Impact of genetic background as a risk factor for atherosclerotic cardiovascular disease: A protocol for a nationwide genetic case-control (CV-GENES) study in Brazil.

Atherosclerotic Cardiovascular Disease (ASCVD) represents the leading cause of death worldwide, and individual screening should be based on behavioral, metabolic, and genetic profile derived from data collected in large population-based studies. Due to the polygenic nature of ASCVD, we aimed to assess the association of genomics with ASCVD risk and its impact on the occurrence of acute myocardial infarction, stroke, or peripheral artery thrombotic-ischemic events at population level. CardioVascular Genes (CV-GENES) is a nationwide, multicenter, 1:1 case-control study of 3,734 patients in Brazil. Inclusion criterion for cases is the first occurrence of one of the ASCVD events. Individuals without known ASCVD will be eligible as controls. A core lab will perform the genetic analyses through low-pass whole genome sequencing and whole exome sequencing. In order to estimate the independent association between genetic polymorphisms and ASCVD, a polygenic risk score (PRS) will be built through a hybrid approach including effect size of each Single Nucleotide Polymorphism (SNP), number of effect alleles observed, sample ploidy, total number of SNPs included in the PRS, and number of non-missing SNPs in the sample. In addition, the presence of pathogenic or likely pathogenic variants will be screened in 8 genes (ABCG5, ABCG8, APOB, APOE, LDLR, LDLRAP1, LIPA, PCSK9) associated with atherosclerosis. Multiple logistic regression will be applied to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI), and population attributable risks will be calculated. Clinical trial registration: This study is registered in clinicaltrials.gov (NCT05515653).

MLPA followed by target-NGS to detect mutations in the dystrophin gene of Peruvian patients suspected of DMD/DMB.

BACKGROUND: We report the molecular analysis of the DMD gene in a group of Peruvian patients with Duchenne/Becker dystrophinopathy. This is the first study to thoroughly characterize mutations in this population. METHODS: We used the combination of multiplex ligation-dependent probe amplification (MLPA) and sequencing analysis of the DMD gene. We recruited Peruvian patients in 2 years from reference national hospitals. We performed DNA tests in 152 patients, checking first exon deletion/duplication by MLPA, and subsequently, if negative, samples were sequenced to detect point mutations. RESULTS: The average age for diagnosis was 9.8 years, suggesting a delay for timely diagnosis and care. We found causal DMD mutations in 125 patients: 72 (57.6%) exon deletions/duplications (41.6% deletions, 16.0% duplications), and 53 (42.4%) point mutations (27.2% nonsense, 9.6% small indels, and 5.6% splice site). CONCLUSION: Due to our genetic background, we expected a higher number of novel and recurrent causal mutations in our sample. Results showed 16% of novel mutations, similar to other well-studied populations.

Precision Medicine for Lysosomal Disorders.

Precision medicine (PM) is an emerging approach for disease treatment and prevention that accounts for the individual variability in the genes, environment, and lifestyle of each person. Lysosomal diseases (LDs) are a group of genetic metabolic disorders that include approximately 70 monogenic conditions caused by a defect in lysosomal function. LDs may result from primary lysosomal enzyme deficiencies or impairments in membrane-associated proteins, lysosomal enzyme activators, or modifiers that affect lysosomal function. LDs are heterogeneous disorders, and the phenotype of the affected individual depends on the type of substrate and where it accumulates, which may be impacted by the type of genetic change and residual enzymatic activity. LDs are individually rare, with a combined incidence of approximately 1:4000 individuals. Specific therapies are already available for several LDs, and many more are in development. Early identification may enable disease course prediction and a specific intervention, which is very important for clinical outcome. Driven by advances in omics technology, PM aims to provide the most appropriate management for each patient based on the disease susceptibility or treatment response predictions for specific subgroups. In this review, we focused on the emerging diagnostic technologies that may help to optimize the management of each LD patient and the therapeutic options available, as well as in clinical developments that enable customized approaches to be selected for each subject, according to the principles of PM.

