Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns we developed Recombulator-X, a new open-source Python tool. The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm. Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. In conclusion, Recombulator-X makes the estimation process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices.

Resolving the recombination pattern of 38 X-STRs from Chinese Han three-generation pedigrees

X-chromosomal markers have been proved as a useful tool for solving complex kinship cases due to its sex-linked inheriting feature. Among these markers, tightly linked X-STR clusters forming haplotypes are highly informative. The analysis of the haplotypes requires determination of linkage disequilibrium. In this study, genetic linkage, recombination fractions and mutation rates of 38 X-STR loci in 177 three-generation pedigrees were investigated. Genetic linkage analysis and calculation of recombination fractions were performed within each pair of markers and clusters. Then mutation rates were calculated. The results showed that, a) 22 recombination events happened within the tightly linked X-STR clusters, which span<1.0 Mb; b) significantly linked marker pairs were observed with the LOD (logarithm of the odds) scores > 2.0 (2.0104 to 54.8316); c) the average mutation rate of the 38 X-STR loci was 1.32 × 10^-3 per meiosis in the Chinese Han population, with DXS10135 and DXS8377 presenting notably high mutation rate (6.5 × 10^-3). Our results confirmed that meiotic recombination was not a simple function of physical distance, so that whether recombination occurred at the closely clustered X-STRs or not should be assumed cautiously considering the stability of haplotypes in inheritance process for kinship analysis. This study supplemented the existing database and laid an experimental foundation for the future study on genetic characteristics, recombination, and mutation of the X-STRs.

Genetic characterization of the highlander Tibetan population from Qinghai-Tibet Plateau revealed by X chromosomal STRs

Tibetans are considered an East Asian ethnic group and primarily live in the high Tibetan plateau, the western Sichuan and Yunnan mountains of central and southern China, and areas throughout the Himalayas and around the Tibetan plateau. These people exhibit rare molecular machinery that allows them to adapt to hypoxic environments in the Qinghai-Tibet Plateau and make them a potential candidate for providing insights related to medical genetic, molecular medicine and human population studies. In the current study, we have genotyped 549 individuals with Investigator Argus X-12 Kit. For 12 X-STRs, a total of 174 unique alleles were found, among them DXS10134 and DXS10135 were the most polymorphic loci. All of the loci were in Hardy-Weinberg Equilibrium (HWE). The numbers of observed haplotypes in Highlander Tibetans males were 161,112, 96 and 108, respectively, whereas haplotype diversities (HD) were 0.9959, 0.9880, 0.9809 and 0.9873, respectively. The combined discrimination power for males (PDm) was 0.999 999 99701 and for females (PDf) was 0.999 999 999 999 9958. This study represents an extensive report on X chromosomal STR markers variation in the Highlander Tibetans population for forensic applications and population genetic studies.

Population genetic data for 12 X-STR loci in the Central Saudi region using investigator Argus X-12 amplification kit

BACKGROUND

X-chromosome short tandem repeat (X-STR) markers are important in forensic identity investigations and kinship analysis.

SUBJECT AND METHODS

In the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator^® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of Saudi Arabia in order to develop an allelic frequency database for the markers included in the kit.

RESULTS

DXS10146 locus was the most informative with 21 alleles, while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci, either as individual markers or as linkage groups, provide genetic information with high discrimination that is appropriate for forensic purposes with polymorphism information content (PIC), power of exclusion (PE), and paternity index (PI) varying from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically closer to the Egyptian and Emirati populations and distant to the Turkish population.

CONCLUSION

The current study revealed that Investigator^® Argus 12 X-STR kit would support the forensic application, kinship testing involving female offspring, and human identification in the Saudi population.

Genetic diversity, forensic feature, and phylogenetic analysis of Guizhou Tujia population via 19 X-STRs

BACKGROUND

X-chromosome short tandem repeats (X-STRs) with unique sex-linkage inheritance models play a complementary role in forensic science. Guizhou is a multiethnic province located in southwest China and some genetic evidence focusing on X-STRs for various minorities was reported. However, population data of Guizhou Tujia are scarce.

METHODS

A total of 507 Guizhou Tujia individuals were profiled using the AGCU X-19 STR kit. Allele frequencies and forensic parameters were calculated. Additionally, population genetic relationships between Guizhou Tujia and other 19 populations were explored.

RESULTS

A total of 257 alleles with the allele frequencies ranged from 0.0013 to 0.6098 were found. The combined power of discrimination in males and females and mean exclusion chances in all case scenarios were all greater than 0.99999. Population comparisons showed Guizhou Tujia had a homogeneity with all Han populations from different administrative regions, and other ethnic populations residing in Guizhou, while had obviously genetic heterogeneity with the Altaic family populations except Xibe.

CONCLUSION

Nineteen X-STRs can afford a reliable and informative database of Guizhou Tujia population for human identification and paternity testing, especially in complex biological relations. The genetic relationships of Chinese are significantly influenced by the geographic position and ethnolinguistic origin.

Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics

The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmission characteristics, besides the obvious clinical impact (sex chromosome aneuploidies are extremely frequent), make the X chromosome an irreplaceable genetic tool for population genetic-based studies as well as for kinship and forensic investigations. In the early 2000s, the number of publications using X-chromosomal polymorphisms in forensic and population genetic applications increased steadily. However, nearly 20 years later, we observe a conspicuous decrease in the rate of these publications. In light of this observation, the main aim of this article is to provide a comprehensive review of the advances and applications of X-chromosomal markers in population and forensic genetics over the last two decades. The foremost relevant topics are addressed as: (i) developments concerning the number and types of markers available, with special emphasis on short tandem repeat (STR) polymorphisms (STR nomenclatures and practical concerns); (ii) overview of worldwide population (frequency) data; (iii) the use of X-chromosomal markers in (complex) kinship testing and the forensic statistical evaluation of evidence; (iv) segregation and mutation studies; and (v) current weaknesses and future prospects.

