LAENALS: epidemiological and clinical features of amyotrophic lateral sclerosis in Latin America.

OBJECTIVE: The Latin American Epidemiologic study of ALS (LAENALS) aims to gather data on ALS epidemiology, phenotype, and risk factors in Cuba, Chile, and Uruguay, to understand the impact of genetic and environmental factors on ALS. METHODS: A harmonized data collection protocol was generated, and a Latin-American Spanish language Register was constructed. Patient data were collected in Uruguay in 2018, in Chile from 2017 to 2019, and in Cuba between 2017 and 2018. Statistical analysis was performed using SPSS 25.0.0 software. Crude cumulative incidence, standardized incidence, and prevalence were calculated in the population aged 15 years and older. RESULTS: During 2017-2019, 90 people with ALS from Uruguay (55.6% men), 219 from Chile (54.6% men), and 49 from Cuba (55.1% men) were included. The cumulative crude incidence in 2018 was 1.73/100,000 persons in Uruguay, 1.08 in Chile and 0.195 in Cuba. Crude prevalence in 2018 was 2.19 per 100,000 persons in Uruguay, 1.39 in Chile and 0.55 in Cuba. Mean age at onset was 61.8 ± 11.96 SD years in Uruguay, 61.9 ± 10.4 SD years in Chile, and 60.21 ± 12.45 SD years in Cuba (p = 0.75). Median survival from onset was 32.43 months (21.93 - 42.36) in Uruguay, 24 months (13.5 - 33.5) in Chile, and 29 months (15 - 42.5) in Cuba (p = 0.006). CONCLUSIONS: These preliminary data from LAENALS confirm the lower incidence and prevalence of ALS in counties with admixed populations. The LAENALS database is now open to other Latin American countries for harmonized prospective data collection.

NAToRA, a relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses.

Genetic and omics analyses frequently require independent observations, which is not guaranteed in real datasets. When relatedness cannot be accounted for, solutions involve removing related individuals (or observations) and, consequently, a reduction of available data. We developed a network-based relatedness-pruning method that minimizes dataset reduction while removing unwanted relationships in a dataset. It uses node degree centrality metric to identify highly connected nodes (or individuals) and implements heuristics that approximate the minimal reduction of a dataset to allow its application to complex datasets. When compared with two other popular population genetics methodologies (PLINK and KING), NAToRA shows the best combination of removing all relatives while keeping the largest possible number of individuals in all datasets tested and also, with similar effects on the allele frequency spectrum and Principal Component Analysis than PLINK and KING. NAToRA is freely available, both as a standalone tool that can be easily incorporated as part of a pipeline, and as a graphical web tool that allows visualization of the relatedness networks. NAToRA also accepts a variety of relationship metrics as input, which facilitates its use. We also release a genealogies simulator software used for different tests performed in this study.

Population structure and relatedness estimates in a Mexican sample.

Population stratification (PS) is a confounding factor in genome-wide association studies (GWASs) and also an interesting process itself. Latin American populations have mixed genetic ancestry, which may account for PS. We have analyzed the relatedness, by means of the identity-by-descent (IBD) estimations, in a sample of 1805 individuals and 1.006.703 autosomal mutations from a case-control study of colorectal cancer in Mexico. When using the recommended protocol for quality control assessment, 402 should have been removed due to relatedness. Our purpose was to analyze this value in the context of an admixed population. For that aim, we reanalyzed the sample using two software designed for admixed populations, obtaining estimates of 110 and 70 related individuals to remove. The results showed that the first estimation of relatedness was an effect of the higher Native American contribution in part of the data samples, being a confounding factor for IBD estimations. We conclude in the importance of considering PS and genetic ancestry in order to avoid spurious results, not only in GWAS but also in relatedness analysis.

Patterns of genetic diversity in Colombia for 38 indels used in human identification.

The current population of Colombia has a genetic heterogeneity resulting from different migrations from other continents and within the country. In addition, there are small groups in their territory that have remained isolated and therefore have a different genetic pool in relation to that of the neighbouring urban populations. This population stratification must be considered in forensic analysis, being more complex for markers with marked intercontinental differentiation. In this study, population differentiation in Colombian admixed, native, and Afro-descendant populations was evaluated for a group of 38 indels described for forensic use. Allelic frequencies and parameters of forensic relevance were determined in each of the groups defined based on population differentiation analyses. In addition to the differences found between population groups, the results show that the set of 38 indels analysed could be useful in studies of individual identification in Colombia. The exclusion power presented by this set of markers suggests the need for joint use with other markers, being able to complement the STRs in paternity cases. High levels of both power of discrimination and exclusion were found when complementing the 38 HID-indels with a second multiplex, for a total of 83 indels.

Association between the TPMT*3C (rs1142345) Polymorphism and the Risk of Death in the Treatment of Acute Lymphoblastic Leukemia in Children from the Brazilian Amazon Region.

