The nudix hydrolase 15 (NUDT15) gene acts in the metabolism of thiopurine, by catabolizing its active metabolite thioguanosine triphosphate into its inactivated form, thioguanosine monophosphate. The frequency of alternative NUDT15 alleles, in particular those that cause a drastic loss of gene function, varies widely among geographically distinct populations. In the general population of northern Brazilian, high toxicity rates (65%) have been recorded in patients treated with the standard protocol for acute lymphoblastic leukemia, which involves thiopurine-based drugs. The present study characterized the molecular profile of the coding region of the NUDT15 gene in two groups, non-admixed Amerindians and admixed individuals from the Amazon region of northern Brazil. The entire NUDT15 gene was sequenced in 64 Amerindians from 12 Amazonian groups and 82 admixed individuals from northern Brazil. The DNA was extracted using phenol-chloroform. The exome libraries were prepared using the Nextera Rapid Capture Exome (Illumina) and SureSelect Human All Exon V6 (Agilent) kits. The allelic variants were annotated in the ViVa^® (Viewer of Variants) software. Four NUDT15 variants were identified: rs374594155, rs1272632214, rs147390019, andrs116855232. The variants rs1272632214 and rs116855232 were in complete linkage disequilibrium, and were assigned to the NUDT15*2 genotype. These variants had high frequencies in both our study populations in comparison with other populations catalogued in the 1000 Genomes database. We also identified the NUDT15*4 haplotype in our study populations, at frequencies similar to those reported in other populations from around the world. Our findings indicate that Amerindian and admixed populations from northern Brazil have high frequencies of the NUDT15 haplotypes that alter the metabolism profile of thiopurines.

Genetic factors associated with COVID-19 disease outcomes are poorly understood. This study aimed to associate genetic variants in the SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, and ABO genes with the risk of severe forms of COVID-19 in Amazonian Native Americans, and to compare the frequencies with continental populations. The study population was composed of 64 Amerindians from the Amazon region of northern Brazil. The difference in frequencies between the populations was analyzed using Fisher’s exact test, and the results were significant when p ≤ 0.05. We investigated 64 polymorphisms in 7 genes; we studied 47 genetic variants that were new or had impact predictions of high, moderate, or modifier. We identified 15 polymorphisms with moderate impact prediction in 4 genes (ABO, CXCR6, FYCO1, and SLC6A20). Among the variants analyzed, 18 showed significant differences in allele frequency in the NAM population when compared to others. We reported two new genetic variants with modifier impact in the Amazonian population that could be studied to validate the possible associations with COVID-19 outcomes. The genomic profile of Amazonian Native Americans may be associated with protection from severe forms of COVID-19. This work provides genomic data that may help forthcoming studies to improve COVID-19 outcomes.

Understanding alternative splicing is crucial to elucidate the mechanisms behind several biological phenomena, including diseases. The huge amount of expressed sequences available nowadays represents an opportunity and a challenge to catalog and display alternative splicing events (ASEs). Although several groups have faced this challenge with relative success, we still lack a computational tool that uses a simple and straightforward method to retrieve, name and present ASEs. Here we present SPLOOCE, a portal for the analysis of human splicing variants. SPLOOCE uses a method based on regular expressions for retrieval of ASEs. We propose a simple syntax that is able to capture the complexity of ASEs.

Estimates show that 5–10% of breast cancer cases are hereditary, caused by genetic variants in autosomal dominant genes; of these, 16% are due to germline mutations in the BRCA1 and BRCA2 genes. The comprehension of the mutation profile of these genes in the Brazilian population, particularly in Amazonian Amerindian groups, is scarce. We investigated fifteen polymorphisms in the BRCA1 and BRCA2 genes in Amazonian Amerindians and compared the results with the findings of global populations publicly available in the 1000 Genomes Project database. Our study shows that three variants (rs11571769, rs144848, and rs11571707) of the BRCA2 gene, commonly associated with hereditary breast cancer, had a significantly higher allele frequency in the Amazonian Amerindian individuals in comparison with the African, American, European, and Asian groups analyzed. These data outline the singular genetic profiles of the indigenous population from the Brazilian Amazon region. The knowledge about BRCA1 and BRCA2 variants is critical to establish public policies for hereditary breast cancer screening in Amerindian groups and populations admixed with them, such as the Brazilian population.