Diagnosis of Mucopolysaccharidoses.

The mucopolysaccharidoses (MPSs) include 11 different conditions caused by specific enzyme deficiencies in the degradation pathway of glycosaminoglycans (GAGs). Although most MPS types present increased levels of GAGs in tissues, including blood and urine, diagnosis is challenging as specific enzyme assays are needed for the correct diagnosis. Enzyme assays are usually performed in blood, with some samples (as leukocytes) providing a final diagnosis, while others (such as dried blood spots) still being considered as screening methods. The identification of variants in the specific genes that encode each MPS-related enzyme is helpful for diagnosis confirmation (when needed), carrier detection, genetic counseling, prenatal diagnosis (preferably in combination with enzyme assays) and phenotype prediction. Although the usual diagnostic flow in high-risk patients starts with the measurement of urinary GAGs, it continues with specific enzyme assays and is completed with mutation identification; there is a growing trend to have genotype-based investigations performed at the beginning of the investigation. In such cases, confirmation of pathogenicity of the variants identified should be confirmed by measurement of enzyme activity and/or identification and/or quantification of GAG species. As there is a growing number of countries performing newborn screening for MPS diseases, the investigation of a low enzyme activity by the measurement of GAG species concentration and identification of gene mutations in the same DBS sample is recommended before the suspicion of MPS is taken to the family. With specific therapies already available for most MPS patients, and with clinical trials in progress for many conditions, the specific diagnosis of MPS as early as possible is becoming increasingly necessary. In this review, we describe traditional and the most up to date diagnostic methods for mucopolysaccharidoses.

Polymorphic variants (p.Ser141Ser and p.Arg737Gly) at the NAGLU gene are really indicative of pseudodeficiency alleles?

Filocamo et al. recently published a paper describing the presence of a pseudodeficiency allele, constituted by p.Ser141Ser and p.Arg737Gly polymorphisms at the NAGLU gene, which leads to a reduced level of the alpha-N-acetyl-D-glucosaminidase activity. Based on analysis performed in Brazilian patients, using a customized gene panel containing SGSH, NAGLU, HGSNAT and GNS we observed that p.Ser141Ser (rs659497) and p.Arg737Gly (rs86312) variants were present in homozygosis in all of our MPS IIIB patients and in the majority of MPS IIIA, IIIC and IIID patients, and there was no significant decrease of the alpha-N-acetyl-D-glucosaminidase enzyme activity in this group when compared with those without the "pseudodeficiency allele". Thus, we suggest that these two variants are not producing a pseudodeficiency allele.

Recent advances in molecular testing to improve early diagnosis in children with mucopolysaccharidoses.

INTRODUCTION: The mucopolysaccharidoses (MPS) are a group of lysosomal storage disorders with high phenotypic and genotypic heterogeneity, making precise diagnosis challenging. Although enzyme activity assay is considered the gold standard for the diagnosis of these disorders, molecular testing can greatly refine this task. New methods for rapid detection of variants are useful to reduce the 'diagnostic odyssey' faced by patients and their family, to lead to appropriate genetic counseling and to select the most appropriate therapy for each case. Areas covered: We review and discuss the advantages, disadvantages and limitations of the modern technologies in the field of molecular diagnosis of MPS, presenting our own experience. Expert commentary: While current molecular genetics testing for MPS mostly relies on PCR and Sanger sequencing, promising alternative techniques have emerged over the last few years, and its application into routine clinical practice is gaining momentum.

