Autosomal SNPs study of a population sample from North of Portugal and a sample of immigrants from the Eastern Europe living in Portugal

The use of autosomal single nucleotide polymorphisms (SNPs) for forensic research has been widely discussed in recent years, mainly because SNPs have important advantages compared to short tandem repeats (STRs).In this study a total of 131 non related individuals from the North of Portugal and 85 immigrant individuals from the Eastern Europe, mainly Ukrainians, equally non related and residing in Portugal, were typed for 52 loci included in the in the SNP for ID 52plex with the SNaPshot™ assay.     

Characterization of GlobalFiler loci in Angolan and Guinean populations inhabiting Southern Portugal

We analyzed the GlobalFiler short tandem repeat (STR) loci for 152 and 70 unrelated individuals from Angolan and Guinean immigrant populations inhabiting Southern Portugal, respectively. After Bonferroni correction, no significant deviations from the Hardy–Weinberg equilibrium and linkage disequilibrium were detected for either population. For the Angolan population, SE33 was the most informative marker. In contrast, D5S818 and D13S317 were the least informative loci. The combined power of discrimination was 99.9999999999999999999999961907%. For the Guinean population, SE33 and D21S1 were the most informative loci, while D13S317 was the least. The combined power of discrimination was 99.99999999999999999999997915%. No significant differences were observed between Angolan, Guinean, and Afro-American populations for any of the analyzed STRs. The South African population presented significant differences at D22S1045 and D10S1248 when compared to Angola, and at D22S1045 when compared to Guinea-Bissau. The MDS plot and neighbor-joining tree analysis revealed that Angolan and Guinean populations are genetically close to African-American and South African populations, and genetically different from Korean, Mexican, European (including American-Caucasian), and Middle Eastern populations.

     

Applicability of the SNPforID 52-plex panel for human identification and ancestry evaluation in a Brazilian population sample by next-generation sequencing

SNP analysis is of paramount importance in forensic genetics. The development of new technologies in next-generation sequencing allowed processing a large number of markers in various samples simultaneously. Although SNPs are less informative than STRs, they present lower mutation rates and perform better when using degraded samples. Some SNP systems were developed for forensic usage, such as the SNPforID 52-plex, from the SNPforID Consortium, containing 52 bi-allelic SNPs for human identification. In this paper we evaluated the informativeness of this system in a Brazilian population sample (n = 340). DNA libraries were prepared using a customized HaloPlex Target Enrichment System kit (Agilent Technologies, Inc.) and sequenced in the MiSeq Personal Sequencer platform (Illumina Inc.). The methodology presented here allowed the analysis of 51 out of 52 SNPforID markers. Allele frequencies and forensic parameters were estimated, revealing high informativeness: the combined match probability and power of exclusion were 6.48 × 10⁻²¹ and 0.9997, respectively. Population admixture analysis indicates high European contribution (more than 70%) and low Amerindian contribution (less than 10%) in our population, while individual admixture analyses were consistent with the majority of individuals presenting high European contribution. This study demonstrates that the 52-plex kit is suitable for forensic cases in a Brazilian population, presenting results comparable with those obtained using a 16 STR panel.     

Genetic characterization of Guinea-Bissau using a 12 X-chromosomal STR system: Inferences from a multiethnic population

A male West African sample from Guinea-Bissau (West-African coast) was genetically analyzed using 12 X chromosomal short tandem repeats that are grouped into four haplotype groups. Linkage disequilibrium was tested (p ≤ 0.0008) and association was detected for the majority of markers in three out of the four studied haplotype clusters. The sample of 332 unrelated individuals analyzed in this study belonged to several recognized ethnic groups (n = 18) which were used to evaluate the genetic variation of Guinea-Bissau’s population. Pairwise genetic distances (F_ST) did not reveal significant differences among the majority of groups. An additional 110 samples from other countries also belonging to West Africa were as well compared with the sample of Guinea-Bissau. No significant differences were found between these two groups of West African individuals, supporting the genetic homogeneity of this region on the X chromosome level. The generation of over 100 DNA West African sequences provided new insights into the repeat sequence structure of some of the present X-STRs. Parameters for forensic evaluation were also calculated for each X-STR, supporting the potential application of these markers in typical kinship scenarios. Also, the high power of discrimination values for samples of female and male origin observed in this study, confirms the usefulness of the present X-STRs in identification analysis.     

