Expression and Clinical Significance of CLCA2 in Pan-Cancer / Expresión y Significado Clínico de CLCA2 en Pan-Cáncer

SUMMARY: The calcium-activated chloride channel (CLCA2) performs a vital function in the intricate process of tumorigenesis. Using a bioinformatics analysis system, we conducted a pan-cancer investigation on CLCA2 to explore its association with tumor prognosis and its involvement in immunology. In order to achieve this objective, we examined the prognostic significance and expression level of CLCA2 in multiple cancer types using the TIMER and Sangerbox databases. The analysis of protein interaction networks revealed proteins linked to CLCA2. To investigate the potential biological functions and enrichment pathways of CLCA2 in cancer, the SangerBox and GSCA databases were utilized. Furthermore, the expression of CLCA2 in different cancer subtypes was evaluated during the analysis. Various functional conditions of cancer cells were then compared with CLCA2 in the CancerSEA database. Using online tools like TISIDB and Assistant for Clinical Bioinformatics, the investigation explored the link between CLCA2 and immune subtypes. Additionally, it assessed immune cell infiltration as part of the analysis. In addition, the application of GDSA was employed to investigate the predictive significance of CLCA2 in relation to drug sensitivity. The research outcomes uncovered abnormal expression patterns of CLCA2 in diverse tumor categories, with its expression level demonstrating a correlation with distinct subtypes of tumors. Strong associations have been observed between enhanced patient survival rates and CLCA2 in specific tumor types. There is a noteworthy connection observed among diverse tumor types, immune cell infiltration, immune subtypes, and CLCA2. The enrichment analysis of KEGG indicates that there may exist a connection between the expression of CLCA2 and renin secretion, pancreatic secretion, as well as other pathways in pan-cancer. CLCA2 appears to primarily activate pathways such as EMT (epithelial-mesenchymal transition), RAS/MAPK, RTK, apoptosis, TSC/mTOR, and PI3K/ AKT in pan-cancer. On the other hand, it seems to inhibit pathways like cell cycle, DNA damage, hormone AR, and hormone ER. Through single-cell functional analysis, it has been confirmed that CLCA2 is associated with diverse cellular functional states, encompassing DNA repair, EMT, hypoxia, invasion, metastasis, and quiescence. Furthermore, a substantial correlation has been observed between the expression of CLCA2 and drug sensitivity towards bosutinib, tipifarnib-P1, as well as other therapeutic agents. This research affirms that various cancer types express CLCA2 and its involvement in tumor advancement and immune penetration. CLCA2 possesses the capability to function as a noteworthy biomarker and target for therapeutic intervention in diverse cancer forms.

