Analysis of four novel X-chromosomal short tandem repeats within 71 kb of the Xp22.3 region

Abstract

DNA testing using X-chromosomal short tandem repeat (X-STR) polymorphisms has been used in maternity/paternity and complex kinship cases. Analyses of repeat sequences, surveys on racial statistics, and development of practical applications for DNA testing continue to be reported. In this study, we identified four novel tetranucleotide STR loci located in the X chromosome, which is the basis of X-STR research. These four tetranucleotide STRs were located within 71 kb of the chromosome Xp22.3 region. Using sequence analysis of the structure of repeat sequences, we identified simple repeat sequences of TAAA, CTTT, TATC, and GATA with rare insertions. We then calculated forensic statistical parameters using base length analysis. In the Japanese population, the polymorphism information content was 0.597-0.687, power of discrimination in females was 0.829-0.884, and power of discrimination in males was 0.635-0.729. As these tetranucleotide STRs are closely linked, we conducted haplotype analysis and detected that three loci (LC149476, LC149479, and LC149480) were in linkage disequilibrium. We demonstrated that the simultaneous analysis of these loci may be useful in complex kinship cases. Because these four loci can be detected by multiplex PCR, the detection of alleles at these loci can be rapidly and easily achieved. We conclude that the X-STR loci detected in this study may be useful tools in complex kinship cases and may increase the reliability of genetic testing.

Forensic DNA Analysis

“…Additional X-STR loci have been developed and validated in order to increase the power of discrimination and assist in the analysis of degraded samples . In 2017, two separate papers focused on the discovery of novel X-STR and the study of the genetic linkage as a useful tool for kinship determination. , A guideline for applications of X-STR in kinship analysis was also published …”

“…113 In 2017, two separate papers focused on the discovery of novel X-STR and the study of the genetic linkage as a useful tool for kinship determination. 114,115 A guideline for applications of X-STR in kinship analysis was also published. 116 ■ SINGLE NUCLEOTIDE POLYMORPHISMS Single nucleotide polymorphims (SNPs) are particularly useful in situations in which the recovered DNA is badly degraded.…”

Applications of X-Chromosome Short Tandem Repeats for Human Identification: A Review

“…In another example, 17 X-STRs loci were utilized by Prieto-Fernández et al [50], with 10 of which were similar to Decaplex GHEP-ISFG, combined with additional 6 other loci (DXS6801, DXS6799, DXS6800, DXS10075, DXS6807, and DXS6803) and one specifically from the Qiagen Investiga-tor® Argus X-12 QS kit. Progressively, evaluation of several other novel X-STRs markers at specific regions (Xp21.1, Xq21.31, Xp22.32, Xq23 and Xp11.4) for resolving complex kinship cases [51][52][53] have also been reported. However, when tested on Japanese population, low PIC (ranging from 0.5606 to 0.7448) was obtained for the two regions analyzed (Xp22.3 and Xp11.4) [51][52][53], indicating that the markers are not well polymorphic.…”

“…Progressively, evaluation of several other novel X-STRs markers at specific regions (Xp21.1, Xq21.31, Xp22.32, Xq23 and Xp11.4) for resolving complex kinship cases [51][52][53] have also been reported. However, when tested on Japanese population, low PIC (ranging from 0.5606 to 0.7448) was obtained for the two regions analyzed (Xp22.3 and Xp11.4) [51][52][53], indicating that the markers are not well polymorphic.…”

“…In a case involving two sisters with paternal dispute, the use of 12 X-STRs could not determine the actual biological father since the two alleged fathers were cousins (with their mothers being sisters) [54]. Considering such a failure in resolving the paternity dispute, Hering et al [55] later suggested the expansion of the German population data by adding two clusters of X-STRs from previous researchers [51,56] in their newly designed hexaplex PCR that was combined with the existing Qiagen Investigator® Argus X-12 QS kit. The fact that the increasing number of X-STRs loci used in multiplexes would proportionately increase the power of discrimination among individuals, attempts by researchers to combine several multiplexes (> 20 X-STRs loci) described previously for reporting the relevant population data [57][58][59] may prove relevant.…”