Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population.

Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.

Functional analysis of CTLA4 promoter variant and its possible implication in colorectal cancer immunotherapy.

Background: Colorectal cancer (CRC) is a prevalent cancer, ranking as the third most common. Recent advances in our understanding of the molecular causes of this disease have highlighted the crucial role of tumor immune evasion in its initiation and progression. CTLA4, a receptor that acts as a negative regulator of T cell responses, plays a pivotal role in this process, and genetic variations in CTLA4 have been linked to CRC susceptibility, prognosis, and response to therapy. Methods: We conducted a case-control study involving 98 CRC patients and 424 controls. We genotyped the CTLA4 c.-319C > T variant (rs5742909) and performed an association analysis by comparing allele frequencies between the patients and controls. To assess the potential functional impact of this variant, we first performed an In Silico analysis of transcription factor binding sites using Genomatix. Finally, to validate our findings, we conducted a luciferase reporter gene assay using different cell lines and an electrophoretic mobility shift assay (EMSA). Results: The case-control association analysis revealed a significant association between CTLA4 c.-319C > T and CRC susceptibility (p = 0.023; OR 1.89; 95% CI = 1.11-3.23). Genomatix analysis identified LEF1 and TCF7 transcription factors as specific binders to CTLA4 c.-319C. The reporter gene assay demonstrated notable differences in luciferase activity between the c.-319 C and T alleles in COS-7, HCT116, and Jurkat cell lines. EMSA analysis showed differences in TCF7 interaction with the CTLA4 C and T alleles. Conclusion: CTLA4 c.-319C > T is associated with CRC susceptibility. Based on our functional validation results, we proposed that CTLA4 c.-319C > T alters gene expression at the transcriptional level, triggering a stronger negative regulation of T-cells and immune tumoral evasion.

Pharmacogenomic profile of actionable molecular variants related to drugs commonly used in anesthesia: WES analysis reveals new mutations.

Background: Genetic interindividual variability is associated with adverse drug reactions (ADRs) and affects the response to common drugs used in anesthesia. Despite their importance, these variants remain largely underexplored in Latin-American countries. This study describes rare and common variants found in genes related to metabolism of analgesic and anaesthetic drug in the Colombian population. Methods: We conducted a study that included 625 Colombian healthy individuals. We generated a subset of 14 genes implicated in metabolic pathways of common medications used in anesthesia and assessed them by whole-exome sequencing (WES). Variants were filtered using two pipelines: A) novel or rare (minor allele frequency-MAF <1%) variants including missense, loss-of-function (LoF, e.g., frameshift, nonsense), and splice site variants with potential deleterious effect and B) clinically validated variants described in the PharmGKB (categories 1, 2 and 3) and/or ClinVar databases. For rare and novel missense variants, we applied an optimized prediction framework (OPF) to assess the functional impact of pharmacogenetic variants. Allelic, genotypic frequencies and Hardy-Weinberg equilibrium were calculated. We compare our allelic frequencies with these from populations described in the gnomAD database. Results: Our study identified 148 molecular variants potentially related to variability in the therapeutic response to 14 drugs commonly used in anesthesiology. 83.1% of them correspond to rare and novel missense variants classified as pathogenic according to the pharmacogenetic optimized prediction framework, 5.4% were loss-of-function (LoF), 2.7% led to potential splicing alterations and 8.8% were assigned as actionable or informative pharmacogenetic variants. Novel variants were confirmed by Sanger sequencing. Allelic frequency comparison showed that the Colombian population has a unique pharmacogenomic profile for anesthesia drugs with some allele frequencies different from other populations. Conclusion: Our results demonstrated high allelic heterogeneity among the analyzed sampled, enriched by rare (91.2%) variants in pharmacogenes related to common drugs used in anesthesia. The clinical implications of these results highlight the importance of implementation of next-generation sequencing data into pharmacogenomic approaches and personalized medicine.

Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples.

RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus in the context of the COVID-19 pandemic. Because of the extreme number of cases in periodic waves of infection, there is a severe financial and logistical strain on diagnostic laboratories. For this reason, alternative implementations and validations of academic protocols that employ the lowest cost and the most widely available equipment and reagents found in different regions are essential. In this study, we report an alternative implementation of the EUA 2019-nCoV CDC assay which uses a previously characterized duplex PCR reaction for the N1 and RNAse P target regions and an additional uniplex reaction for the N2 target region. Taking advantage of the Abbott m2000 Sample Preparation System and NEB Luna Universal Probe One-Step RT-qPCR kit, some of the most widely available and inexpensive nucleic acid extraction and amplification platforms, this modified test shows state-of-the-art analytical and clinical sensitivities and specificities when compared with the Seegene Allplex-SARS-CoV-2 assay. This implementation has the potential to be verified and implemented by diagnostic laboratories around the world to guarantee low-cost RT-PCR tests that can take advantage of widely available equipment and reagents.

Characterization of ADME Gene Variation in Colombian Population by Exome Sequencing.

In genes related to drug pharmacokinetics, molecular variations determine interindividual variability in the therapeutic efficacy and adverse drug reactions. The assessment of single-nucleotide variants (SNVs) is used with growing frequency in pharmacogenetic practice, and recently, high-throughput genomic analyses obtained through next-generation sequencing (NGS) have been recognized as powerful tools to identify common, rare and novel variants. These genetic profiles remain underexplored in Latin-American populations, including Colombia. In this study, we investigated the variability of 35 genes included in the ADME core panel (absorption, distribution, metabolism, and excretion) by whole-exome sequencing (WES) of 509 unrelated Colombian individuals with no previous reports of adverse drug reactions. Rare variants were filtered according to the minor allele frequencies (MAF) <1% and potential deleterious consequences. The functional impact of novel and rare missense variants was assessed using an optimized framework for pharmacogenetic variants. Bioinformatic analyses included the identification of clinically validated variants described in PharmGKB and ClinVar databases. Ancestry from WES data was inferred using the R package EthSEQ v2.1.4. Allelic frequencies were compared to other populations reported in the public gnomAD database. Our analysis revealed that rare missense pharmacogenetic variants were 2.1 times more frequent than common variants with 121 variants predicted as potentially deleterious. Rare loss of function (LoF) variants were identified in 65.7% of evaluated genes. Regarding variants with clinical pharmacogenetic effect, our study revealed 89 sequence variations in 28 genes represented by missense (62%), synonymous (22.5%), splice site (11.2%), and indels (3.4%). In this group, ABCB1, ABCC2, CY2B6, CYP2D6, DPYD, NAT2, SLC22A1, and UGTB2B7, are the most polymorphic genes. NAT2, CYP2B6 and DPYD metabolizer phenotypes demonstrated the highest variability. Ancestry analysis indicated admixture in 73% of the population. Allelic frequencies exhibit significant differences with other Latin-American populations, highlighting the importance of pharmacogenomic studies in populations of different ethnicities. Altogether, our data revealed that rare variants are an important source of variability in pharmacogenes involved in the pharmacokinetics of drugs and likely account for the unexplained interindividual variability in drug response. These findings provide evidence of the utility of WES for pharmacogenomic testing and into clinical practice.

Association Between the LZTFL1 rs11385942 Polymorphism and COVID-19 Severity in Colombian Population.

Genetic and non-genetic factors are responsible for the high interindividual variability in the response to SARS-CoV-2. Although numerous genetic polymorphisms have been identified as risk factors for severe COVID-19, these remain understudied in Latin-American populations. This study evaluated the association of non-genetic factors and three polymorphisms: ACE rs4646994, ACE2 rs2285666, and LZTFL1 rs11385942, with COVID severity and long-term symptoms by using a case-control design. The control group was composed of asymptomatic/mild cases (n = 61) recruited from a private laboratory, while the case group was composed of severe/critical patients (n = 63) hospitalized in the Hospital Universitario Mayor-Méderi, both institutions located in Bogotá, Colombia. Clinical follow up and exhaustive revision of medical records allowed us to assess non-genetic factors. Genotypification of the polymorphism of interest was performed by amplicon size analysis and Sanger sequencing. In agreement with previous reports, we found a statistically significant association between age, male sex, and comorbidities, such as hypertension and type 2 diabetes mellitus (T2DM), and worst outcomes. We identified the polymorphism LZTFL1 rs11385942 as an important risk factor for hospitalization (p < 0.01; OR = 5.73; 95% CI = 1.2-26.5, under the allelic test). Furthermore, long-term symptoms were common among the studied population and associated with disease severity. No association between the polymorphisms examined and long-term symptoms was found. Comparison of allelic frequencies with other populations revealed significant differences for the three polymorphisms investigated. Finally, we used the statistically significant genetic and non-genetic variables to develop a predictive logistic regression model, which was implemented in a Shiny web application. Model discrimination was assessed using the area under the receiver operating characteristic curve (AUC = 0.86; 95% confidence interval 0.79-0.93). These results suggest that LZTFL1 rs11385942 may be a potential biomarker for COVID-19 severity in addition to conventional non-genetic risk factors. A better understanding of the impact of these genetic risk factors may be useful to prioritize high-risk individuals and decrease the morbimortality caused by SARS-CoV2 and future pandemics.

