Analysis of genetic ancestry in the admixed Brazilian population from Rio de Janeiro using 46 autosomal ancestry-informative indel markers

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

doi:10.3109/03014460.2012.742138

Cited by 60 publications

(62 citation statements)

References 21 publications

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“…33 Recently, using a set of AIM-INDELs, we estimated the ancestry proportions of individuals from Amazonas, Belém, and Rio de Janeiro populations in Brazil. 33,37 We concluded that this panel has accuracy and is suitable to estimate genetic ancestry in highly admixed populations such as the Brazilian. 33,37 Herein, we aimed to establish the QMVR of BAT-25, BAT-26, NR-21, NR-24, and NR-27 markers, in a Brazilian healthy population, to evaluate the feasibility of MSI status determination of tumors without the need of matching normal DNA.…”

Section: Introductionmentioning

confidence: 88%

“…33,37 We concluded that this panel has accuracy and is suitable to estimate genetic ancestry in highly admixed populations such as the Brazilian. 33,37 Herein, we aimed to establish the QMVR of BAT-25, BAT-26, NR-21, NR-24, and NR-27 markers, in a Brazilian healthy population, to evaluate the feasibility of MSI status determination of tumors without the need of matching normal DNA. Furthermore, we intend to determine the ancestry of Brazilian individuals using specific AIMINDELs and correlate with their QMVR.…”

Section: Introductionmentioning

confidence: 88%

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Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers

et al. 2013

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Microsatellite instability (MSI) testing has been advocated for all newly diagnosed colorectal cancer patients. One of the most common tests is composed by a pentaplex panel of mononucleotides markers , which allows the analysis of MSI in tumors without the need of reference DNA. For that, it is fundamental to establish a quasi-monomorphic variation range (QMVR) for each marker. Herein, we aimed to establish the QMVR in a Brazilian healthy population, to evaluate the feasibility of MSI determination of tumors, without the matching normal DNA. Furthermore, we intend to assess their ancestry using specific ancestry-informative markers (AIMs) and correlate with QMVR. The QMVR was assessed in 214 individuals, through a pentaplex PCR followed by fragment analysis. The ancestry analysis was done by 46 AIMs in a single multiplex PCR followed by capillary electrophoresis. Following QMVR establishment, we observed 23 individuals with alleles outside the QMVR. Importantly, none of them exhibited more than one marker outside the range. Therefore, individuals with instability at Z2 markers would be accurately classified as MSI. The European ancestry proportion was the most frequent (67.5%), followed by the African (19.6%). The comparison of the individuals with alleles within (n ¼ 191) and outside (n ¼ 23) the QMVR showed statistical difference in the proportions of European and African alleles, confirming the higher polymorphic nature of African ancestry. In conclusion, the present study reports an accurate methodology to assess MSI status without matched-normal DNA and independently of the ethnicity, even in the highly admixed population of Brazil.

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Section: Introductionmentioning

confidence: 88%

Section: Introductionmentioning

confidence: 88%

Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers

et al. 2013

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“…4,5 Other studies, in contrast, have demonstrated a significant association between self-declared color/ ethnicity and genetic ancestry. [6][7][8] In the present study we evaluate the correlation between selfreported skin color and genetic ancestry, and describe the patterns of genetic structure and admixture stratification in two cities from the Northeast region of Brazil: Fortaleza, capital of the state of Ceará, and Salvador, capital of the state of Bahia. The two capitals are 1300 km apart, and have different demographic histories with respect to African slavery and European immigration.…”

Section: Introductionmentioning

confidence: 99%

The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions

et al. 2014

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The degree of admixture in Brazil between historically isolated populations is complex and geographically variable. Studies differ as to what the genetic and phenotypic consequences of this mixing have been. In Northeastern Brazil, we enrolled 522 residents of Salvador and 620 of Fortaleza whose distributions of self-declared color were comparable to those in the national census. Using the program Structure and principal components analysis there was a clear correlation between biogeographic ancestry and categories of skin color. This correlation with African ancestry was stronger in Salvador (r=0.585; P<0.001) than in Fortaleza (r=0.236; P<0.001). In Fortaleza, although self-declared blacks had a greater proportion of European ancestry, they had more African ancestry than the other categories. When the populations were analyzed without pseudoancestors, as in some studies, the relationship of 'race' to genetic ancestry tended to diffuse or disappear. The inclusion of different African populations also influenced ancestry estimates. The percentage of unlinked ancestry informative markers in linkage disequilibrium, a measure of population structure, was 3-5 times higher in both Brazilian populations than expected by chance. We propose that certain methods, ascertainment bias and population history of the specific populations surveyed can result in failure to demonstrate a correlation between skin color and genetic ancestry. Population structure in Brazil has important implications for genetic studies, but genetic ancestry is irrelevant for how individuals are treated in society, their health, their income or their inclusion. These track more closely with perceived skin color than genetic ancestry.

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“…To conduct this study, we used the highest cutoff point value of the AIMs (65%), which provided a reasonable number of individuals per ancestries groups. We believe that this cutoff value is appropriate because it is greater than the average value of the European AIMs described for Ouro Preto's population (50.3-53.9%) [18], and is the average of which is observed to southeastern Brazilian population (55.2-79.9%) [5,[22][23][24]. Although the prevalence of obesity, type 2 diabetes, and hypertension differs between ethnic groups, there are few correlation studies between genetic ancestry and risk phenotypes for these diseases.…”

Section: Discussionmentioning

confidence: 95%

Genetic Ancestry Is Associated With Systolic Blood Pressure and Glucose in Brazilian Children and Adolescents

et al. 2016

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Analysis of genetic ancestry in the admixed Brazilian population from Rio de Janeiro using 46 autosomal ancestry-informative indel markers

Cited by 60 publications

References 21 publications

Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers

Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers

The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions

Genetic Ancestry Is Associated With Systolic Blood Pressure and Glucose in Brazilian Children and Adolescents

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