The HumD21S11 system of short tandem repeat DNA polymorphisms in Japanese and Chinese

Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation

Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

The structure of a variant allele which is considered to be 30.3 in the STR locus D21S11

We found a variant allele which is considered to be 30.3 in the STR locus D21S11 in a mother and child during a paternity test. The allele had consisted of the insertion of three bases (TCA) or the deletion of one base (T after C) between the five TCTA repeats and the six TCTA repeats within the last variable region of three variable regions.

Tetrameric short tandem repeat (STR) system D15S233 (wg1d1): sequencing and frequency data in the japanese and Chinese populations

We evaluated the forensic usefulness of D15S233 (wg1d1), a tetrameric short tandem repeat (STR) locus, in the Japanese and Chinese populations. Typing was performed by denaturing polyacrylamide gel electrophoresis followed by silver staining. Nine different alleles were found in 472 Japanese chromosomes and seven in 186 Chinese chromosomes. 102 alleles sequenced were composed of two kinds of repeats (AGGA and GGGA). All alleles differed in size by one tetranucleotide repeat unit, and no insertion or deletion was found. The expected unbiased heterozygosities in Japanese and Chinese were 0.766 and 0.785, respectively. No significant deviations from the Hardy-Weinberg equilibrium were found in either population. We retyped all samples using an alternative pair of flanking primers in order to detect any spurious appearances of homozygotes due to sequence variation at the primer annealing site. One heterozygous sample had unbalanced density bands when the original primer set was used, but equal density bands when our newly designed primer set was used. Sequencing analysis revealed that the sparser allele had one nucleotide substitution near the 5' end of the annealing site of the original primer region. Thus, all apparently homo/heterozygous samples were thought to be truly homo/heterozygous. We also applied the D15S233 locus to paternity testing and forensic identification. Our results suggest that this locus should be a very useful STR locus for forensic practice in Japanese and Chinese.

Quadruplex fluorescent STR typing system (HUMVWA, HUMTH01, D21S11 and HPRT) with sequence-defined allelic ladders identification of a new allele at D21S11

A protocol for simultaneous amplification of the tetrameric STR loci HUMVWA, HUMTH01, D21S11 and HPRT has been developed in this study. Fluorescent amplified alleles were detected by laser scanning on the ALF DNA sequencer, and identified with locus specific allelic ladders. A sequencing survey of these STR loci was performed in 40 selected individuals from three major ethnic groups and confirmed the data reported previously. At the D21S11 locus, a new allele of 207 bp, was found in a Belgian Caucasian individual and designated as allele 25.2. Sequence analysis of this allele revealed that it contained a 14 bp deletion of (TCTA)3 TA at the beginning of the constant region. A nonconsensus allele of 245 bp, described and designated as allele 33.2.3(2x) by Brinkmann et al. (1996), was identified in an individual of central African origin. In addition, three new sequence variants of the allele 29, 30 and 32 were observed at D21S11.