Haplotype data and forensic evaluation of 23 Y-STR and 12 X-STR loci in eight ethnic groups from Eritrea

Forensic autosomal and gonosomal short tandem repeat marker reference database for populations in Burkina Faso

Tandem repeat genetic profiles used in forensic applications varies between populations. Despite the diversity and security issues in the Sahel that require the identification of victims (soldiers and civilians), Burkina Faso (BF) remains understudied. To fill this information gap, 396 unrelated individuals from BF were genotyped using a MICROREADER 21 ID System kit. All 20 short tandem repeat (STR) loci tested passed the Hardy-Weinberg equilibrium (HWE) test. The combined powers of exclusion for duos (CPE duos) and trios (CPE trios) for the 20 tested loci were 0.9999998 and 0.9999307, respectively. The probability that two individuals would share the same DNA profiles among the BF population was 9.80898 × 10-26. For the X-chromosome STR analysis, 292 individuals were included in this study using a MICROREADER 19X Direct ID System kit. Among the 19 loci, no significant deviations from HWE test were observed in female samples after Bonferroni correction (p < 0.05/19 = 0.0026), except for loci GATA165B12 and DXS7423. The results showed that the combined power of exclusion (CPE) and the combined power of discrimination in females (CPDF) and males (CPDM) were 0.999999760893, 0.999999999992, and 1, respectively. Comparison with other African sub-populations showed that geographical proximity is a reliable indicator of genetic relatedness.

Analysis of Y-STR diversity and DNA methylation variation among Black and Indian males from KwaZulu-Natal, South Africa

Y-chromosome short tandem repeats (Y-STRs) are essential in understanding genetic structure and diversity of human populations and, most importantly, in identification of male perpetrators in criminal investigations. DNA methylation differences have been reported in human populations and methylation pattern at the CpG sites found within or flanking the Y-STR sites could also aid in human identification. Studies based on DNA methylation (DNAm) at Y-STRs are currently limited. The current study aimed to analyze the Y-STR diversity in South African Black and Indian individuals living in KwaZulu-Natal, Durban, South Africa, with the Yfiler™ Plus Kit and to analyze DNAm patterns in Y-STR markers CpG sites. DNA from 247 stored saliva samples were isolated and quantified. Across the 27 Y-STR loci in the Yfiler™ Plus Kit, 253 alleles were observed in 113 South African Black and Indian males, 112 unique haplotypes were observed, and one haplotype appeared twice (two Black individuals). No statistically significant differences were observed in the genetic diversity between the two population groups (Fst = 0.028, p-value ≥ 0.05). The kit showed a high discrimination capacity (DC) of 0.9912 and an overall haplotype diversity (HD) = 0.9995 among the sampled population groups. DYS438 and DYS448 markers displayed 2 and 3 CpG sites, respectively. Based on the two-tailed Fisher's Exact test, there were no statistically significant differences in the DNAm levels at DYS438 CpGs of Black and Indian males (p > 0.05). The Yfiler™ Plus Kit can be considered highly discriminatory among South African Black and Indian males. Studies on the South African population using Yfiler™ Plus Kit are scarce. Hence, accumulating Y-STR data on the diverse South African population will enhance the representation of South Africa in STR databases. Knowing which Y-STR markers are significantly informative for South Africa is essential for developing Y-STR kits better suited for the different ethnic groups. And to the best of our knowledge, DNA methylation analysis in Y-STR for different ethnic groups has never been done before. Complementing Y-STR data with methylation knowledge could provide population-specific information for forensic identification.

Population genetic analysis of 12 X-STR markers in Slovakia

Background: During the last 20 years, X-chromosomal STR markers have become widely used in forensic genetics and paternity testing. Nevertheless, to exploit their full potential in any given population, a reliable reference dataset needs to be established. Since no relevant studies concerning these markers have been performed on the Slovak population so far, we decided to analyse several commonly used markers in this population.Aim: To create an informative set of Slovak population data concerning X-STR markers.Subjects and methods: We genotyped 378 individuals and analysed 12 loci (DXS10148, DX10135, DXS8378, DXS7132, DXS10079, DXS10074, DXS10103, HPRTB, DXS10101, DXS10146, DXS10134 and DXS742) localised in four distinct linkage groups.Results: Our analysis showed that the most informative marker is DXS10135 (PIC = 0,927) and the most informative linkage group (LG) is LG1 with 149 different haplotypes. This analysis also confirmed linkage disequilibrium for two pairs of markers (DX10101-DX10103 and DX10101-HPRTB) within LG3 in female samples. No statistically significant departure from HWE was observed for any locus. Moreover, the interpopulation comparison of 8 European populations based on haplotype frequencies showed no statistically significant FST values in any LG, except for LG2 in comparison with the German population.Conclusion: We created a haplotype database for forensic analyses and kinship testing in Slovakia, as well as the CE dataset which can be used to further increase the decision power in similar analyses in the future.

Forensic Applications of Markers Present on the X Chromosome

Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.

Y-23 mediated genetic data analysis of endogamous Brahmin population of Rajasthan, India

India's largest state Rajasthan is known for its variable population groups including castes, communities and tribes. In the present article, Y-STR polymorphisms of hundred unrelated healthy male volunteers from the Brahmin population of Rajasthan, India were investigated using the Powerplex® Y-23 PCR amplification kit. Total 94 distinct haplotypes were obtained out of them 93 were singletons. Haplotype Diversity (HD) and Discrimination Capacity (DC) for the population were 0.644 and 0.9894 respectively. The Intra-population relationship between the present population data and other reported Indian populations was examined through Multidimensional Scaling (MDS) Plot, which shows the Brahmin population of Rajasthan lies in a cluster with the Brahmin populations of Haryana and Maharashtra. Data generated with 23 Y-STR markers is submitted on Y chromosome haplotype reference database (YHRD) (yhrd.org) and it will robust the forensic database of the Rajasthan population of India.

A reference database of forensic autosomal and gonosomal STR markers in the Tigray population of Ethiopia

Allele frequencies of 21 autosomal STR markers (AmpF/STR GlobalFiler) and haplotype frequencies of 27 Y- and 12 X-STR markers (AmpF/STR YFiler Plus and Investigator Argus X-12, respectively) were investigated in the Tigray population of Ethiopia, representing the main population group in the Tigray regional state of Ethiopia and neighboring Eritrea. For autosomal STR allele frequencies, the average random match probability in the Tigray sample was 2.1 × 10^-27. The average locus by locus F_ST distance calculated comparing autosomal STR allele frequencies from Tigray and from a broad regional reference dataset currently available for the Horn of Africa was 0.003. The Tigray male sample displayed high Y-STR diversity, with complete individualization of haplotypes using the AmpF/STR YFiler Plus panel. Analysis of molecular variance did not detect significant heterogeneity between Y-STR haplotypes observed in the present study and those previously reported in the literature for other Tigray population samples from Ethiopia and Eritrea. Study of the X-STR landscape in Tigray evidenced several distinctive features including: the molecular characterization of a novel null allele at locus DXS10146 with frequency > 1%; allele dependency between loci within linkage groups I and III; significant differences in haplotype distribution compared to other Horn of Africa populations, that should be taken into account in kinship analysis. The collected data can be used as a reference STR database by local forensic genetics services and in genetic identification procedures of victims of human trafficking in the Mediterranean Sea, which frequently involve individuals originating from the Horn of Africa.