Genetic polymorphism analyses of three novel X chromosomal short tandem repeat loci in the Xp22.3 region

X chromosomal short tandem repeats (X-STRs) can be useful for haplotype analysis in DNA testing, particularly for complex kinship testing or when one parent is absent. We searched downstream of four previously detected loci in the Xp22.3 region (LC149476, LC149479, LC149480, and LC149484) and detected and analyzed three novel short tandem repeats (STRs), LC317283, LC317284, and LC317285, with the repeat sequences TATAA, TTTA, and TATC, respectively. The forensic statistical values in Japanese subjects were confirmed to be noninferior to existing loci, with values for polymorphism information content, the power of discrimination in males (PDm), and the power of discrimination in females (PDf) of 0.5606-0.7448, 0.6078-0.7774, and 0.7990-0.9178, respectively. Haplotype analysis also revealed linkage disequilibrium between LC317283 and the four known loci (LC149476, LC149479, LC149480, and LC149484) and between two other novel loci (LC317284 and LC317285). Analysis of three family samples suggested that these STRs could be useful in complex kinship testing, so we developed an X-STR multiplex polymerase chain reaction (PCR) system for the seven loci and confirmed its ability to provide favorable amplification. We anticipate that the identified loci and developed multiplex PCR system will be beneficial to the field of forensic medicine.

Paternal and maternal mutations in X-STRs: A GHEP-ISFG collaborative study

The GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit Qiagen. A total of 16 laboratories gathered data from 1,612 father/mother/daughter trios, which were used to estimate both maternal and paternal mutation rates, when pooled together with other already published data. Data on fathers and mothers' age at the time of birth of the daughter were also available for ∼93 % of the cases. Population analyses were computed considering the genetic information of a subset of 1,327 unrelated daughters, corresponding to 2,654 haplotypes from residents in several regions of five countries: Argentina, Brazil, Ecuador, Portugal and Spain. Genetic differentiation analyses between the population samples from the same country did not reveal signs of significant stratification, although results from Hardy-Weinberg and linkage disequilibrium tests indicated the need of larger studies for Ecuador and Brazilian populations. The high genetic diversity of the markers resulted in a large number of haplotype combinations, showing the need of huge databases for reliable estimates of their frequencies. It should also be noted the high number of new alleles found, many of them not included in the allelic ladders provided with the kit, as very diverse populations were analyzed. The overall estimates for locus specific average mutation rates varied between 7.5E-04 (for DXS7423) and 1.1E-02 (for DXS10135), the latter being a troublesome figure for kinship analyses. Most of the found mutations (∼92 %) are compatible with the gain or loss of a single repeat. Paternal mutation rates showed to be 5.2 times higher than maternal ones. We also found that older fathers were more prone to transmit mutated alleles, having this trend not been observed in the case of the mothers.

Genetic analysis of 12 X-STRs for forensic purposes in Liaoning Manchu population from China

X-chromosomal short tandem repeats (X-STRs) have been widely used in forensic practice involving complicated cases of kinship and also play an increasingly important role in population genetics. X-STRs have been studied in regional populations of China but there is a lack of data for the Manchu population. In this study, we have investigated the forensic genetic properties of 12 X-STRs in the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 772 Manchu (male = 514, female = 258) individuals from the Xiuyan and Huanren Manchu autonomous counties of Liaoning province. We observed a total of 166 alleles at 12 X-STR loci with allele frequencies ranging from 0.001295to 0.615285. The most polymorphic locus was DXS10135 with 24 alleles while DXS7423 was the least polymorphic locus with 5 alleles. We found significant linkage disequilibrium (LD) between the following pairs of markers for males: DXS10103/DXS10101, DXS10135/DXS10146, DXS10101/DXS10148, DXS10135/DXS10148, DXS7423/DXS10148 and DXS10079/DXS10148. For females, LD was only observed for DXS10103/DXS10101. The combined power of discrimination was 0.9999999979699 for males and 0.999999999999998 for females. The numbers of observed haplotypes in Manchu males were 310, 172, 182 and 172 in four linkage groups; LG1, LG2, LG3 and LG4, respectively, however, these linkage groups did not form stable haplotypes as indicated by linkage equilibrium (LE) of STRs within the groups and significant LD between the groups. This study represents an extensive report on X-STR marker variation in the Manchu population for forensic applications and population genetic studies.

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

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.

DNA Commission of the International Society for Forensic Genetics (ISFG): Guidelines on the use of X-STRs in kinship analysis

Forensic genetic laboratories perform an increasing amount of genetic analyses of the X chromosome, in particular to solve complex cases of kinship analysis. For some biological relationships X-chromosomal markers can be more informative than autosomal markers, and there are a large number of markers, methods and databases that have been described for forensic use. Due to their particular mode of inheritance, and their physical location on a single chromosome, some specific considerations are required when estimating the weight of evidence for X-chromosomal marker DNA data. The DNA Commission of the International Society for Forensic Genetics (ISFG) hereby presents guidelines and recommendations for the use of X-chromosomal markers in kinship analysis with a special focus on the biostatistical evaluation. Linkage and linkage disequilibrium (association of alleles) are of special importance for such evaluations and these concepts and the implications for likelihood calculations are described in more detail. Furthermore it is important to use appropriate computer software that accounts for linkage and linkage disequilibrium among loci, as well as for mutations. Even though some software exist, there is still a need for further improvement of dedicated software.