Genetic analysis of three US population groups using an X-chromosomal STR decaplex

Gomes, Iva; Prinz, Mechthild; Pereira, Rui; Meyers, Carole; Mikulasovich, Rebecca S.; Amorim, António; Carracedo, Ángel; Gusmão, Leonor

doi:10.1007/s00414-006-0146-2

Cited by 60 publications

(63 citation statements)

References 24 publications

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“…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].…”

Section: Discussionsupporting

confidence: 80%

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

et al. 2016

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Polymorphic genetic markers located on the X chromosome might become a complement in particular forensic identification when the biological kinship are deficient. We analyzed forensic statistical parameters of 33 X-chromosome InDel polymorphisms in a sample of 320 individuals from Argentina. The X-chromosome InDel polymorphism (X-InDel) panel was amplified in a single multiplex PCR reaction. Hardy-Weinberg Equilibrium was determined in the female cohort, whereas the male cohort was used to calculate linkage disequilibrium (LD) tested by an extension of Fisher's exact test, D', and Chi-square values. Regarding LD, 15 markers were organized and grouped into six blocks containing two or three linked loci each, namely block I (MID356-MID357), block II (MID448804-MID3703-MID218), block III (MID3705-MID3706-MID304737), block IV (MID197147-MID3754), block V (MID3664-MID284601-MID103547), and block VI (MID3763-MID3728). The haplotype diversity was higher than 0.99 in all cases. Blocks III and VI showed the highest match probability in the studied population, whereas block II showed the lowest. The accumulated power of discrimination was 99.9999991 % in women and 99.9992925 % in men. The mean exclusion chance in trios and duos were 99.9891736 and 99.6099391 %, respectively. Since 15 markers are associated as haplotypic blocks, for a conservative treatment of the data, statistical evaluation should consider their haplotypic frequencies and the remaining 18 markers can be evaluated as independent loci.

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Section: Discussionsupporting

confidence: 80%

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

et al. 2016

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“…Markers were selected taking into account the gene diversity values reported in different populations (e.g., [3,5,8,13,14,[17][18][19][20]23]); and the potential for multiplexing. Preference was given to simple rather than complex STRs, following the ISFG recommendations concerning locus selection for forensic applications [11].…”

Section: Multiplex Optimizationmentioning

confidence: 99%

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

et al. 2008

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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.

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“…The population origin of an individual could be valuable information to identify a suspect. Therefore, genetic loci with large differences in frequency among ethnically defined populations, such as haplogroups of mitochondrial DNA (mtDNA) [1][2][3], microsatellites [4][5][6][7], and single nucleotide polymorphisms (SNPs) [8,9], have been studied. However, to date, the genetic markers that determine the population origin of an individual have not been confirmed.…”

Section: Introductionmentioning

confidence: 99%

Variants of the melanocortin 1 receptor gene (MC1R) and P gene as indicators of the population origin of an individual

Masui¹,

Nakatome

Matoba

2008

Int J Legal Med

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The population origin of an individual is often requested to be determined from specimens left at a crime scene for identifying a suspect and individual identity. The melanocortin 1 receptor gene (MC1R) and P gene are associated with human pigmentation. Although several studies have reported that these genes are highly polymorphic in human populations, it is unclear if the allele variants can be used to determine the population origin of an individual. We aimed to determine the ethnic origin of an individual by using single nucleotide polymorphisms (SNPs). Eighteen SNPs in the MC1R gene and P genes were genotyped in 52 individuals by the direct sequencing method, and 4 SNPs (MC1R gene: R163Q and P gene: IVS5 + 1001, IVS13 + 113, and H615R) were selected on the basis of differences in frequencies. Subsequently, we genotyped these four SNPs in 422 volunteers from six ethnically defined populations using a polymerase chain reaction-based assay. The results revealed that the allele variants were present with high frequencies in Asian populations but were low in European and African populations. On the basis of these results, we defined a specific combination of a genotype (R163Q) and a diplotype group (IVS5 + 1001, IVS13 + 113, and H615R). This study indicates that the specific combination of a genotype and a diplotype group would be effective in estimating the population origin of an individual from a list of population groups.

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Genetic analysis of three US population groups using an X-chromosomal STR decaplex

Cited by 60 publications

References 24 publications

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

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

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

Variants of the melanocortin 1 receptor gene (MC1R) and P gene as indicators of the population origin of an individual

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