.