Homologous Recombination Repair (HRR) testing has become increasingly important in clinical genomic labs due to the use of poly-ADP-ribose polymerase (PARP) inhibitor therapy for epithelial ovarian, fallopian tube, or peritoneum cancer. While sequencing and copy number variation analysis can identify patients with a pathogenic mutation in BRCA1 or BRCA2 who can benefit from PARPi therapy, there are also patients who may benefit but do not have these mutations. To address this, our lab has developed a test called HRD-One, in partnership with SOPHiA GENETICS, that can detect sequence variants in genes involved in HRR, as well as genomic scars that indicate Homologous Recombination Deficiency (HRD), which may be present even when a pathogenic variant is not detected. We tested 59 high-grade serous epithelial ovarian cancer samples using HRD-One and found that it had an overall categorical concordance of 94.74% with Myriad’s myChoice® score, which is a commercial HRD test. 12 out of 13 samples that carried a pathogenic or likely pathogenic variant in BRCA1/2 also had a positive HRD-One score, and 9 samples in which a pathogenic variant in BRCA1/2 was not identified had a positive score in both HRD-One and myChoice®. Of the samples that passed quality control, we observed an average of 1.62 points variation between replicates on a scale from -25.0 to +25.0. We also found that low-confidence results were associated with a low DNA input and the age of FFPE blocks, while the estimated tumor percentage in the block, NGS library yield, and score of genomic instability did not have a significant association. We determined that blocks older than 3 years or with a DNA input of less than 25ng are not reliable for producing high-quality results. Finally, we validated the HRD-One test with SOPHiA Homologous Recombination Solution (Library Prep kit II) and correlated it to myChoice®, and found that the AmoyDx® HRD Focus Panel had the same sensitivity but a higher number of false positive samples and therefore lower specificity. Overall, we have shown that HRD-One can provide a reproducible and concordant score for inferring HRD, and an HRD-One score of 2.0 or greater predicts HRD and correlates to Myriad’s myChoice® score of 42 in high-grade serous epithelial ovarian cancers samples that meet our minimum quality criteria.

Neural circuits emerge during development through dynamic interactions between genetic instructions and environmental cues that shape cell fate, connectivity, and the timing of myelination. In developmental disorders such as autism, abnormalities in sensory processing, social cognition, and motor behavior are thought to arise from disruptions in these processes. Here, we investigated early-life molecular changes following prenatal exposure to valproic acid (VPA), an environmentally induced model of autism. We integrated cortical gene expression analysis using RNA sequencing/qPCR, alternative splicing profiling, in situ myelin quantification, plasma serotonin determination, and machine learning-assisted classification of blood serum molecular profiles using infrared spectroscopic (FTIR) data. Our findings revealed downregulation of myelin-associated genes and upregulation of synapse-related genes in the frontal cortex of young VPA-exposed rats. qPCR confirmed reduced cortical expression of Mobp and PLP1 along with increased Penk and C1ql3 expression. Alternative splicing analysis identified numerous novel transcript variants, enriched in synaptic-related genes, indicating widespread post-transcriptional remodeling in VPA animals. These molecular alterations were accompanied by a significant reduction in myelin content within the cingulate and motor cortex of adult animals. Peripheral molecular profiling showed elevated plasma serotonin in VPA-treated animals and demonstrated that a support vector machine trained on serum FTIR spectra classified VPA-exposed animals with 85% accuracy. Collectively, our findings suggest that prenatal VPA exposure induces early dysregulation of myelin organization, synaptic gene networks, and RNA splicing programs, potentially leading to long-term impairments in neuronal communication and processing efficiency. Furthermore, our results highlight serum spectroscopic signatures as promising peripheral biomarkers for autism, warranting further investigation.