Machine Learning for Prediction of Stable Warfarin Dose in US Latinos and Latin Americans.

Populations used to create warfarin dose prediction algorithms largely lacked participants reporting Hispanic or Latino ethnicity. While previous research suggests nonlinear modeling improves warfarin dose prediction, this research has mainly focused on populations with primarily European ancestry. We compare the accuracy of stable warfarin dose prediction using linear and nonlinear machine learning models in a large cohort enriched for US Latinos and Latin Americans (ULLA). Each model was tested using the same variables as published by the International Warfarin Pharmacogenetics Consortium (IWPC) and using an expanded set of variables including ethnicity and warfarin indication. We utilized a multiple linear regression model and three nonlinear regression models: Bayesian Additive Regression Trees, Multivariate Adaptive Regression Splines, and Support Vector Regression. We compared each model's ability to predict stable warfarin dose within 20% of actual stable dose, confirming trained models in a 30% testing dataset with 100 rounds of resampling. In all patients (n = 7,030), inclusion of additional predictor variables led to a small but significant improvement in prediction of dose relative to the IWPC algorithm (47.8 versus 46.7% in IWPC, p = 1.43 × 10-15). Nonlinear models using IWPC variables did not significantly improve prediction of dose over the linear IWPC algorithm. In ULLA patients alone (n = 1,734), IWPC performed similarly to all other linear and nonlinear pharmacogenetic algorithms. Our results reinforce the validity of IWPC in a large, ethnically diverse population and suggest that additional variables that capture warfarin dose variability may improve warfarin dose prediction algorithms.

Association between Paraoxonase-1 p.Q192R Polymorphism and Coronary Artery Disease susceptibility in the Colombian Population.

BACKGROUND: Paraoxonase-1 (PON1), a glycoprotein associated with serum high-density lipoprotein (HDL), has a central role in metabolizing lipid peroxides, exhibiting antiatherogenic properties. The polymorphism p.Q192R has been previously associated with coronary artery disease (CAD) susceptibility and clopidogrel response. PURPOSE: We aimed at investigating the association of PON1 p.Q192R with CAD and clopidogrel response in Colombian population. PATIENTS AND METHODS: The study was conducted among 163 patients diagnosed with CAD and treated with clopidogrel. The allele frequencies for the PON1 192Q and 192R alleles were determined in cases and Latin-American controls obtained from the public database gnomAD (n = 17,711). Response to clopidogrel was determined by assessing the platelet function using the INNOVANCE PFA-200 System. We determined the association between PON1 p.Q192R polymorphism, increased susceptibility to CAD and high on-treatment platelet reactivity (HPR) by using odds ratio (OR) and 95% confidence interval (CI) on four genetic models. RESULTS: The allele frequencies for the PON1 192Q and 192R alleles were 0.60 and 0.40, respectively. The allele distribution was found to be statistically different from the control group and other ethnic groups. The allele 192R was positively associated with decreased susceptibility to CAD under a dominant model (OR, 0.58; 95% CI, 0.42-0.8; P < 0.01). We found no association between the polymorphism and HPR. CONCLUSION: We propose that PON1 p.Q192R is a potentially useful marker for CAD susceptibility in the Colombian population and lacks association with HPR under clopidogrel treatment.

Genetic Profile of the Dystrophin Gene Reveals New Mutations in Colombian Patients Affected with Muscular Dystrophinopathy.

