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

Abstract

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (> or =1 in 5 x 10(5)) and females (> or =1 in 3 x 10(9)), as well as high mean exclusion chance in father/daughter duos (> or =99.953%) and in father/mother/daughter trios (> or =99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.

Potential forensic use of a 33 X-InDel panel in the Argentinean population

“…Therefore, the aim of this work was to evaluate the potential forensic suitability of additional genetic markers to be included in the routine forensic casework toolbox. Regardless of LD, the results obtained with the X-InDel panel for accumulated power of discrimination in males and females, as well as the mean exclusion chances in duos and trios, were slightly lower than other studied InDels [26,34,35], X-STR [6,36,37], and X-SNPs [38,39], but comparable with the X-chromosomal 21-InDel panel proposed by Edelman et al [40].…”

“…The analysis of forensic parameters showed that the values obtained for PD F , PD M , MEC T , and MEC D for this panel were slightly lower than those of other InDels [26,34,35,41] or STR panels [6]. Nevertheless, due to the low mutation rates of InDels, this panel could be used as a complement in cases displaying few microsatellite transmission incompatibilities.…”

“…Although STRs are the markers of choice, occasionally, the results might be uninformative or inconclusive, particularly in deficient paternity cases or when degraded material is the only DNA source. Hence, complementary analyses such as polymorphisms located on Y [3,4] and X [5,6] chromosomes or mitochondrial DNA (mtDNA) are frequently required [7,8]. The transmission pattern of the human X chromosome differs between genders, escaping recombination in males, whereas in females, it occurs at a lower rate than for autosomes leading to higher levels of linkage disequilibrium (LD) [9].…”

DNA human identification for the family rights: One year of agreement between UNESP/Laboratory of Paternity and Public Defender Service in São Paulo State

“…PCR amplification of autosomal (AS) short tandem repeat (STR) markers was carried out using the PowerPlex 1 16 System (Promega) from December/2011 to February/2012; after that PowerPlex 1 18D System (Promega) was used from March to July and PowerPlex 1 21 System (Promega) from August to December of 2012. When necessary, 12 Y-STR (PowerPlex 1 Y System, Promega) and 10 X-STR [1] markers were analyzed. The latter were amplified as proposed by Martins et al [2].…”

Aplicabilidade do cromossomo X no DNA forense

“…O polimorfismo presente nesse cromossomo vem atraindo cada dia mais a atenção de pesquisadores. Inúmeros estudos na população brasileira demonstraram que vários marcadores moleculares situados no cromossomo X já são validados para uso forense, sendo que estes apresentam resposta no que tange sobre a variabilidade desses polimorfismos na população (CAINÉ et al, 2007;CAINÉ et al, 2010;GUSMÃO et al, 2009;LEITE et al, 2009;MARTINS et al, 2008a;MARTINS et al, 2009;MARTINS et al, 2010a;MARTINS et al, 2010b;PENNA et al, 2011;RODRIGUES et al, 2010;RODRIGUES et al, 2011;SILVA et al, 2010;TAVARES et al, 2008). Na rotina forense, os marcadores do tipo STR mais utilizados são os localizados nos cromossomos autossômicos e no Y (TOMAS et al, 2015).…”