X-chromosome STR sequence variation, repeat structure, and nomenclature in humans and chimpanzees.

Qualitative information on the sequence composition of the allele and locus structure of the X-STRs DXS8378, DXS9898, DXS6789, GATA31E08, and GATA172D05 was generated in this study. Sequence data were obtained from chimpanzees (Pan troglodytes) and diverse human population groups including Africans, Caucasians, Asians, African-Americans, and Hispanics. Results revealed DXS8378 as the most stable locus. On the other hand, DXS9898 and GATA172D05 showed unstable regions identified through chimpanzee-human sequence comparison. At DXS6789, intra-allelic variation was found in all human populations, i.e., alleles with same fragment sizes showed structural differences only detected by sequencing. At the GATA31E08 locus, a previously unreported variation between humans and chimpanzees was identified in an adjacent region upstream from the repeat. This resulted in the addition of two repeat units and the proposal of a new allele nomenclature at this locus. Also, the sequence analyses did not detect ethnic differences between the studied population samples that would justify the use of these markers to help identify ethnic origin in an anthropological context.

Characterization of a novel dimorphism in the 5' flanking region of the short tandem repeat (STR) locus, c-fes/fps (FES).

The FES short tandem repeat (STR) locus contains seven to 14 repeats of the tetranucleotide sequence ATTT. A novel 10 base pair dimorphism in the 5' flanking region of the FES locus was characterized in four broad populations: African-American, Hispanic, Caucasian, and Asian. The absence of the 10 base pair sequence, or (-) allele, was closely linked to FES STR alleles with 10 or fewer repeats. The presence of the 10 base pair sequence, or (+) allele, was closely linked to FES STR alleles with 12 or more repeats. The (-) and (+) alleles occurred equally often in FES STR allele 11. The nucleotide sequence (5'-GGCTGTTTTG-3') of the (+) allele, located 179 base pairs upstream of the FES STR, was determined to be consistent within and among the four populations. Statistical and sequence analysis confirmed the linkage between the two polymorphic sites. The results indicate that the exclusion rate of the FES locus is increased, above that for the STR alone, when both polymorphic characteristics are considered.