BACKGROUND: Duchenne and Becker muscular dystrophies (DMD/BMD) are the most common human dystrophinopathies with recessive X-linked inheritance. Dystrophin gene deletions and duplications are the most common mutations, followed by point mutations. The aim of this study is to characterize the mutational profile of the dystrophin gene in Colombian patients with DMD/BMD. MATERIAL AND METHODS: Mutational profiling was determined in 69 affected patients using Sanger sequencing, next-generation sequencing (NGS) and/or multiplex ligation dependent-probes amplification (MLPA). Genetic variants were classified according to molecular consequence and new variants were determined through database and literature analysis. RESULTS: Mutational profile in affected patients revealed that large deletions/duplications analyzed by MLPA accounted for 72.5% of all genetic variations. By using Sanger sequencing or NGS, we identified point mutations in 15.9% and small deletions in 11.6% of the patients. New mutations were found, most of them were point mutations or small deletions (10.1%). CONCLUSION: Our results described the genetic profile of the dystrophin gene in Colombian patients with DMD and contribute to efforts to identify molecular variants in Latin American populations. For our population, 18.8% of cases could be treated with FDA or MDA approved molecular therapies based on specific mutations. These data contribute to the establishment of appropriate genetic counseling and potential treatment.

Genetic and Molecular Aspects of Drug-Induced QT Interval Prolongation.

Long QT syndromes can be either acquired or congenital. Drugs are one of the many etiologies that may induce acquired long QT syndrome. In fact, many drugs frequently used in the clinical setting are a known risk factor for a prolonged QT interval, thus increasing the chances of developing torsade de pointes. The molecular mechanisms involved in the prolongation of the QT interval are common to most medications. However, there is considerable inter-individual variability in drug response, thus making the application of personalized medicine a relevant aspect in long QT syndrome, in order to evaluate the risk of every individual from a pharmacogenetic standpoint.

A Pharmacogenetic Study of CYP2C19 in Acute Coronary Syndrome Patients of Colombian Origin Reveals New Polymorphisms Potentially Related to Clopidogrel Therapy.

Clopidogrel, an oral platelet P2Y12 receptor blocker, is used in the treatment of acute coronary syndrome. Interindividual variability in treatment response and the occurrence of adverse effects has been attributed to genetic variants in CYP2C19. The analysis of relevant pharmacogenes in ethnically heterogeneous and poorly studied populations contributes to the implementation of personalized medicine. We analyzed the coding and regulatory regions of CYP2C19 in 166 patients with acute coronary syndrome (ACS) treated with clopidogrel. The allele frequencies of CYP2C19 alleles *1, *2, *4, *17, *27 and *33 alleles were 86.1%, 7.2%, 0.3%, 10.2%, 0.3% and 0.3%, respectively. A new potentially pathogenic mutation (p.L15H) and five intronic variants with potential splicing effects were detected. In 14.4% of the patients, a new haplotype in strong linkage disequilibrium was identified. The clinical outcome indicated that 13.5% of the patients presented adverse drugs reactions with a predominance of bleeding while 25% of these patients were carriers of at least one polymorphic allele. We propose that new regulatory single-nucleotide variants (SNVs) might potentially influence the response to clopidogrel in Colombian individuals.

A Novel Splice-Site Mutation in the ELN Gene Suggests an Alternative Mechanism for Vascular Elastinopathies.

The ELN gene encodes elastin, a fundamental protein of the extracellular matrix that confers elasticity to different tissues including blood vessels. The formation of elastin fibers is a complex process involving monomer coacervation and subsequent crosslinking. Mutations in exons 1-29 of the ELN gene have been linked to supravalvular aortic stenosis (SVAS) whereas mutations in exons 30-33 are associated with autosomal dominant cutis laxa (ADCL). This striking segregation has led to the hypothesis that distinct molecular mechanisms underlie both diseases. SVAS is believed to arise through haploinsufficiency while ADCL is hypothesized to be caused by a dominant negative effect. Here, we describe a patient with SVAS harboring a novel splice-site mutation in the last exon of ELN. The location of this mutation is not consistent with current knowledge of SVAS, since all mutations reported in the C-terminus have been found in ADCL patients, and a thorough evaluation did not reveal significant skin involvement in this case. RT-PCR analysis of skin tissue showed that C-terminal mutations in the region can lead to the production of aberrant transcripts through intron retention and activation of cryptic splice sites and suggest that disruption of the very last exon can lead to functional haploinsufficiency potentially related to SVAS.

Possible Genetic Determinants of Response to Phenytoin in a Group of Colombian Patients With Epilepsy.