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.     

Study of InDel genetic markers with forensic and ancestry informative interest in PALOP’s immigrant populations in Lisboa

The migratory phenomenon in Portugal has become one of the main factors for the genetic variability. In the last few years, a new class of autosomal insertion/deletion markers—InDel—has attracted interest in forensic genetics. Since there is no data for InDel markers of Portuguese-speaking African countries (PALOP) immigrants living in Lisboa, our aim is the characterization of those groups of individuals by typing them with at least 30 InDel markers and to compare different groups of individuals/populations. We studied 454 bloodstain samples belonging to immigrant individuals from Angola, Guinea-Bissau, and Mozambique. DNA extraction was performed with the Chelex® 100 method. After extraction, all samples were typed with the Investigator® DIPplex method. Through the obtained results, allelic frequencies show that all markers are at Hardy-Weinberg equilibrium, and we can confirm that those populations show significant genetic distances between themselves, between them, and the host Lisboa population. Because of this, they introduce genetic variability in Lisboa 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.     

Allelic frequency distribution of 17 STRs from Identifiler and PowerPlex-16 in Central Portugal area and the Azores archipelago

This study analyzes the allelic frequency distribution of 17 STRs contained in the AmpFlSTR Identifiler (Applied Biosystems) and PowerPlex16 System (Promega) commercial kits for two large population samples from the Azores archipelago (Portugal) (N = 475) and from Central Portugal (N = 2125). Likewise, it includes a comparative study among the population groups analyzed in this paper and those which history points out as originating from the first settlers of the Azores.All loci were highly polymorphic. The Central Portuguese area and the Azores archipelago population samples are in Hardy–Weinberg equilibrium for the 17 markers analyzed.     

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.     

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15?C17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.     

Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system

The Y-chromosome STRs (short tandem repeat) markers are routinely utilized in the resolution of forensic casework related to sexual assault. For this, the forensic community has adopted a set of eleven (core) Y-STR that is incorporated in all commercial diagnostic systems. Our previous studies of Y-STR polymorphisms in the South African population identified low levels of diversity and discrimination capacity for many commercial marker sets, determining a limited applicability of these systems to the local population groups. To overcome this shortcoming, we designed a Y-STR 10-plex system that shows higher discriminatory capacity (DC) than available commercial systems. The markers were selected from a population group of 283 individuals with African, European and Asian ancestry genotyped at 45 Y-STRs, applying an optimization based selection procedure to achieve the highest possible DC with the minimal number of markers. The 10-plex was satisfactorily subjected to developmental validation tests following the SWGDAM guidelines and shows potential for its application to genealogical and evolutionary studies.     

Allele frequencies of three STRs of the human von Willebrand factor gene (vWF) in a Brazilian population sample

Allele frequencies were calculated for three tetrameric short tandem repeats (STRs) located in intron 40 of the human von Willebrand factor (vWA, vWF1 and vWF2) in 352 white individuals sampled from an urban population from the northeastern region of the State of São Paulo, Brazil. The exact test did not indicate any significant deviation from HWE for any of the three investigated loci. The allele frequencies of vWA and vWF1 showed unimodal and bimodal distributions, respectively, and the frequencies of vWF2 in our sample exhibited bimodal or even trimodal patterns. These differing patterns could reflect the differential action of one selective factor or of the distribution of mutations in these STRs, although the STRs are very close to one another and belong to the same gene. The frequency of paternity exclusions observed for each of these three loci conform to the theorectical expectations. The lack of difficulties regarding the methodology of typing and the forensic value of statistical parameters confirm the usefulness of these systems to study Brazilian populations.     

Forensic effectiveness and genetic distribution of 23 autosomal STRs included in Verifiler Plus TM multiplex in a population sample from Madhya Pradesh,India

We report here the first ever global study on genetic polymorphism using a Verifiler PlusTM autosomal STR multiplex system. The study evaluated genetic characteristics of 23 autosomal STRs in 200 unrelated residents of Guna district of Madhya Pradesh, India. Allele frequencies and forensic parameters are reported. Population comparison analysis was also performed using NJ tree and PCA plot. Penta E marker showed highest power of discrimination (0.938) among all 23 studied markers. The study also presents the first ever global forensic assessment in Indian population on D6S1043 marker (PD 0.937). The results demonstrated that all the 23 markers were highly polymorphic and the Verifiler PlusTM kit is suitable for forensic purposes in Indian population.     

