DXS6797 contains two STRs which can be easily haplotyped in both sexes

Abstract

DXS6797 is a complex X-chromosomal locus which contains two variable short tandem repeats (STRs) (motif ATCT) separated by 128 non-polymorphic nucleotides. The two STRs can be cleaved apart by Taq I digestion. Conventionally, DXS6797 is typed by measuring the overall amplicon length, providing only eight alleles [polymorphism information content (PIC) 0.733, mean exclusion chance (MEC) 0.712]. Separate amplification would increase the discrimination but obscure the haplotype constellation in females. Therefore, we proceed by amplifying the whole sequence containing both repeats (DXS6797 I and DXS6797 II) using a Fam-labelled forward primer and a Tamra-labelled reverse primer. We then measure the length of the entire double-labelled amplicon and a Taq-I-digested aliquot to infer, for both males and females, compound haplotypes consisting of DXS6797 I and DXS6797 II repeat length. This procedure has the potential to provide 42 DXS6797 haplotypes. If the crossover rate between both STRs is assumed to be <1.5x10(-6), DXS6797 haplotypes could be used for kinship testing like STR alleles. In our German sample (780 X chromosomes), we determined 27 haplotypes (PIC 0.842, MEC 0,834) and in 220 meioses, we found no new mutations.

Japanese population data for eight X-STR loci using two new quadruplex systems

“…DXS6797 locus contains two STRs separated by 128 nonpolymorphic nucleotides. Although haplotype analysis of both the STRs would increase the amount of information compared with that of the complex double STR [23], in this study, we investigated the length of the complex double STRs amplicon. PCR amplification and allele typing with the systems were successful for all eight loci (Fig.…”

DXS10079, DXS10074 and DXS10075 are STRs located within a 280-kb region of Xq12 and provide stable haplotypes useful for complex kinship cases

“…We previously combined STR clusters from known markers [9,19] and were able to establish clusters that span 2-5 cM. In another case, we established a haplotyping procedure for two very closely linked pairs of STRs [16]. We have conducted an amended GenBank search to find STR clusters that provide highly stable haplotypes and present three newly established markers, DXS10079, DXS10074 and DXS10075, which can potentially produce 2,548 haplotypes.…”

X chromosomal recombination—a family study analysing 39 STR markers in German three-generation pedigrees

“…It can be assumed that such marker clusters segregate as stable haplotypes because of linkage disequilibrium. Several studies exist for closely linked markers [5][6][7][8][9]. Information about recombination patterns of the female X chromosome is very important for the application of ChrX haplotyping in kinship analysis.…”