Indel markers: Genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material

Manta, Fernanda S. N.; Caiafa, Alexandre; Pereira, Rui; Silva, Dayse A.; Amorim, António; Carvalho, E.F.; Gusmão, Leonor

doi:10.1016/j.fsigen.2011.12.008

Cited by 32 publications

(14 citation statements)

References 16 publications

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“…Panama and Southeast Brazil are those with the highest values (PD is 0.9999999999999995 and 0.9999999999999990, respectively; PE is 0.9987 and 0.9979, respectively). Previous reports using the same 38 indel set as in this study showed very similar results in population samples from Brazil, Portugal, and Spain [8,31,32].…”

Section: Forensically Relevant Parameterssupporting

confidence: 86%

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

Pereira

Alves

Aler

et al. 2018

Forensic Science International: Genetics

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A collaborative effort was carried out by the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) to promote knowledge exchange between associate laboratories interested in the implementation of indel-based methodologies and build allele frequency databases of 38 indels for forensic applications. These databases include populations from different countries that are relevant for identification and kinship investigations undertaken by the participating laboratories. Before compiling population data, participants were asked to type the 38 indels in blind samples from annual GHEP-ISFG proficiency tests, using an amplification protocol previously described. Only laboratories that reported correct results contributed with population data to this study. A total of 5839 samples were genotyped from 45 different populations from Africa, America, East Asia, Europe and Middle East. Population differentiation analysis showed significant differences between most populations studied from Africa and America, as well as between two Asian populations from China and East Timor. Low F values were detected among most European populations. Overall diversities and parameters of forensic efficiency were high in populations from all continents.

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Section: Forensically Relevant Parameterssupporting

confidence: 86%

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

Pereira

Alves

Aler

et al. 2018

Forensic Science International: Genetics

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“…The samples from Alagoas and Santa Isabel were selected from previous research projects belonging to healthy unrelated individuals used as controls in association studies, which involved the State hospitals as well as the Federal University of Alagoas and the Research Institute FIOCRUZ (Oswaldo Cruz Foundation). The Terena samples were those previously included in Manta et al [22]. …”

Section: Methodsmentioning

confidence: 99%

Revisiting the Genetic Ancestry of Brazilians Using Autosomal AIM-Indels

et al. 2013

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There are many different studies that contribute to the global picture of the ethnic heterogeneity in Brazilian populations. These studies use different types of genetic markers and are focused on the comparison of populations at different levels. In some of them, each geographical region is treated as a single homogeneous population, whereas other studies create different subdivisions: political (e.g., pooling populations by State), demographic (e.g., urban and rural), or ethnic (e.g., culture, self-declaration, or skin colour). In this study, we performed an enhanced reassessment of the genetic ancestry of ~ 1,300 Brazilians characterised for 46 autosomal Ancestry Informative Markers (AIMs). In addition, 798 individuals from twelve Brazilian populations representing the five geographical macro-regions of Brazil were newly genotyped, including a Native American community and a rural Amazonian community. Following an increasing North to South gradient, European ancestry was the most prevalent in all urban populations (with values up to 74%). The populations in the North consisted of a significant proportion of Native American ancestry that was about two times higher than the African contribution. Conversely, in the Northeast, Center-West and Southeast, African ancestry was the second most prevalent. At an intrapopulation level, all urban populations were highly admixed, and most of the variation in ancestry proportions was observed between individuals within each population rather than among population. Nevertheless, individuals with a high proportion of Native American ancestry are only found in the samples from Terena and Santa Isabel. Our results allowed us to further refine the genetic landscape of Brazilians while establishing the basis for the effective application of an autosomal AIM panel in forensic casework and clinical association studies within the highly admixed Brazilian populations.

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“…They are widely distributed throughout the genome and derived from single mutation events which occur at a very low frequency. Moreover, some of them might be informative as ancestry markers since they may display significant allele frequency differences among geographically separated populations, whereas others might be a complement in human identification tests [22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

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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Indel markers: Genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material

Cited by 32 publications

References 16 publications

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

Revisiting the Genetic Ancestry of Brazilians Using Autosomal AIM-Indels

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

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