Study of DXS9895 and DXS7130: Population data from North of Portugal

The study of X-chromosomal short tandem repeats (X-STRs) can complement data obtained with autosomal and Y-STRs. This population study only concerns two X-STRs in order to add complementary data obtained with other X-STRs already studied by our laboratory. DXS9895 and DXS7130 were used to study a population sample of North of Portugal (101 female and 118 male samples). DNA was amplified in a multiplex reaction mix and the automatic detection was performed using capillary electrophoresis. Allele frequencies and several forensic parameters were calculated.     

Allele frequencies of seven X-linked STR loci in Chinese Han population from Zhejiang Province

Allele frequencies and forensic parameters of seven X-chromosome STRs (DXS981, DXS7424, DXS101, DXS7133, DXS6789, GATA165B12 and GATA31E08) were estimated from a sample of unrelated individuals (383 females and 313 males) belonging to Chinese Han population in Zhejiang Province, a region located in the east of China. Combining the seven X-linked markers, high mean exclusion chance and power of discrimination values were obtained. Amplification was performed in a single multiplex PCR reaction. Due to the small PCR products (<202 bp), the use of these STRs can increase the probability that a degraded sample can be typed.     

Results for five sets of forensic genetic markers studied in a Greek population sample

A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex^®, Argus X-12 and PowerPlex^® Y23. No significant deviation from Hardy–Weinberg expectations was observed for any of the studied markers after Holm–Šidák correction. Statistically significant (P < 0.05) levels of linkage disequilibrium were observed between markers within two of the studied X-chromosome linkage groups. AMOVA analyses of the five sets of markers did not show population structure when the individuals were grouped according to their geographic origin. The Greek population grouped closely to the other European populations measured by F_ST^* distances. The match probability ranged from a value of 1 in 2 × 10⁷ males by using haplotype frequencies of four X-chromosome haplogroups in males to 1 in 1.73 × 10²¹ individuals for 16 autosomal STRs.     

Forensic evaluation of the AmpFℓSTR Identifiler kit in nine Mexican native populations from the pre-Columbian Mesoamerican region

Allele frequency distribution and forensic parameters of the AmpF?STR Identifiler kit was determined in nine Mexican Amerindian populations based on 1,040 unrelated individuals from the pre-Columbian region known as Mesoamerica. Hardy-Weinberg equilibrium was demonstrated for most of the short tandem repeats (STRs) in all nine populations. The power of discrimination and exclusion were higher than 0.99999 and 0.997942, respectively. In addition, a brief overview of the genetic relatedness and structure (F _st?=?2.62 %; p?=?0.00000) between these populations is presented.     

Allele frequencies of 11 X-chromosomal loci in a population sample from Ghana

Eleven X-chromosomal short tandem repeats (STRs) from two multiplex PCR approaches (DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377, and DXS7423), located in four different X-chromosomal linkage groups, were typed in a population sample from Ghana, Africa. After genotyping unrelated men (129) and women (114) from the Ashanti population, forensic efficiency parameters such as polymorphism information content and mean exclusion chance were calculated. A deviation from the Hardy–Weinberg equilibrium could not be found. The investigation of 11 father–daughter and seven mother–son meioses revealed no mutations in any STR analyzed. Our data were compared with European, African-American, and Asian populations from the literature. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Allele frequencies for 11 X chromosomal short tandem repeats in a population from Turkey

X chromosomal STRs are nowadays an important part of forensic genetic analysis, especially in complex kinship cases. In this study, allele frequencies and forensic efficiency parameters of the 11 X chromosomal STRs DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377 and DXS7423 in an admixed population from Turkey are presented.     

Population data for 30 insertion–deletion markers in a Korean population

This study reports on the forensic parameters of 30 insertion–deletion polymorphisms (Indels) (Investigator DIPplex® kit) in 100 individuals from a Korean population. The match probability ranged from 0.353 to 0.789, and the combined power of discrimination reached 0.99999999995. The DIPplex® kit is more discriminative in Koreans than six COfiler® short tandem repeats (STRs), but less discriminative than nine Profiler Plus® STRs. This study further demonstrated that some Indels in the DIPplex® kit could be used as Asian ancestry informative markers through a comparison with other population data.