DXYS267: DYS393 and its X chromosome counterpart.
The GATA repeat DYS393 was reported in 1987 among other Y-specific short tandem repeats. It has since been used for forensic and evolutionary studies. We decided to test its Y-specificity when we found that female DNA gave amplicons, in agreement with recent GDB-recorded experiences on radiation hybrids. Parent-child triplets revealed that heterozygous daughters always carried the same paternally derived amplicon which, however, was not amplified in their fathers' DNAs. The X-assignment was verified in larger families. A half-new primer set with a new reverse DYS393 primer, outside the old one, resulted in X amplicons in females as well as Y and X amplicons in males. This new primer set defines the new DXYS267 (GDB Data Curation). DNA-sequencing revealed four base pair differences between the Y- and the X-sequences. Two are within the reverse primer site sequence, thus probably causing preferential hybridization to the Y sequence when using the conventional primers. The two others are within the repeat array, giving the regular repeat GATA in the Y-sequence, and TATA and GACA, respectively, in the X-sequence. Allele frequency distribution in DYS393 was studied in 300 unrelated Norwegian males, allele distribution in the X-locus in 48 Norwegian women. Even if allele repeat numbers are overlapping between the loci, leading to identical fragment lengths, the allele distribution is different between DYS393 and the X-chromosome locus. The differences between the two homologous loci on the Y and X indicate a considerable lap of time since common ancestry. To avoid co-amplification of the X-locus in DYS393 typing, primer A was elongated to include one of the sequence differences between the two loci. This to a considerable extent improved the specificity of the DYS393 primers.
Dupuy
B M
BM
University of Oslo, Institute of Forensic Medicine, Rikshospitalet, 0027, Oslo, Norway. b.m.dupuy@labmed.uio.no
Gedde-Dahl
T
T
Olaisen
B
B
D000225:Adenine; D000483:Alleles; D020029:Base Pairing / Q000235:genetics; D002678:Chimera / Q000235:genetics; D002874:Chromosome Mapping; D003596:Cytosine; D004247:DNA / Q000235:genetics; D017931:DNA Primers; D019143:Evolution, Molecular; D005260:Female; D005554:Forensic Medicine; D005784:Gene Amplification; D005787:Gene Frequency; D014644:Genetic Variation; D006147:Guanine; D006579:Heterozygote; D006801:Humans; D008297:Male; D009664:Norway; D011110:Polymorphism, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences / Q000235:genetics*; D013941:Thymine; D014960:X Chromosome / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*
D017931:DNA Primers; D006147:Guanine; D003596:Cytosine; D004247:DNA; D000225:Adenine; D013941:Thymine