title: New sequence variants detected at DXS10148, DXS10074 and DXS10134 loci.
abstract: A great amount of population and forensic genetic data are available for X-STRs supporting the need for having a common and accurate nomenclature among laboratories allowing for better communication, data exchange, and data comparison. DXS10148, DXS10074 and DXS10134 are commonly used X-STRs particularly due to their inclusion in the commercial kit Investigator Argus X-12 (Qiagen). Samples from West Africa and Iraq were sequenced for all three X-STRs allowing the detection of new DNA sequence variants. At DXS10148, variation was detected at four bases downstream from the flanking region from the repeat motif. The sequence AAGG-AAAG has been detected for the first time as a varying (AAGG-AAAG)1-3 motif, in the present work. One additional string when compared to the common one (AAGG-AAAG)2 adds eight bases to the fragment size of the tetranucleotide STR. This means that 2 repeats are added in these cases to the fragment size of the allele, while the presence of only one copy will reduce the expected allele size by 2 repeats. At DXS10074 two varying stretches consisting of AC and AG dinucleotide repeats were observed in the upstream flanking region, six bases from the main repeat core that also influence the expected allele size. DXS10134 revealed a simpler nomenclature in the Guinea-Bissau sample set when compared to the previously described allele nomenclature. This detected new hidden variation also has impact on the actual allele nomenclature at this locus as it contributes to a new class of short alleles so far undetected in other studies.
authors.affiliation: Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany. Electronic address: iva.gomes@uk-koeln.de.
authors.forename: Iva
authors.initials: I
authors.lastname: Gomes
authors.affiliation: Human Genetics Laboratory, University of Madeira, Funchal, Portugal.
authors.forename: António
authors.initials: A
authors.lastname: Brehm
authors.affiliation: DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Brazil; IPATIMUP, Institute of Pathology and Molecular Immunology of the University of Porto, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
authors.forename: Leonor
authors.initials: L
authors.lastname: Gusmão
authors.affiliation: Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Schneider
mesh_terms: D000354:Africa, Western; D000483:Alleles; D041321:Chromosomes, Human, X; D005260:Female; D053803:Forensic Genetics / Q000379:methods*; D005787:Gene Frequency; D056426:Genetic Loci; D014644:Genetic Variation; D005828:Genetics, Population; D006169:Guinea-Bissau; D006239:Haplotypes; D006801:Humans; D007493:Iraq; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic
keywords: Guinea-Bissau; Investigator Argus X-12; Iraq; West Africa; X chromosome; X-STRs