Population and forensic data for three sets of forensic genetic markers in four ethnic groups from Iran: Persians,Lurs, Kurds and Azeris

A total of 255 individuals (Persians, Lurs, Kurds and Azeris) from Iran were typed for three sets of forensic genetic markers with the NGM SElect™, DIPplex^® and Argus X-12 kits. Statistically significant deviations (P ≤ 0.002) from Hardy–Weinberg expectations were observed for the insertion-deletion markers HLD97 and HLD93 after Holm–Šidák correction. Statistically significant (P < 0.05) levels of linkage disequilibrium were observed between markers within two of the four studied X-chromosomal linkage groups. AMOVA analyses of the three sets of markers did not show population structure when the individuals were grouped according to their ethnic group. The Iranian population grouped closely to populations living geographically near to Iran based on pairwise F_ST distances. The matching probabilities ranged from 1 in 3.2 × 10⁷ males by using haplotype frequencies of four X-chromosomal haplogroups to 1 in 3.4 × 10²¹ individuals for the 16 autosomal STRs.     

Analysis of 49 autosomal SNPs in an Iraqi population

Forty-nine of the 52 autosomal single nucleotide polymorphisms (SNPs) in the SNPforID 52plex were typed in 101 unrelated Iraqis living in Denmark. No significant deviation from HWE was found in all but one of the 49 SNP systems and no significant pairwise linkage disequilibrium was observed for any SNP pair. When 18 worldwide populations were compared (including populations in Iraq, Turkey, Israel, Pakistan, India, China, Taiwan, Japan, Siberia, Algeria, Somalia, Uganda, Mozambique, Angola, Nigeria, Denmark, Portugal, Spain), a significant global F_ST value was obtained. All but six F_ST values were statistically significant when pairwise comparisons were performed between the 18 populations. The Iraqi population did not show significant difference from the population in Turkey and it grouped together with other Middle-Eastern populations when a multidimensional scaling plot was drawn based on the pairwise F_ST values. The combined mean match probability and the typical paternity index for trios were 8.3 × 10⁻²⁰ and 259,000, respectively, for the Iraqi population.     

Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups

Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on F_ST and R_ST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (F_ST > 0.05; P < 0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa.     

Y-chromosome STR haplotypes in males from Greenland

A total of 272 males from Greenland were typed for 11 Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex^® Y System (Promega). A total of 146 different haplotypes were observed and the haplotype diversity was 0.9887. The number of haplotypes seen once was 108 and the most common haplotype was observed in 12 males. A significant F_ST value was observed (F_ST = 0.012, P < 0.00001) when comparing the population of 15 locations in Greenland assigned to 7 groups. The significance could mainly be attributed to the subpopulation of males from Tasiilaq (East of Greenland). The R_ST value was not statistically significant (R_ST = 0.016, P = 0.15).     

Population data for 12 Y-chromosome STR loci in a sample from El Salvador

Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 150 unrelated male individuals from El Salvador, Central America. A total of 131 haplotypes were identified by the 12 Y-STR loci of which 118 were unique. The haplotype diversity (99.08%) and the proportion of different haplotypes (87.33%) were estimated. R_ST genetic distances were calculated between El Salvador and other populations from Southern and Central America, Europe and Africa. The highest R_ST genetic distances were found when comparing El Salvador with African populations (0.334 ? R_ST ? 0.395). The lowest non-significant distance was found in the comparison with Honduras. The observed genetic distances between El Salvador and Southern and Central Native groups presented a wide range of values (from 0.024 to 0.210) that can be explained by the differences in the proportion of European versus Amerindian contributions in these population groups. The Multi Dimensional Scaling (MDS) plot analysis, based on pairwise R_ST values, showed that the general population of El Salvador is closer to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Southern/Central American cluster of Native and Mestizo populations.     

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.     

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.     

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.     

