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

• DOI: 10.1007/s00414-017-1553-2
• Publication Date: 2017-02-27T08:01:13Z
• Authors: Takeki Nishi; Kenji Fukui; Kimiharu Iwadate
• Keywords: Male; 0301 basic medicine; Chromosomes, Human, X; Polymorphism, Genetic; Sequence Analysis, DNA; Polymerase Chain Reaction; Linkage Disequilibrium; 03 medical and health sciences; Asian People; Gene Frequency; Haplotypes; Japan; Humans; Female; Microsatellite Repeats

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.