Enhancing SARS-CoV-2 Lineage Surveillance through the Integration of a Simple and Direct qPCR-Based Protocol Adaptation with Established Machine Learning Algorithms.

Emerging and evolving Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages, adapted to changing epidemiological conditions, present unprecedented challenges to global public health systems. Here, we introduce an adapted analytical approach that complements genomic sequencing, applying a cost-effective quantitative polymerase chain reaction (qPCR)-based assay. Viral RNA samples from SARS-CoV-2 positive cases detected by diagnostic laboratories or public health network units in Ceará, Brazil, were tracked for genomic surveillance and analyzed by using paired-end sequencing combined with integrative genomic analysis.

Assessing the Risk Stratification of Breast Cancer Polygenic Risk Scores in a Brazilian Cohort.

Polygenic risk scores (PRSs) for breast cancer have a clear clinical utility in risk prediction. PRS transferability across populations and ancestry groups is hampered by population-specific factors, ultimately leading to differences in variant effects, such as linkage disequilibrium and differences in variant frequency (allele frequency differences). Thus, locally sourced population-based phenotypic and genomic data sets are essential to assess the validity of PRSs derived from signals detected across populations.

Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil.

Admixed populations have not been examined in detail in cancer genetic studies. Here, we inferred the local ancestry of cancer-associated single nucleotide polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population. SNP array was used to genotype 73 unrelated individuals aged 80-102 years.

The structure of first-cousin marriages in Brazil.

This paper deals with the frequency and structure of first-cousin marriages, by far the most important and frequent type of consanguineous mating in human populations. Based on the analysis of large amounts of data from the world literature and from large Brazilian samples recently collected, we suggest some explanations for the asymmetry of sexes among the parental sibs of first-cousin marriages. We suggest also a simple manner to correct the method that uses population surnames to assess the different Wright fixation indexes F, F and F taking into account not only alternative methods of surname transmission, but also the asymmetries that are almost always observed in the distribution of sexes among the parental sibs of first-cousins.

A population-based study of inter-generational attitudes towards consanguineous marriages in north-eastern Brazil.

The aim of this cross-sectional study was to investigate beliefs, attitudes and reproductive behaviours in relation to consanguinity in a population living in the backlands of north-eastern Brazil. Data were collected by face-to-face interview from 147 high school students aged 13-20 years and from 532 elderly individuals aged 60 years and over from Brejo dos Santos in the state of Paraíba in 2017. The frequency of consanguineous marriage was found to have increased over the generations, being 15.

Origin and age of the causative mutations in KLC2, IMPA1, MED25 and WNT7A unravelled through Brazilian admixed populations.

The mutation age and local ancestry of chromosomal segments harbouring mutations associated with autosomal recessive (AR) disorders in Brazilian admixed populations remain unknown; additionally, inbreeding levels for these affected individuals continue to be estimated based on genealogical information. Here, we calculated inbreeding levels using a runs of homozygosity approach, mutation age and local ancestry to infer the origin of each chromosomal segments containing disorder-causing mutations in KLC2, IMPA1, MED25 and WNT7A. Genotyped data were generated from 18 patients affected by AR diseases and combined to the 1000 genome project (1KGP) and Simons genome diversity project (SGDP) databases to infer local ancestry.

Ancestry Informative Marker Panel to Estimate Population Stratification Using Genome-wide Human Array.

Case-control studies are a powerful strategy to identify candidate genes in complex diseases. In admixed populations, association studies can be affected by population stratification, leading to spurious genetic associations. Ancestry informative markers (AIMs) can be used to minimise this effect.