BACKGROUND: Epilepsy is a serious health problem worldwide. Despite the introduction of new antiepileptic drugs (AEDs) almost 30% of these patients have drug-resistant forms of the disease (DRE), with a significant increase in morbi-mortality. OBJECTIVE: Our objective was to assess the impact of some genetic factors and its possible association with treatment response and adverse drug reactions (ADRs) to phenytoin in 67 adult Colombian patients with epilepsy. METHODS: We conducted an analytical, observational, prospective cohort study to screen four polymorphisms in pharmacogenes: CYP2C9*2-c.430C>T (rs1799853), CYP2C9*3-c.1075A>C (rs1057910), ABCB1-c.3435T>C (rs1045642), and SCN1A-IVS5-91G>A (rs3812718), and their association with treatment response. Patients were followed for 1 year to confirm the existence of DRE (non-response) and ADRs using an active pharmacovigilance approach, followed by a consensus in order to classify ADRs according to causality, preventability, intensity and their relation with phenytoin dose, the duration of treatment, and susceptibility factors (DoTS methodology). RESULTS: A little more than half of evaluated subjects (52.2%) were non-responding to phenytoin. Regarding the genotype-phenotype correlation there was no association between polymorphisms of SCN1A and ABCB1 and DRE (non-response) (p = 0.34), and neither with CYP2C9 polymorphisms and the occurrence of ADRs (p = 0.42). We only found an association between polymorphic alleles of CYP2C9 and vestibular-cerebellar ADRs (dizziness, ataxia, diplopia, and dysarthria) (p = 0.001). Alleles CYP2C9*2-c.430C>T and CYP2C9*3-c.1075A>C were identified as susceptibility factors to ADRs in 24% of patients. CONCLUSIONS: Decreased function alleles of CYP2C9 were highly predictive of vestibular-cerebellar ADRs to phenytoin in our study (p = 0.001). However, the genetic variants CYP2C9*2-c.430C>T, CYP2C9*3-c.1075A>C, ABCB1-c.3435T>C, and SCN1A-IVS5-91G>A, were not associated with treatment response in our study.

A Pharmacogenomic Dissection of a Rosuvastatin-Induced Rhabdomyolysis Case Evokes the Polygenic Nature of Adverse Drug Reactions.

Rosuvastatin, is a widely-used statin for the treatment of hypercholesterolemia and the prevention of cardiovascular diseases. Although rosuvastatin is well tolerated, about 3/10.000 patients can suffer severe myopathy. Rhabdomyolysis is a severe medical condition that causes injury to the skeletal muscle, electrolyte imbalances, acute renal failure and extreme creatine kinase (CK) elevation. Little is known regarding the molecular involvement of rosuvastatin-induced rhabdomyolysis (RIR). It has been demonstrated that genomic variants associated with decreased enzymatic activity of proteins are important determinants in plasmatic and skeletal muscle distribution of rosuvastatin and its toxicity. Until now, no interactions of ticagrelor, ezetimibe and rosuvastatin have been described with the consideration of pharmacogenomics predisposition. The present report involves a whole-exome sequencing (WES), in a patient affected by rosuvastatin-induced rhabdomyolysis. A pharmacogenomic dissection was performed by analyzing a comprehensive subset of candidate genes (n=160) potentially related to RIR. The genes were selected according to their implication in drug metabolism or inherited myopathies. Using an innovative approach of bioinformatics analysis, considering rare and common variants, we identified 19 genomic variations potentially related to the pharmacokinetic/pharmacodynamic modifications of rosuvastatin, ezetimibe and ticagrelor. The affected genes are involved in Phase I metabolism (CYP2C19, CYP2E1, CYP1A1, CYP2D6 and CYP2C9), Phase II metabolism (UGT2B15 and UGT2B7), influx transportation (SLCO1B3 and SLCO2B1), efflux transportation (ABCG8, ABCB11, ABCC4 and ABCB1), drug targeting (NPC1L1) and inherited myopathy etiology (OBSCN). We report three rare, potentially pathogenic molecular variants in CYP2C19, NPC1L1 and OBSCN genes. Pharmacogenetic analysis indicated that the patient was a carrier of inactivating alleles in several pharmacogenes involved in drug toxicity. The whole-exome sequencing and bioinformatics analysis presented here represents an innovative way to identify genomic variants contributing with RIR´s origin and evokes the polygenic nature of adverse drug reactions.

Copy number variation profiling in pharmacogenetics CYP-450 and GST genes in Colombian population.