El canal de cloruro activado por calcio (CLCA2) desempeña una función vital en el proceso de tumorigénesis. Utilizando un sistema de análisis bioinformático, llevamos a cabo una investigación pan-cáncer en CLCA2 para explorar su asociación con el pronóstico tumoral y su participación en la inmunología. Para lograr este objetivo, examinamos la importancia pronóstica y el nivel de expresión de CLCA2 en múltiples tipos de cáncer utilizando las bases de datos TIMER y Sangerbox. El análisis de las redes de interacción de proteínas reveló proteínas vinculadas a CLCA2. Para investigar las posibles funciones biológicas y las vías de enriquecimiento de CLCA2 en el cáncer, se utilizaron las bases de datos SangerBox y GSCA. Además, durante el análisis se evaluó la expresión de CLCA2 en diferentes subtipos de cáncer. Luego se compararon varias condiciones funcionales de las células cancerosas con CLCA2 en la base de datos CancerSEA. Utilizando herramientas en línea como TISIDB y Assistant for Clinical Bioinformatics, la investigación exploró el vínculo entre CLCA2 y los subtipos inmunes. Además, evaluó la infiltración de células inmunitarias como parte del análisis y se empleó la aplicación de GDSA para investigar la importancia predictiva de CLCA2 en relación con la sensibilidad al fármaco. Los resultados de la investigación descubrieron patrones de expresión anormales de CLCA2 en diversas categorías de tumores, y su nivel de expresión demuestra una correlación con distintos subtipos de tumores. Se han observado fuertes asociaciones entre mayores tasas de supervivencia de los pacientes y CLCA2 en tipos de tumores específicos. Se observa una conexión notable entre diversos tipos de tumores, infiltración de células inmunitarias, subtipos inmunitarios y CLCA2. El análisis de enriquecimiento de KEGG indica que puede existir una conexión entre la expresión de CLCA2 y la secreción de renina, la secreción pancreática y otras vías en el pancáncer. CLCA2 parece activar principalmente vías como EMT (transición epitelial-mesenquimatosa), RAS/MAPK, RTK, apoptosis, TSC/mTOR y PI3K/AKT en pan-cáncer. Por otro lado, parece inhibir vías como el ciclo celular, el daño del ADN, la hormona AR y la hormona ER. Mediante análisis funcional unicelular, se ha confirmado que CLCA2 está asociado con diversos estados funcionales celulares, que abarcan la reparación del ADN, la EMT, la hipoxia, la invasión, la metástasis y la inactividad. Además, se ha observado una correlación sustancial entre la expresión de CLCA2 y la sensibilidad al fármaco hacia bosutinib, tipifarnib-P1, así como a otros agentes terapéuticos. Esta investigación indica que varios tipos de cáncer expresan CLCA2 y su participación en el avance tumoral y la penetración inmune. CLCA2 posee la capacidad de funcionar como un biomarcador notable y como un objetivo para la intervención terapéutica en diversas formas de cáncer.

Implementación asistencial de estudios genómicos aplicados al diagnóstico molecular / Implementation of genomic studies applied to molecular diagnostics

El Hospital Garrahan ha sido pionero en el diagnóstico molecular de patologías pediátricas en Argentina. Los avances tecnológicos de las últimas décadas en el área de la biología molecular, sentaron las bases para la optimización y ampliación del diagnóstico molecular a partir de la secuenciación masiva en paralelo de múltiples genes. El presente trabajo describe el proceso de implementación de los estudios de secuenciación de nueva generación y el desarrollo de la Unidad de Genómica en un hospital público pediátrico de alta complejidad, así como su impacto en las capacidades diagnósticas de enfermedades poco frecuentes de origen genético. La creación del Grupo Interdisciplinario de Estudios Genómicos constituyó la vía institucional para la toma de decisiones que implican la implementación de nuevos estudios genómicos y el establecimiento de prioridades diagnósticas, extendiendo la disponibilidad del diagnóstico molecular a más disciplinas. La Unidad de Genómica trabaja en diseñar las estrategias que permitan la mayor optimización de los recursos con los que cuenta el hospital, teniendo en cuenta el equipamiento disponible, las prioridades establecidas y la frecuencia de las distintas patologías. Se demuestra el salto significativo operado en nuestras capacidades diagnósticas, tanto en la variedad de enfermedades como en el número de genes analizados, habiendo estudiado a la fecha alrededor de 2.000 pacientes, muchos de los cuales ven de este modo finalizada su odisea diagnóstica. Los estudios de NGS se han convertido en una herramienta de la práctica diaria para la atención de un número importante de pacientes de nuestro hospital. Continuaremos trabajando para ampliar su aplicación a la mayor cantidad de patologías, a través de los mecanismos institucionales ya existentes (AU)

The Garrahan Hospital has been a pioneer in the molecular diagnosis of pediatric diseases in Argentina. The technological advances of the last decades in the area of molecular biology have laid the foundations for the optimization and expansion of molecular diagnostics through massive parallel sequencing of multiple genes. This study describes the process of implementation of next-generation sequencing studies and the development of the Genomics Unit in a public pediatric tertiary hospital, and its impact on the capacity to diagnose rare diseases of genetic origin. The creation of the Interdisciplinary Group of Genomic Studies constituted the institutional pathway for decision-making involving the implementation of new genomic studies and the establishment of diagnostic priorities, extending the availability of molecular diagnostics to additional disciplines. The Genomics Unit is working to design strategies that allow for optimization of the resources available to the hospital, taking into account the equipment available, the priorities established, and the frequency of the different diseases. It demonstrates the significant leap in our diagnostic capabilities, both in the variety of diseases and in the number of genes analyzed. To date, around 2,000 patients have been studies, many of whom have thus completed their diagnostic odyssey. NGS studies have become a tool in daily practice for the care of a significant number of patients in our hospital. We will continue working to expand its application to as many diseases as possible, through the existing institutional mechanisms (AU)

