DXYS267: DYS393 and its X chromosome counterpart

The GATA repeat DYS393 was reported in 1987 among other Y-specific short ta ndem 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 am plicons, in agreement with recent GDB-recorded experiences on radiation hyb rids. Parent-child triplets revealed that heterozygous daughters always car ried 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-seque ncing revealed four base pair differences between the Y- and the X-sequence s. Two are within the reverse primer site sequence, thus probably causing p referential hybridization to the Y sequence when using the conventional pri mers. 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 Norw egian males, allele distribution in the X-locus in 48 Norwegian women. Even if allele repeat numbers are overlapping between the loci, leading to iden tical fragment lengths, the allele distribution is different between DYS393 and the X-chromosome locus. The differences between the two homologous loc i 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 el ongated to include one of the sequence differences between the two loci. Th is to a considerable extent improved the specificity of the DYS393 primers. (C) 2000 Elsevier Science Ireland Ltd. All rights reserved.