Curiosities of X chromosomal markers and haplotypes

X-chromosomal STRs: Metapopulations and mutation rates

The analysis of STRs located on the X chromosome has been one of the strategies used to address complex kinship cases. Its usefulness is, however, limited by the low availability of population haplotype frequency data and lack of knowledge on the probability of mutations. Due to the large amount of data required to obtain reliable estimates, it is important to investigate the possibility of grouping data from populations with similar profiles when calculating these parameters. To better understand the partition of genetic diversity among human populations for the X-STRs most used in forensics, an analysis was carried out based on data available in the literature and new data (23,949 haplotypes in total; from these 10,445 new) obtained through collaborative exercises within the Spanish and Portuguese Working Group of the International Society for Forensic Genetics. Based on the available population data, a similarity in X-STR profiles was found in European populations, and in East Asian populations, except for some isolates. A greater complexity was found for African, South American, and South and Southeast Asian populations, preventing their grouping into large metapopulations. New segregation data on 2273 father/mother/daughter trios were also obtained, aiming for a more thorough analysis of X-STR mutation rates. After combining our data with published information on father/mother/daughter trios, no mutations were detected in 13 out of 37 loci analyzed. For the remaining loci, mutation rates varied between 2.68 × 10-4 (DXS7133) and 1.07x10-2 (DXS10135), being 5.2 times higher in the male (4.16 ×10-3) than in the female (8.01 ×10-4) germline.

Variability and forensic efficiency of 12 X-STR markers in Namibian populations

STR loci localized on the X chromosome provide information additional to the autosomal markers routinely analyzed in forensic genetics, integrating genetic systems as Y-STRs and mitochondrial DNA in the investigation of complex kinship scenarios and mass disaster cases.In this study we genotyped 12 X-STR loci in 251 male samples from four populations of Namibia in southern Africa using the Investigator Argus X-12 kit (Qiagen, Hilden, Germany). Forensic efficiency parameters indicated high power of discrimination in the considered populations. As part of our investigation, we highlighted partial linkage associations between loci within known linkage groups (LGs) and identified several occurrences of previously unreported out-of-ladder (OL) alleles.Genetic distances between the Namibian populations here investigated and other African (Eritrea, Ethiopia, Somalia, Guinea, Cape Verde) and non-African (Germany, China, Philippines) populations using loci grouped in LGs mirrored their biogeographical distribution differently for each linkage group. Haplotype sharing within each LG revealed a high degree of population-specific types, hinting to the potential of these markers for ancestry applications.These results highlight the importance to produce specific and freely available population databases especially for multi-ethnic countries. This novel dataset is expected to be of interest for population studies that need an accessible reference dataset of African regions not currently well represented, as well as possible relevance for forensic applications focusing on the biogeographic origin of samples.

Extended population genetic analysis of 12 X-STRs - Exemplified using a Norwegian population sample

The use of X-chromosomal markers to resolve questions of relatedness has experienced a significant increase during the last years in forensic genetics. Perhaps primarily due to the emergence of commercial kits, but equally important due to an increased awareness of the utility of those markers. The X-chromosomal inheritance pattern entails that some cases, for instance paternal half-sisters, can potentially be resolved using a few X-chromosomal markers alone. For the statistical assessment in kinship cases it is of importance to have relevant population frequency data. In the present study 631 unrelated males from a Norwegian population sample are analyzed. The resulting haplotypes are compared to previously studied population samples and a deeper analysis of the linkage disequilibrium (LD) structure is conducted. We demonstrate that the power to detect LD will be low when few males, say below 300, are analyzed. We use entropy to describe the degree of LD between multiallelic loci and describe how this measure varies between different studied populations. Large population frequency databases have been recommended when using X-chromosomal markers, and we show that by combining reference databases from genetically similar populations, more precise haplotype frequency estimates can be obtained for rare haplotypes which improves the statistical assessment of the weight of evidence. In addition, we promote the use of simulations to assess the utility of STR markers in contrast to standard forensic parameters. Specifically we perform extensive simulations on cases where X-chromosomal markers are important and illustrate how the results can be used to infer the information gained from these markers.

Kinship assignment with the ForenSeq™ DNA Signature Prep Kit: Sources of error in simulated and real cases

Kinship recognition between anonymous DNA samples is becoming a relevant issue in forensics, more so with the increasing number of DNA profiles in databanks. Also, NGS-based genotyping is being increasingly used in routine personal identification, to simultaneously type large numbers of markers of different kind. In the present work, we explored computationally and experimentally the performance of the ForenSeq™ DNA Signature Prep Kit in identifying the true relationship between two anonymous samples, distinguishing it from other possible relationships. We analyzed with Familias R series of 10,000 pairs with 9 different simulated relationships, corresponding to different degrees of autosomal sharing. For each pair we obtained likelihood ratios for five kinship hypotheses vs. unrelatedness, and used their ranking to identify the preferred relationship. We also typed 21 subjects from two pedigrees, representing from parent-child to 4th cousins relationships. As expected, the power for identifying the true relationship decays in the order of autosomal sharing. Parent-child and full siblings can be robustly identified against other relationships. For half-siblings the chance of reaching a significant conclusion is already small. For more distant relationships the proportion of cases correctly and significantly identified is 10% or less. Bidirectional errors in kinship attribution include the suggestion of relatedness when this does not exist (10-50%), and the suggestion of independence in pairs of individuals more than 4 generations apart (25-60%). The real cases revealed a relevant effect of genotype miscalling at some loci, which could only be partly avoided by modulating the analysis parameters. In conclusion, with the exception of first degree relatives, the kit can be useful to inform additional investigations, but does not usually provide probatory results.

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.

A microhap panel for kinship analysis through massively parallel sequencing technology

It is widely recognized that microhaps are powerful markers for different forensic purposes, mainly due to their advantages of both short tandem repeats and single nucleotide polymorphisms, including multiple alleles, low mutation rate, and absence of stutter peaks. In the present study, a panel of 60 microhap loci was developed and utilized in forensic kinship analysis as a preliminary study. Genotyping of microhap was performed by massively parallel sequencing and haplotypes were directly achieved from sequence reads of 73 samples from Chinese Han population. We observed that 49 out of 60 loci have effective number of alleles greater than 3.0 and 10 out of 60 have values above 4.0, with an average value of 3.5598. The heterozygosity values were in a range from 0.5840 to 0.8546 with an average of 0.7268 and the cumulative power of exclusion value of the 60 loci is equal to 1-4.78 × 10^-18 . Moreover, we demonstrated the applicability of this method by different relationship inference problems, including identification of single parent-offspring, full-sibling, and second-degree relative. The results indicated that the assembled microhap panel provided more power for relationship inference, than commonly used short tandem repeats or single nucleotide polymorphism system.