Transferência tecnológica durante a pandemia de covid-19: relato do primeiro treinamento prático presencial no Brasil / Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical training course in Brazil / Transferencia de tecnología durante la epidemia de COVID-19 en Brasil: informe de la primera formación práctica presencial

O relato descreveu o primeiro curso presencial visando capacitar profissionais de saúde pública na realização de vigilância genômica em tempo real, durante períodos pandêmicos. Relato de experiência sobre um curso teórico-prático com foco em pesquisa e vigilância genômica, incluindo tecnologias de sequenciamento móvel, bioinformática, filogenética e modelagem epidemiológica. O evento contou com 162 participantes e foi o primeiro grande treinamento presencial realizado durante a epidemia de covid-19 no Brasil. Não foi detectada infecção pelo SARS-CoV-2 ao final do evento em nenhum participante, sugerindo a segurança e efetividade de todas as medidas de segurança adotadas. Os resultados do evento sugerem que é possível executar capacitação profissional com segurança durante pandemias, desde que seguidos todos os protocolos de segurança.

The objective of this report was to describe the first face-to-face course aimed at training public health professionals in performing real-time genomic surveillance during the pandemic period. Experience report on a theoretical-practical course focusing on genomic research and surveillance, including mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological modeling. There were 162 participants in the event and it was the first major face-to-face training course conducted during the COVID-19 epidemic in Brazil. No cases of SARS-CoV-2 infection was detected among the participants at the end of the event, suggesting the safety and effectiveness of all safety measures adopted. The results of this experience suggest that it is possible to conduct professional training safely during pandemics, as long as all safety protocols are followed.

Este estudio tuvo como objetivo describir el primer curso presencial para capacitar a los profesionales de la salud pública para llevar a cabo la vigilancia genómica en tiempo real durante los períodos de pandemia. Este es un informe de experiencia en un curso teórico-práctico centrado en la investigación y vigilancia genómica, que incluye secuenciación móvil, bioinformática, filogenética y tecnologías de modelado epidemiológico. Este evento contó con la asistencia de 162 participantes y fue la primera gran capacitación presencial realizada durante la epidemia de COVID-19 en Brasil. No se detectó infección por SARS-CoV-2 al final del evento en ningún participante, lo que sugiere la seguridad y efectividad de todas las medidas de seguridad adoptadas. Por lo tanto, los resultados del evento sugieren que es posible realizar entrenamientos profesionales de manera segura durante pandemias, siempre y cuando se sigan todos los protocolos de seguridad.

Detección y cuantificación de SARS-CoV-2 en plantas de tratamiento de aguas residuales de diferentes ciudades de Chile: hacia la implementación de una vigilancia centinela permanente / Detection and quantification of SARS-CoV-2 wastewater treatment plants from different cities in Chile; towards to a permanent sentinel surveillance

INTRODUCCIÓN: La cuantificación de SARS-CoV-2 en aguas residuales es una herramienta que permite determinar la tendencia de la circulación viral en un área geográfica determinada. OBJETIVO: Cuantificar el virus SARS-CoV-2 en 15 plantas de tratamiento de aguas residuales en diferentes ciudades de Chile para establecer una comparación con las variables de: i) casos activos por cada 100.000 habs.; ii) positividad diaria (casos nuevos); y iii) fases del plan de confinamiento. METODOLOGÍA: SARS-CoV-2 se concentró a partir de muestras de aguas residuales. Para obtener el número de genomas del virus por litro se realizó una cuantificación absoluta utilizando qRT-PCR. RESULTADOS: Entre enero y junio de 2021 se procesaron 253 muestras, siendo todas positivas para la presencia del virus. Asimismo, se logró determinar que la tasa de casos activos por cada 100.000 habs. es la variable que mejor se ajusta a las tendencias obtenidas con la cuantificación de la carga viral en las aguas residuales. CONCLUSIONES: La cuantificación de SARS-CoV-2 en las aguas residuales de manera permanente es una herramienta eficiente para determinar la tendencia del virus en un área geográfica determinada y, en conjunto con una vigilancia genómica, puede constituirse en una vigilancia centinela ideal generando alertas sobre futuros brotes.

