New sequence variants detected at DXS10148, DXS10074 and DXS10134 loci. (January 2016)

• Record Type: Journal Article
• Authors: Gomes, Iva; Brehm, António; Gusmão, Leonor; Schneider, Peter M.
• Is Part Of: Forensic science international. Volume 20(2016:Jan.)
• Page Start: 112
• Page End: 116
• Publication Date: 2016-01
• Subjects: Investigator Argus X-12 -- X-STRs -- X chromosome -- West Africa -- Iraq -- Guinea-Bissau; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2015.10.005
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: Newly detected sequence variants at commonly used X-STR loci. First time report of a varying AAGG-AAAG motif in the flanking region of DXS10148. Detection of AC and AG varying stretches at DXS10074 upstream flanking region. New, simpler nomenclature detected at DXS10134. 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.