BACKGROUND: Copy Number variation (CNVs) in genes related to drug absorption, distribution, metabolism and excretion (ADME) are relevant in the interindividual variability of drug response. Studies of the CNVs in ADME genes in Latin America population are lacking. The objective of the study was to identify the genetic variability of CNVs in CYP-450 and GST genes in a subgroup of individuals of Colombian origin. METHODS: Genomic DNA was isolated from 123 healthy individuals from a Colombian population. Multiplex Ligation-Dependent Probe Amplification (MLPA) was performed for the identification of CNVs in 40 genomic regions of 11 CYP-450 and 3 GST genes. The genetic variability, allelic and genotypic frequencies were analyzed. RESULTS: We found that 13 out of 14 genes had CNVs: 5 (35.7%) exhibited deletions and duplications, while 8 (57.1%) presented either deletions or duplications.. 33.3% of individuals carried deletions and duplications while 49.6% had a unique type of CNV (deletion or duplication). The allelic frequencies of the CYP and GST genes were 0 to 47.6% (allele null), 0 to 17.5% (duplicated alleles) and 37 to 100% (normal alleles). CONCLUSIONS: Our results describe, for the first time, the genomic profile of CNVs in a subgroup of Colombian population in GST and CYP-450 genes. GST genes indicated greater genetic variability than CYP-450 genes. The data obtained contributes to the knowledge of genetic profiles in Latin American subgroups. Although the clinical relevance of CNVs has not been fully established, it is a valuable source of pharmacogenetic variability data with potential involvement in the response to medications.

Frecuencia de mutación y de variantes de secuencia para los genes BRCA1 y BRCA2 en una muestra de mujeres colombianas con sospecha de síndrome de cáncer de mama hereditario: serie de casos / Frequency of sequence mutations and variants for the BRCA1 and BRCA2 genes in a sample of Colombian women with suspected hereditary breast cancer syndrome: Case series

Describir variantes de secuencia en los genes BRCA1 y BRCA2 en una muestra de pacientes colombianas con historia personal o familiar de cáncer de mama sugestiva de riesgo genético.Materiales y métodos: serie de casos compuesta por 67 pacientes que fueron remitidas para estudio genético por sospecha de síndrome de cáncer de mama y ovario hereditario (HBOC). De los 67 casos, 42 (62,7 %) cumplieron con los criterios de indicación médica de la National Comprehensive Cancer Network (NCCN) del 2013, y en ellos se realizó secuenciación completa de los genes BRCA1 y BRCA2. Se determinó la frecuencia de mutación, variantes de secuencia y significancia clínica de las variantes halladas con base en Breast Cancer Information Core (BIC).Resultados: se identificaron mutaciones para el gen BRCA1 en seis pacientes (14,3 %), no se documentó mutación para el gen BRCA2, además se detectaron 43 variantes genéticas en 27 pacientes (64,2 % de 42 casos). De estas, 21 (48,8 %) fueron identificadas en el gen BRCA1 y 22 (51,2 %) en el gen BRCA2. Dentro de estas variantes, se identificaron 5 mutaciones patogénicas solo en el gen BRCA1, de las cuales solo una había sido reportada previamente en Colombia.Conclusiones: este estudio identifica variantes genéticas patogénicas en el gen BRCA1 no descritas en estudios previos en la población colombiana y otras conocidas en diferentes poblaciones; permitiendo de esta forma ampliar el conocimiento sobre las variantes en población colombiana de los genes BRCA1 y BRCA2. Sin embargo, se requieren más estudios con suficiente poder y calidad metodológica para poder estimar la frecuencia de mutaciones y de variantes de secuencia para estos genes en mujeres colombianas con sospecha de síndrome de cáncer de mama u ovario hereditario...

