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

Abstract

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.

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

“…GATA31E08 has been previously described by Shin et al [20] and alleles were named according to the total number of AGAT repeats. However, upstream to this STR, there is an AGGG unit that can be present in two or three copies [9]. Therefore, the repeat structure should be changed to (AGGG) 2-3 (AGAT) n and reference samples genotypes should be changed by adding two additional repeats (see Table 2).…”

Evaluation of DXS9902, DXS7132, DXS6809, DXS7133, and DXS7423 in humans and chimpanzees: sequence variation, repeat structure, and nomenclature

“…1) using the PRIMER3 software (http://frodo.wi.mit.edu). Polymerase chain reaction (PCR), thermocycling, and sequencing reaction conditions were the same as in Gomes et al [11] except for annealing temperatures (T m ) used for amplification of chimpanzee samples which was 58°C for all loci. DXS7423 was the only locus that presented unspecific PCR products in chimpanzee using the human primer set.…”

“…During several studies, some unusual results called attention to the probable use of different nomenclatures by different laboratories for the same X-STR marker (e.g., [9,11,16,20,22,23]). As additional research to help provide more accurate and secure genotyping results, the selection of X-chromosomal markers in the current and previous work [11] was based on those included in the X-linked decaplex recently developed by the Spanish-Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG) [15,16]. This multiplex system has been applied in the genetic characterization of several populations [10,16,28] and is still a tool for current and future projects.…”

“…This multiplex system has been applied in the genetic characterization of several populations [10,16,28] and is still a tool for current and future projects. Consequently, as an extension of preceding work [11], in this study, we aimed to investigate the sequence structural variation of the Xlinked loci DXS9902, DXS7132, DXS6809, DXS7133, and DXS7423 in different human population groups, as well as in chimpanzees. Comparisons of Homo sapiens and Pan troglodytes genomes allowed a more precise analysis of the sequence structure of the loci studied in this work, as well as inferences on possible evolving mutational mechanisms.…”

Forensic DNA Analysis

“…The Y and X chromosome both contain STR loci that could be shown to be as polymorphic as autosomal STRs (Roewer et al 1992;Kayser et al 1997;Szibor 2007;Gomes et al 2009). These gonosomal markers provide additional information about male or female relationships and have been successfully applied to routine kinship testing and historical investigations (Foster et al 1998;Rolf et al 2001;Ayadi et al 2007;Immel et al 2011).…”