Thirty autosomal insertion-deletion polymorphisms analyzed using the Investigator® DIPplex Kit in populations from Iraq,Lithuania, Slovenia,and Turkey

Thirty autosomal insertion-deletion (InDel) polymorphisms were analyzed in four populations from Iraq, Lithuania, Slovenia, and Turkey using the commercial kit Investigator® DIPplex. Genotyping issues were encountered for five of the 30 InDels. They were most probably caused by polymorphisms located in the primer binding sites. Population and forensic parameters were calculated. No significant deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were detected. The observed heterozygosities ranged from 33% to 61% depending on the marker and the population. The combined probability of exclusion for the 30 markers was 99.7% in all four populations and the matching probabilities were 1 in 3–4 × 10¹² individuals. The multidimensional scaling plot drawn from F_ST distances showed a good concordance between the relative position of the 15 populations included in the plot and their geographic locations.     

Polish population data on 15 autosomal STRs of AmpFlSTR NGM PCR kit

The objective of the research was to provide a comprehensive database of autosomal microsatellite loci included in AmpFlSTR NGM PCR kit for a population of Poland considering possible genetic differentiation of a forensic interest. Fifteen STR markers were analyzed in 2041 unrelated individuals residing in eight geographically different regions. All the loci were found to be in Hardy–Weinberg equilibrium. The combined probability of match is 3.52 × 10⁻¹⁹ and the combined Power of Exclusion is 0.9999998. The F_ST estimate over all 15 STRs is 0.0051 for the Polish population. We established that a combined NGM database may be employed for a Polish population.     

European Network of Forensic Science Institutes (ENFSI): Evaluation of new commercial STR multiplexes that include the European Standard Set (ESS) of markers

To support and to underpin the European initiative to increase the European set of standard markers (ESS), by the addition of five new loci, a collaborative project was organised by the European Network of Forensic Science Institutes (ENFSI) DNA working group in order to assess the new multiplex kits available. We have prepared allele frequency databases from 26 EU populations. Concordance studies were carried out to verify that genotyping results were consistent between kits. Population genetics studies were conducted and it was estimated that F_ST < 0.001. The results showed that the kits were comparable to each other in terms of performance and major discrepancy issues were highlighted. We provide details of allele frequencies for each of the populations analysed per laboratory.     

Verifying the geographic origin of mahogany (Swietenia macrophylla King) with DNA-fingerprints

Illegal logging is one of the main causes of ongoing worldwide deforestation and needs to be eradicated. The trade in illegal timber and wood products creates market disadvantages for products from sustainable forestry. Although various measures have been established to counter illegal logging and the subsequent trade, there is a lack of practical mechanisms for identifying the origin of timber and wood products. In this study, six nuclear microsatellites were used to generate DNA fingerprints for a genetic reference database characterising the populations of origin of a large set of mahogany (Swietenia macrophylla King, Meliaceae) samples. For the database, leaves and/or cambium from 1971 mahogany trees sampled in 31 stands from Mexico to Bolivia were genotyped. A total of 145 different alleles were found, showing strong genetic differentiation (δ_Gregorious = 0.52, F_ST = 0.18, G_ST(Hedrick) = 0.65) and clear correlation between genetic and spatial distances among stands (r = 0.82, P < 0.05). We used the genetic reference database and Bayesian assignment testing to determine the geographic origins of two sets of mahogany wood samples, based on their multilocus genotypes. In both cases the wood samples were assigned to the correct country of origin. We discuss the overall applicability of this methodology to tropical timber trading.     

Forensic and population genetic characteristics of 62 X chromosome SNPs revealed by multiplex PCR and MALDI-TOF mass spectrometry genotyping in 4 North Eurasian populations

X chromosome genetic markers are widely used in basic population genetic research as well as in forensic genetics. In this paper we analyze the genetic diversity of 62 X chromosome SNPs in 4 populations using multiplex genotyping based on multi-locus PCR and MALDI-TOF mass spectrometry, and report forensic and population genetic features of the panel of X-linked SNPs (XSNPid). Studied populations represent Siberian (Buryat and Khakas), North Asian (Khanty) and Central Asian (Kazakh) native people. Khanty, Khakas and Kazakh population demonstrate average gene diversity over 0.45. Only East Siberian Buryat population is characterized by lower average heterozygosity (0.436). AMOVA analysis of genetic structure reveals a relatively low but significant level of genetic differentiation in a group of 4 population studied (F_ST = 0.023, p = 0.0000). The XSNPid panel provides a very high discriminating power in each population. The combined probability of discrimination in females (PDf) for XSNPid panel ranged between populations from 0.99999999999999999999999982 in Khakas to 0.9999999999999999999999963 in Buryats. The combined discriminating power in males (PDm) varies from 0.999999999999999792 to 0.9999999999999999819. The developed multiplex set of X chromosome SNPs can be a useful tool for population genetic studies and for forensic identity and kinship testing.     