Acute lymphoblastic leukemia (ALL) is the leading cause of death from pediatric cancer worldwide. However, marked ethnic disparities are found in the treatment of childhood ALL with less effective results and higher mortality rates being obtained in populations with a high level of Native American ancestry. Genetic variations of the patient can affect resistance to ALL chemotherapy and potentially play an important role in this disparity. In the present study, we investigated the association of 16 genetic polymorphisms with the cell and metabolic pathways of the chemotherapeutic agents used in the treatment of ALL with the risk of death in treating childhood ALL in patients with a high contribution of Amerindian ancestry, coming from the Brazilian Amazon. The study included 121 patients with B-cell ALL treated with the BFM-2002 protocol. We are the first to identify the association between the TPMT gene rs1142345 polymorphism and the high risk of death in treating childhood ALL. Patients with the CC genotype had an approximately 25.5 times higher risk of dying during treatment of the disease than patients with other genotypes (p = 0.019). These results may help elucidate how the patient's genetic characteristics contribute to the mortality disparity in populations with a high contribution of Native American ancestry. The rs1142345 variant of the TPMT gene could be used as a potential marker to early stratify patients at high risk of death in treating childhood ALL in the investigated population.

Male lineages in Brazilian populations and performance of haplogroup prediction tools.

The use of Y-chromosomal genetic markers in forensic investigations demands the establishment of reliable and representative DNA databases of different reference populations. The genetic characterization of the Y chromosome variation in human populations requires the analyses of haplotype frequencies allied to haplogroup determination. The present study aimed to contribute to the Brazilian database by providing 1,382 Yfiler Plus individual profiles, from 11 Brazilian states. The Yfiler Plus markers showed high haplotype diversities in all Brazilian populations (>0.9970), allowing high intra-population discrimination in forensic investigations. Pairwise genetic distances showed a homogeneity between Brazilian populations (FST ≤ 0.0043; non-differentiation p-values ≥ 0.0212), indicating that admixed populations from Brazil can be represented in a single Yfiler Plus haplotype database, for forensic purposes. The performance of Haplogroup Predictor and NevGen software in haplogroup prediction based on Yfiler Plus and Yfiler haplotypes was evaluated in a subset of 416 Brazilian samples that were also genotyped for 51 Y-SNPs. In 25% of the samples, no classification or errors were found for at least one of the prediction tools or marker sets. NevGen presented lower error rates (5.52% and 8.65% with Yfiler Plus and Yfiler, respectively) than Haplogroup Predictor (16.11% with Yfiler Plus and 13.70% with Yfiler). In conclusion, both haplogroup prediction tools can be useful to direct the SNP typing, but present large error rates to be used in forensic analysis, especially in predicting African haplogroups in admixed South American populations.

Comparative Study of 10 X-STR Markers in Populations of Northeast Argentina.

In northeast Argentina, different Amerindian communities share territory and history with settlers, mainly Europeans. Due to miscegenation, the current Argentinean population has a particular structure that can be described through X chromosome variation. The objectives of this study were to describe the variation of 10 X-chromosome short tandem repeats (X-STRs) in urban populations of the Argentinean regions known as Gran Chaco and Mesopotamia, report the forensic parameters of these STRs, and estimate the European and indigenous genetic components in these regions. Population and forensic parameters were estimated for 419 individuals from the analyzed populations, including two indigenous groups, Wichí and Mocoví, previously reported. Population structure was estimated through FST and RST distances and analysis of molecular variance. The indigenous American and European components were assessed with STRUCTURE. X-STRs showed a high level of genetic variability in urban and indigenous populations. Indigenous people of the Gran Chaco region showed significant differentiation from the urban samples (FST = 5.5%) and among themselves (FST = 5.3%). Genetic differentiation among urban groups was almost negligible, except that the population from Misión Nueva Pompeya differed from the rest of the city populations. Forensic parameters indicate that these X-STRs are useful as a complement to paternity tests. The set of 10 STRs could be a good tool for examining population differences.

Genetic Differentiation in a Sample from Northern Mexico City Detected by HLA System Analysis: Impact in the Study of Population Immunogenetics.

The major histocompatibility complex is directly involved in the immune response, and thus the genes coding for its proteins are useful markers for the study of genetic diversity, susceptibility to disease (autoimmunity and infections), transplant medicine, and pharmacogenetics, among others. The polymorphism of the system also allows researchers to use it as a proxy for population genetics analysis, such as genetic admixture and genetic structure. In order to determine the immunogenetic characteristics of a sample from the northern part of Mexico City and to use them to analyze the genetic differentiation from other admixed populations, including those from previous studies of Mexico City population, we analyzed molecular typing results of donors and patients from the Histocompatibility Laboratory of the Central Blood Bank of the Centro Médico Nacional La Raza selected according to their geographic origin. HLA-A, -B, -DRB1, and -DQB1 alleles were typed by polymerase chain reaction with sequence-specific primers. Allelic and haplotype frequencies, as well as population genetics parameters, were obtained by maximum likelihood methods. The most frequent haplotypes found were HLA-A*02/-B*39/-DRB1*04/-DQB1*03:02P, HLA-A*02/-B*35/-DRB1*04/-DQB1*03:02P, HLA-A*68/-B*39/-DRB1*04/-DQB1*03:02P, and HLA-A*02/-B*35/-DRB1*08/-DQB1*04. Importantly, the second most frequent haplotype found in our sample (HLA-A*02/-B*35/-DRB1*04/-DQB1*03:02P) has not been previously reported in any mixedancestry populations from Mexico but is commonly encountered in Native American human groups, which can reflect the impact of migration dynamics in the genetic conformation of the northern part of Mexico City, and the limitations of previous studies with regard to the genetic diversity of the analyzed groups. Differences found in haplotype frequencies demonstrated that large urban conglomerates cannot be analyzed as one homogeneous entity but, rather, should be understood as a set of structures in which social, political, and economical factors influence their genesis and dynamics.

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

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.