Expanded Croatian 12 X-STR loci database with an overview of anomalous profiles

Abstract

In order to implement X-chromosome short tandem repeat (X-STR) typing into routine forensic practice, reference database of a given population should be established. Therefore we extended already published data with additional 397 blood samples from unrelated Croatian citizens, and analyzed the total of 995 samples (549 male and 446 female) typed by Investigator Argus X-12 Kit. To test genetic homogeneity of consecutively processed five historic-cultural regions covering the entire national territory, we calculated pairwise Fst genetic distances between regions based on allele and full haplotype frequencies. Since the comparison did not yield any statistically significant difference, we integrated STR profile information from all regions and used the whole data set to calculate forensic parameters. The most informative marker is DXS10135 (polymorphism information content (PIC = 0.929) and the most informative linkage group (LG) is LG1 (PIC = 0.996). We confirmed linkage disequilibrium (LD) for seven marker pairs belonging to LG2, LG3 and LG4. By including LD information, we calculated cumulative power of discrimination that amounted to 0.999999999997 in females and 0.999999005 in males. We also compared Croatia with 13 European populations based on haplotype frequencies and detected no statistically significant Fst values after Bonferroni correction in any LG. Multi-dimensional scaling plot revealed tight grouping of four Croatian regions amongst populations of southern, central and northern Europe, with the exception of northern Croatia. In this study we gave the first extensive overview of aberrant profiles encountered during Investigator Argus X-12 typing. We found ten profiles consistent with single locus duplication followed by tetranucleotide tract length polymorphism. Locus DXS10079 is by far the most frequently affected one, presumably mutated in eight samples. We also found four profiles consistent with X-chromosome aneuploidy (three profiles with XXX pattern and one profile with XXY pattern). In conclusion, we established integral forensic Croatian X-chromosome database, proved forensic pertinence of Investigator Argus X-12 Kit for the entire Croatian population and identified locus DXS10079 as a potential duplication hotspot.

Genetic polymorphism and variability in the Guangdong Hakka, Teochew, and Cantonese groups: A comprehensive analysis of 19 X‐STRs

“…(2011) also observed that significant LD was found only between DXS10103 and DXS10101. In practice, the ability to detect LD is correlated with sample size, and larger sample size is required to establish all allele pairs (Kling et al., 2015; Mršić et al., 2018). Thus, in this case, the pooled Guangdong Han showed more locus pairs with LD than the Cantonese, Teochew, and Hakka results at larger sample sizes.…”

Forensic Applications of Markers Present on the X Chromosome

“…The Investigator Argus X-12 kit was also used in this study, and 914 complete haplotypes were obtained for the markers included in the kit. Knowing the uniqueness provided by the X-STR markers, several research groups conducted studies to assess the population distribution of countries such as Brazil, Switzerland, Italy, India, Croatia, and countries on the African continent, among others [ 9 , 15 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 ]. Table 1 lists some population studies that explore X-STR markers, published in the last ten years.…”

“…DXS10146 and DXS10135 markers presented 38 alleles, revealing the most polymorphic alleles. The most informative locus among the population studies mentioned is DXS10135, shown in 11 different studies [ 9 , 15 , 35 , 39 , 40 , 42 , 43 , 45 , 46 , 49 ]. This is due to the high PIC (polymorphism information content) value of this locus in the different populations [ 51 ].…”

Population genetic analysis of 12 X-chromosomal STRs in a Swiss sample

“…All variants are listed in Table S6. Most of them have been described previously [8][9][10][11][12][13][14][15][16][17]. However, we list 12 alleles in Table S6 for which we could not find a reference to date.…”

“…In addition to frequent off-ladder alleles, a couple of multi-allelic patterns were discovered. Most of them (6 out of 9) are in DXS10079, a locus for which duplications can be observed frequently [ 9 , 17 ]. Contrary to off-ladder alleles and allele duplications, obvious allele dropouts occurred scarcely, with just one partial dropout in DXS10101 and a potential dropout in DXS10146, inferred from the constantly reduced height of the remaining peak in a female sample.…”