To describe sequence variants in the BRCA1 and BRCA2 genes in a sample of Colombian patients with a personal or family history of breast cancer suggestive of genetic risk.Materials and methods: Case series consisting of 67 patients referred for genetic testing because of suspected hereditary breast and ovarian cancer syndrome (HBOC). Of the 67 cases, 42 (62.7%) met the medical indication criteria of the 2013 National Comprehensive Cancer Network (NCCN) and they were subjected to the entire sequencing of the BRCA1 and BRCA2 genes. A determination was made of the frequency of sequence mutation, variants, and of the clinical significance of the variants found based on the Breast Cancer Information Core (BIC).Results: Mutations were identified for the BRCA 1 gene in six patients (14.3%), no mutation was documented for the BRCA 2 gene, and 43 genetic variants were found in 27 patients (64.2% of 42 cases). Of these, 21 (48.8%) were identified in the BRCA1 gene and 22 (51.2%) in the BRCA 2 gene. Among these variants, 5 pathogenic mutations were found only in the BRCA1 gene and, of those, only 1 had been reported previously in Colombia.Conclusions: This study identifies pathogenic genetic variants in the BRCA1 gene not described previously in the Colombian population, as well as others known in different populations. Therefore, it helps expand knowledge regarding the variants of the BRCA1 and BRCA2 genes in the Colombian population. However, additional studies are required with sufficient power and methodological quality to estimate the frequency of sequence mutations and variants for the BRCA1 and BRCA2 genes in Colombian women suspected of having the hereditary breast or ovarian cancer syndrome...

Pérdida de heterocigocidad e identificación de portadoras de distrofia muscular de Duchenne: un caso familiar con evento de recombinación / Loss of heterozygosity and carrier identification in Duchenne muscular dystrophy: a familiar case with recombination event / Perda de heterozigosidade e identificação de portadoras de distrofia muscular de Duchenne: um caso familiar com evento de recombinação

La distrofia muscular de Duchenne y Becker (DMD/DMB) es una entidad de herencia recesiva ligada al cromosoma X que se presenta con debilidad muscular y es causada por mutaciones en el gen de la distrofina. La pérdida de heterocigocidad permite identificar a las mujeres portadoras de deleción en el gen de la distrofina mediante haplotipos. Objetivo: identificar mujeres portadoras en una familia con un paciente afectado por DMD mediante análisis de pérdida de heterocigocidad. Materiales y métodos: se analizaron nueve miembros de una familia con un afectado de DMD. Se hizo extracción de ADN y amplificación de diez STR del gen de la distrofina; se construyeron haplotipos, y se determinó el estado de portadora de deleción en dos de las seis mujeres analizadas, quienes mostraron pérdida de heterocigocidad de tres STR. Se establecieron algunos eventos de recombinación. Resultados: dos de las seis mujeres analizadas, mostraron pérdida de heterocigocidad en tres de los diez STR genotipificados, indicando su estado de portadora de deleción en este fragmento del gen de la distrofina. Con la segregación familiar de los haplotipos se establecieron eventos de recombinación. Conclusiones: mediante pérdida de heterocigocidad es posible establecer el estado de portadora de deleción en el gen de la distrofina con un 100% de certeza. La construcción de haplotipos identifica el cromosoma X portador de la deleción en familiares del caso índice. Se evidenció un evento de recombinación en una de las hermanas del afectado, lo que hace indeterminado su estado de portadora.

Duchenne/Becker Muscular Dystrophy (DMD/BMD) is an X-linked recessive disease characterized by muscular weakness. It is caused by mutations on the dystrophin gen. Loss of heterozygosity allows us to identify female carriers of deletions on the dystrophin gen. Objective: identify female carriers in a family with a patient affected by DMD. Material and methods: nine family members and the affected child were analyzed using DNA extraction and posterior amplification of ten STRs on the dystrophin gen. Haplotypes were constructed and the carrier status determined in two of the six women analyzed due to loss of heterozygosity in three STRs. Additionally, we observed a recombination event. Conclusions: loss of heterozygosity allows us to establish with a certainty of 100% the carrier status of females with deletions on the dystrophin gen. By the construction of haplotypes we were able to identify the X chromosome with the deletion in two of the six women analyzed. We also determined a recombination event in one of the sisters of the affected child. These are described with a high frequency (12%). A possible origin for the mutation is a gonadal mosaicism in the maternal grandfather or in the mother of the affected child in a very early stage in embryogensis. This can be concluded using the analysis of haplotypes.