A forensic DNA profiling system for Northern European brown bears (Ursus arctos)

A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6 ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy–Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (F_ST) was 0.09. The average estimate of inbreeding (F_IS) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1 × 10^?9 and the total average probability of sibling identity was lower than 1.3 × 10^?4. The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.     

Quantification of GABAA receptors in the rat brain with [123I]Iomazenil SPECT from factor analysis-denoised images

PurposeIn vivo imaging of GABA_A receptors is essential for the comprehension of psychiatric disorders in which the GABAergic system is implicated. Small animal SPECT provides a modality for in vivo imaging of the GABAergic system in rodents using [¹²³I]Iomazenil, an antagonist of the GABA_A receptor. The goal of this work is to describe and evaluate different quantitative reference tissue methods that enable reliable binding potential (BP) estimations in the rat brain to be obtained.MethodsFive male Sprague–Dawley rats were used for [¹²³I]Iomazenil brain SPECT scans. Binding parameters were obtained with a one-tissue compartment model (1TC), a constrained two-tissue compartment model (2TC_c), the two-step Simplified Reference Tissue Model (SRTM2), Logan graphical analysis and analysis of delayed-activity images. In addition, we employed factor analysis (FA) to deal with noise in data.ResultsBP_ND obtained with SRTM2, Logan graphical analysis and delayed-activity analysis was highly correlated with BP_F values obtained with 2TC_c (r = 0.954 and 0.945 respectively, p < 0.0001). Equally significant correlations were found between values obtained with 2TC_c and SRTM2 in raw and FA-denoised images (r = 0.961 and 0.909 respectively, p < 0.0001). Scans of at least 100 min are required to obtain stable BP_ND values from raw images while scans of only 70 min are sufficient from FA-denoised images. These images are also associated with significantly lower standard errors of 2TC_c and SRTM2 BP values.ConclusionReference tissue methods such as SRTM2 and Logan graphical analysis can provide equally reliable BP_ND values from rat brain [¹²³I]Iomazenil SPECT. Acquisitions, however, can be much less time-consuming either with analysis of delayed activity obtained from a 20-minute scan 50 min after tracer injection or with FA-denoising of images.     

Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations

Forty Y-STR loci were analyzed in 1128 males from the following six Chinese ethnic populations: Han (n = 300), Hui (n = 244), Korean (n = 100), Mongolian (n = 100), Uighur (n = 284) and Tibetan (n = 100), utilizing two new generation multiplex Y-STR systems, AGCU Y24 STR and GFS Y24 STR genotyping kits, which allow for the genotyping of 24 loci from a single amplification reaction in each system. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.441658) and DYS437 (0.496977), and the greatest diversity corresponds to markers DYS385a/b (0.969919) and DYS527a/b (0.94676). A considerable number of duplicate and off-ladder alleles were also revealed. Additionally, there were 1111 different haplotypes identified from the total 1128 samples, of which 1095 were unique. Notably, no shared haplotypes between populations were observed. The estimated overall haplotype diversity (HD) was 0.999085, and its discrimination capacity (DC) was 0.970745. An MDS plot based on the genetic distances between populations showed the genetic similarity of the southern Han population to the Northern populations of Hui, Korean, Mongolian and Uighur and a clear genetic departure of the Tibetan population from other populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of the Y STR profile. However, because the haplotype based Fst values are extremely small within the present data (0.000153 with 40 Y-STRs), no substructure correction is required to estimate the rarity of a haplotype comprising 40 markers. In summary, the results of our study indicate that the 40 Y-STRs have a high level of polymorphism in Chinese ethnic groups and could therefore be a powerful tool for forensic applications and population genetic studies.     