Detección de la mutación E8SJM en el gen LIPA, por PCR en tiempo real, para la investigación de la enfermedad por almacenamiento de ésteres de colesterol / Detection of the E8SJM mutation in the LIPA gene, by real-time PCR, for the investigation of cholesteryl ester storage disease

Introducción: La enfermedad por Almacenamiento de Ésteres de Colesterol (CESD; Cholesteryl Ester Storage Disease) es una enfermedad de depósito lisosomal, su presentación es bastante variable y su diagnóstico constituye un desafío. Además, existe un número de anomalías observadas en los pacientes con CESD que se sobreponen a diagnósticos más comunes, siendo probable que sea subdiagnosticada. La mayoría de pacientes relatados hasta el momento son portadores de la mutación E8SJM en el gen LIPA. En este sentido, el auxilio en el diagnóstico es fundamental pues existen opciones de terapia en desarrollo. Diseño: Estudio observacional. Objetivo: Estandarizar la técnica de PCR en tiempo real para la detección de la mutación más frecuente, E8SJM, en muestras de sangre periférica y de biopsia hepática para el auxilio diagnóstico de CESD y futuros estudios de prevalencia de la mutación. Institución: Centro de Terapia Génica del Hospital de Clínicas de Porto Alegre (HCPA), Brasil. Material biológico: Muestras de ADN extraídas de sangre periférica y tejido hepático parafinado. Principales medidas de resultados: Presencia/Ausencia de la mutación E8SJM. Resultados: Se estandarizó la reacción de PCR en tiempo real, la mutación fue detectada correctamente y posteriormente validada por secuenciación de Sanger. La mutación fue analizada en 137 muestras y encontrada en apenas una paciente que ingresó al Servicio de Genética Médica del HCPA con diagnóstico clínico y bioquímico de CESD/Wolman. Conclusiones: La técnica de PCR en tiempo real es ideal para la detección rápida y en gran escala de la mutación frecuente asociada a CESD.

Introduction: Cholesteryl Ester Storage Disease (CESD) is a lysosomal storage disorder, its presentation is highly variable and its diagnosis challenging. In addition, there are several abnormalities observed in patients with CESD who overlap with more common diagnoses and are likely to be underdiagnosed. Most patients reported to date are carriers of the E8SJM mutation in the LIPA gene. In this sense, diagnostic assistance is essential because there are options for therapy in development, as well as mutation prevalence studies. Design: Observational research. Objective: To standardize the real-time PCR technique for the detection of the most frequent mutation, E8SJM, in peripheral blood and liver biopsy specimens for the diagnosis of CESD and future mutation prevalence studies. Institution: Center of Gene Therapy of the Hospital de Clinicas de Porto Alegre (HCPA), Brazil. Biological material: DNA samples extracted from peripheral blood and paraffinembedded liver tissue. Main outcome measures: Presence / Absence of E8SJM mutation. Results: The PCR reaction was standardized in real time; the mutation was correctly detected and validated by Sanger sequencing. The mutation was analyzed in 137 samples and found in only one patient who entered the Medical Genetics Service of the HCPA with clinical and biochemical diagnosis of CESD/Wolman. Conclusions: The real-time PCR technique is ideal for rapid and large-scale detection of the frequent CESD-associated mutation.

Investigation of newborns with abnormal results in a newborn screening program for four lysosomal storage diseases in Brazil.

Lysosomal storage diseases (LSDs) are genetic disorders, clinically heterogeneous, mainly caused by defects in genes encoding lysosomal enzymes that degrade macromolecules. Several LSDs already have specific therapies that may improve clinical outcomes, especially if introduced early in life. With this aim, screening methods have been established and newborn screening (NBS) for some LSDs has been developed. Such programs should include additional procedures for the confirmation (or not) of the cases that had an abnormal result in the initial screening. We present here the methods and results of the additional investigation performed in four babies with positive initial screening results in a program of NBS for LSDs performed by a private laboratory in over 10,000 newborns in Brazil. The suspicion in these cases was of Mucopolysaccharidosis I - MPS I (in two babies), Pompe disease and Gaucher disease (one baby each). One case of pseudodeficiency for MPS I, 1 carrier for MPS I, 1 case of pseudodeficiency for Pompe disease and 1 carrier for Gaucher disease were identified. This report illustrates the challenges that may be encountered by NBS programs for LSDs, and the need of a comprehensive protocol for the rapid and precise investigation of the babies who have an abnormal screening result.