A distrofia muscular de Duchenne e Becker (DMD/DMB) é uma entidade de herança recessiva ligada ao cromossoma X que se apresenta com debilidade muscular e é causada por mutações no gene da distrofia. A perda de heterozigosidade permite identificar às mulheres portadoras de deleção no gene da distrofina mediante haplótipos. Objetivo: identificar mulheres portadoras em uma família com um paciente afetado de DMD mediante análises de perda de heterozigosidade. Materiais e métodos: se analisaram nove membros de uma família com um afetado de DMD. De fez extração de ADN e amplificação de dez STR do gene da distrofina; construíram-se haplótipos, e determinou-se o estado de portadora de deleção em duas das seis mulheres analisadas, as quais mostraram perda de heterozigosidade de três STR. Estabeleceram-se alguns eventos de recombinação. Resultados: duas das seis mulheres analisadas mostraram perda de heterozigosidade em três dos dez STR genotipados, indicando seu estado de portadora de deleção neste fragmento do gene da distrofina. Com a segregação familiar dos haplótipos se estabeleceram eventos de recombinação. Conclusões: mediante perda de heterozigosidade é possível estabelecer o estado de portadora de deleção no gene da distrofina com um 100% de certeza. A construção de haplótipos identifica o cromossoma X portador da deleção em familiares do caso índice. Evidenciou-se um evento de recombinação em uma das irmãs do afetado, o que faz indeterminado seu estado de portadora.

Análisis clínic y molecular de una pacientecon pentasomia del cromoooma x. / Clinical and Molecular Analysis of a Patient with X-Chromosome Pentasomy.

Introducción: la Pentasomia del X (49,XXXXX) es una alteración cromosómica poco frecuente, que afecta a mujeres y fue descrita en 1963 por Kesaree y Wooley. Hasta la fecha se han reportado menos de 30 casos en la literatura. Se presenta un caso de pentasomia del cromosoma X, y mediante técnicas de biología molecular (microsatélites) se determino el origen materno de los cromosomas X adicionales. Caso clínico: paciente de 28 meses, con talla baja proporcionada, braquicefalia, fascies característica, genitales externos femeninos con labios mayores hipoplásicos, braquidactilia, clinodactilia bilateral del quinto dedo, luxación de rodilla derecha, deformidad en varo. Se realizó cariotipo en sangre periférica que reportó un complemento cromosómico 49,XXXXX. Materiales y métodos: se realizó extracción de ADN y PCR para la amplificación de ocho microsatélites o STR’s tetra y dinucleotídicos situados a lo largo del cromosoma X. Los productos amplificados se analizaron en el secuenciador ALF EXPRESS. Con la información alélica se realizó la construcción del haplotipo y el análisis de dosis génica mediante la determinación del área bajo la curva. Resultados y discusión: el análisis de los ocho STR’s realizados en la paciente y sus padres, permitió establecer que los cromosomas X extras corresponden a información alélica heredada de la madre. Se analizan los resultados y los eventos que se han documentado como relacionados con los fenómenos de no disyunción. Conclusión: el origen de la doble no disyunción que generó la pentasomia es materna, en donde un ovulo tetrasómico, con cuatro copias de cromosoma X fue fecundado con un espermatozoide monosómico normal.

Introduction: Pentasomy X is a rare chromosomal disorder which affects women. It was first described in 1963 by Kesaree and Wooley. Up to date, less than 30 cases have been reported. We report a case of 28 month old female patient with clinical features of Pentasomy X. Cytogenetic and molecular analysis revealed that her karyotype was 49,XXXXX and that the additional X chromosomes were maternal in origin. Case report: We present a 28 month old female patient with short stature, brachycephaly, characteristic facies, with female external genitalia, hypoplasic labia majora, brachydactyly, bilateral clinodactyly of the fifth finger, dislocation of the right knee with genu varum deformities. Chromosome analysis revealed a karyotype of 49, XXXXX. Materials and methods: We performed DNA extraction and subsequent PCR amplification of 8 microsatellites (STR’s) throughout the X chromosome. The amplified products were analyzed in the ALF EXPRESS sequencer. The allelic information obtained was used to construct haplotypes and to analyze gene dosage through the determination of the area under the curve. Results and discussion: Through the analysis of eight STR’s in the patient and her parents we were able to determine that the extra X chromosomes were inherited from the mother. We analyze our results and other well documented events that have been related to non-disjunctions. Conclusion: We confirmed through molecular analysis of X-linked DNA markers that the aneuploidy developed from two maternal non-disjunctions.

PCR en toxoplasmosis / PCR in toxoplasmosis

La Reacción en Cadena de la Polimerasa o PCR, constituye una metodología sensible y específica que permite la identificación de segmentos génicos mediante la amplificación selectiva de secuencias de ADN particulares. Las técnicas de Biologia Molecular han sido adaptadas a la identificación de Toxoplasma gondii en diversas muestras biológicas de animales y humanos como sangre, orina, liquido cefalorraquideo, humor vitreo y liquido amniótico.