Genomic ancestry of rural African‐derived populations from Southeastern Brazil

Kimura, Lilian; Ribeiro-Rodrigues, Elzemar Martins; Auricchio, Maria Teresa Balester de Mello; Vicente, João Pedro; Santos, Sidney Emanuel Batista dos; Mingroni-Netto, Regina Célia

doi:10.1002/ajhb.22335

Cited by 27 publications

(22 citation statements)

References 30 publications

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“…Scliar et al (2009); 9. Kimura et al (2013); a subset of these communities was also studied for two Alu insertions, and the values used to estimate parental contributions (Cotrim et al , 2004), but the results obtained showed inconsistencies among the populations and were not considered; 10. Francez et al (2011a); 11.…”

Section: Tablementioning

confidence: 99%

Interethnic admixture and the evolution of Latin American populations

2014

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A general introduction to the origins and history of Latin American populations is followed by a systematic review of the data from molecular autosomal assessments of the ethnic/continental (European, African, Amerindian) ancestries for 24 Latin American countries or territories. The data surveyed are of varying quality but provide a general picture of the present constitution of these populations. A brief discussion about the applications of these results (admixture mapping) is also provided. Latin American populations can be viewed as natural experiments for the investigation of unique anthropological and epidemiological issues.

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Section: Tablementioning

confidence: 99%

Interethnic admixture and the evolution of Latin American populations

2014

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“…It has been shown that European ancestry is evenly preponderant across the country; the African contribution has reached the highest proportion in the Northeast (∼30.3%), followed in decreasing order by the Southeast (∼18.9%), South (∼12.7%), and North (∼10.9%) regions, while the Amerindian contribution is the highest in the North (∼19.4%) region, and relatively evenly spread across the other regions (Santos et al 2010; Pena et al 2011). An unexpected high Amerindian contribution is also found in semi-isolated communities founded by African-slaves refugees, the “quilombos” (Lopes Maciel et al 2011; Kimura et al 2013; Gontijo et al 2014). Our colonization history also accounts for the high incidence of some diseases.…”

Section: Introductionmentioning

confidence: 98%

Genetics and genomics in Brazil: a promising future

Passos‐Bueno

Bertola

Horovitz

et al. 2014

Molec Gen & Gen Med

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“…In the present study we examine the accuracy of HLA imputation in a highly admixed Brazilian population (with 40% African, 39% European and 21% Native American average ancestries [13]) using the 1000 Genomes HLA and SNP data as a training set. Our interest is motivated by the importance of admixed populations in studies with a focus on admixture mapping (e.g.…”

Section: Introductionmentioning

confidence: 99%

HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set

Nunes

Zheng

Torres³

et al. 2016

Human Immunology

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Methods to impute HLA alleles based on dense single nucleotide polymorphism (SNP) data provide a valuable resource to association studies and evolutionary investigation of the MHC region. The availability of appropriate training sets is critical to the accuracy of HLA imputation, and the inclusion of samples with various ancestries is an important pre-requisite in studies of admixed populations. We assess the accuracy of HLA imputation using 1000 Genomes Project data as a training set, applying it to a highly admixed Brazilian population, the Quilombos from the state of São Paulo. To assess accuracy, we compared imputed and experimentally determined genotypes for 146 samples at 4 HLA classical loci. We found imputation accuracies of 82.9%, 81.8%, 94.8% and 86.6% for HLA-A, -B, -C and -DRB1 respectively (two-field resolution). Accuracies were improved when we included a subset of Quilombo individuals in the training set. We conclude that the 1000 Genomes data is a valuable resource for construction of training sets due to the diversity of ancestries and the potential for a large overlap of SNPs with the target population. We also show that tailoring training sets to features of the target population substantially enhances imputation accuracy.

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Genomic ancestry of rural African‐derived populations from Southeastern Brazil

Cited by 27 publications

References 30 publications

Interethnic admixture and the evolution of Latin American populations

Interethnic admixture and the evolution of Latin American populations

Genetics and genomics in Brazil: a promising future

HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set

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