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.

HLA genes can exhibit extensive variations in frequency, especially in highly admixed populations, such as that of Brazil. In this study, we demonstrated NGS‐based HLA typing in our laboratory using an Illumina HiSeq 2500 sequencing platform and downstream analysis. We herein describe and compare the allele and haplotype frequencies of the populations in Barra Mansa (BM) and Rio de Janeiro (RJ), using the acquired genetic data. Sequences encompassing 7 HLA loci (HLA‐A, HLA‐B, HLA‐C, HLA‐DRB1, HLA‐DQB1, HLA‐DPA1, and HLA‐DPB1) were amplified from a total of 1435 bone marrow samples donated by volunteers recruited in BM (37.56%) and RJ (62.44%) using polymerase chain reactions, and were sequenced using five distinct HiSeq 2500 runs. Alleles were analyzed to generate 2‐locus haplotypes and extended haplotypes encompassing more than two loci. The most frequent haplotype was A*01:01:01~C*07:01:01~B*08:01:01~DRB1*03:01:01~DQB1*02:01:01~DPA1*01:03:01~DPB1*04:01:01 in both populations. The populations of BM and RJ exhibited a significant difference in genetic composition (P = .03) but not in genetic variance (P = .45). However, some groups of subjects, classified based on self‐declared ethnicity, particularly Branca and Preta, displayed significant genetic variance (P < .05). In conclusion, these genetic data indicate no differences in HLA loci between the populations of these two cities, but were informative with respect to variations in ancestry composition.

Identification of the novel HLA‐A*02:916 allele that differs from HLA‐A*02:01:01:01 in exon 5.

No abstract

Characterization of an HLA‐C*04:01:01 variant, HLA‐C*04:01:01:76.

reaction (PCR) and sequenced on an ABI 3500xl Genetic Analyzer (Thermo Fisher Scientific, Waltham, Massachusetts). Sequences were analyzed with AccuType software (TBG Corp., New Taipei City, Taiwan).The name, HLA-C*07:499, has been officially assigned by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System in March 2020. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report, 2 names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report.

Characterization of two novel HLA‐DQA1*05:05:01 variants, HLA‐DQA1*05:05:01:22 and ‐DQA1*05:05:01:23.

Characterization of the first HLA‐B*15:31 variant, called HLA‐B*15:31:01:02.