Yo-Yo intermittent recovery test versus the Université de Montréal Track Test: Relation with a high-intensity intermittent exercise

The first purpose of this study was to determine whether the peak velocity (V_Yo-Yo) achieved during the Yo-Yo intermittent recovery test (Yo-Yo) and the maximal aerobic velocity (MAV) determined from the Université de Montréal Track Test (UMTT) could be used interchangeably. The second purpose was to check that the V_Yo-Yo is related to the intermittent exercise performance, which consisted of repeated 90 m distance runs in 15 s performed until exhaustion, alternated with 15 s of passive recovery (15/15). Fourteen amateur soccer players performed, in a random order, the 15/15 and two incremental field-tests: the Yo-Yo and the UMTT. The results of this study showed that MAV was significantly correlated to the V_Yo-Yo (r = 0.79, p < 0.01). However, the error was not constant, when the V_Yo-Yo and the MAV values were higher than 16.3 km h^?1, the MAV values tends to be higher than the V_Yo-Yo, while when the V_Yo-Yo and the MAV values were lower than 16.3 km h^?1, the MAV values tends to be lower than the V_Yo-Yo. MAV and V_Yo-Yo were significantly correlated to the time to exhaustion of the 15/15 (r = 0.74 and r = 0.72, respectively) and show that both tests are similarly related to the high-intensity intermittent exercise performance.     

3T diffusion-weighted MRI in the response assessment of colorectal liver metastases after chemotherapy: Correlation between ADC value and histological tumour regression grading

PurposeThe purpose of the study was to correlate the apparent diffusion coefficient (ADC) values of diffusion-weighted MR imaging (DW-MRI) by 3T device with the histological tumour regression grading (TRG) analysis of colorectal liver metastases after preoperative chemotherapy.Materials and methodsOur study included thirty-five patients with colorectal liver metastases who had undergone MRI by 3T device (GE DISCOVERY MR750; GE Healthcare) after preoperative chemotherapy. DW-MRI was performed using a single-shot spin-echo echo-planar sequence with multiple b-values (0, 150, 500, 1000, 1500 s/mm²), thus obtaining an ADC map. For each liver lesion (more than 1 cm in diameter) the fitted ADC values were calculated by two radiologists in conference and three ROIs were drawn: around the entire tumour (ADC_e), at the tumour periphery (ADC_p) and at the tumour center (ADC_c). All ADC values were correlated with histopathological findings after surgery. Hepatic metastases were pathologically classified into five groups on the basis of TRG. Statistical analysis was performed on a per-lesion basis utilizing the one-way analysis of variance (ANOVA). This retrospective study was approved by our institutional review board; written informed consent was obtained from all patients.ResultsA total of 106 colorectal liver metastases were included for image analysis. TRG1, TRG2, TRG3, TRG4 and TRG5 were observed in 4, 14, 36, 35 and 17 lesions, respectively. ADC_e and ADC_p values were significantly higher in lesions classified as TRG1 (2.40 ± 0.12 × 10⁻⁹ m²/s and 2.28 ± 0.26 × 10⁻⁹ m²/s, respectively) and as TRG2 (1.40 ± 0.31 × 10⁻⁹ m²/s and 1.44 ± 0.35 × 10⁻⁹ m²/s), compared to TRG3 (1.16 ± 0.13 × 10⁻⁹ m²/s and 1.01 ± 0.18 × 10⁻⁹ m²/s), TRG4 (1.10 ± 0.26 × 10⁻⁹ m²/s and 0.97 ± 0.24 × 10⁻⁹ m²/s), and TRG5 (0.93 ± 0.17 × 10⁻⁹ m²/s and 0.82 ± 0.28 × 10⁻⁹ m²/s). ADC_e, ADC_p and ADC_c values were significantly different in TRG classes (p < 0.0001). Statistical correlations were found between the ADC_e, ADC_p, ADC_c values and the TRG classes (Spearman correlation coefficient were −0.568, −0.542 and −0.554, respectively).ConclusionOur study showed a significant correlation between ADC values of 3T DW-MRI and histological TRG of colorectal liver metastases after preoperative chemotherapy.