BACKGROUND: The quantification of SARS-CoV-2 in wastewater is a tool that allows determining the trend of viral circulation in a particular geographical area. AIM: To quantify the SARS-CoV-2 virus in 15 wastewater treatment plants in different Chilean cities to establish a comparison with the variables of: i) Active cases per 100,000 inhabitants; ii) daily positivity (novel cases); and iii) phases of the lockdown strategy. METHODS: SARS-CoV-2 was concentrated from wastewater samples. To obtain the number of virus genomes per liter, absolute quantification was performed using qRT-PCR. RESULTS: Between January and June 2021, 253 samples were processed, all of which were positive for the presence of the virus. Likewise, it will be determined that the rate of active cases per 100,000 inhabitants is the variable that best fits the trends obtained with the quantification of the viral load in wastewater. CONCLUSIONS: The quantification of SARS-CoV-2 in wastewater as a continuous strategy is an efficient tool to determine the trend of the viral circulation in a delimited geographical area and, combined with genomic surveillance, it can constitute an ideal sentinel surveillance alert on future outbreaks.

sideRETRO: uma ferramenta de bioinformática dedicada à identificação deinserções polimórficas, germinativas ou somáticas, de pseudogenes processados / sideRETRO: a bioinformatics tool for identifying somatic and polymorphic insertions of processed pseudogenes

Os avanços metodológicos e instrumentais decorrentes do Projeto Genoma Humano formaram o arcabouço necessário para o surgimento das tecnologias de sequenciamento de DNA de Nova Geração, as quais se caracterizam por um custo reduzido, uma baixa demanda operacional e a produção de um grande volume de dados por experimento. Concomitantemente a isso, o aumento no poder de processamento computacional permitiu o desenvolvimento de análises genéticas em larga escala, de modo que, atualmente, é possível estudar características genômicas individualizadas e, até então, pouco ou nunca exploradas. Dentre essas características, aquelas relacionadas às variações estruturais em genomas têm recebido bastante atenção. Os pseudogenes processados, ou retrocópias, são variações estruturais causadas pela duplicação de genes codificadores mediante à transposição de seu RNA mensageiro maduro pela maquinaria enzimática de LINE- 1. As retrocópias podem estar fixadas, ou seja, presentes em todos os genomas de uma dada espécie, os quais são representados pela montagem modelo do genoma de referência, ou podem não estar fixadas, sendo polimórficas, germinativas ou somáticas. No entanto, o conhecimento acerca das retrocópias não fixadas ainda é limitado devido à falta de ferramentas de bioinformática dedicadas a sua identificação e anotação em dados de sequenciamento de DNA. Posto isso, este trabalho apresenta o sideRETRO um programa computacional especializado na detecção de pseudogenes processados ausentes do genoma de referência, mas presentes em dados de sequenciamento de genoma completo e exoma de outros indivíduos. Além de apontar para a presença de retrocópias não fixadas, o sideRETRO é capaz de anotar várias outras características relacionadas a esses evento, tais como: a coordenada genômica de inserção do pseudogene processado, a qual constitui o cromossomo, o ponto de inserção e a fita de DNA (líder or retardada); o contexto genômico do evento (exônico, intrônico ou intergênico); a genotipagem (presente ou ausente) e a haplotipagem (em homozigose ou heterozigose). Para atestar a eficiência da ferramenta, o sideRETRO foi executado para dados simulados e para dados reais validados experimentalmente por um grupo independente. Portanto, em resumo, nesta tese são descritos o desenvolvimento e o uso do sideRETRO uma ferramenta computacional robusta e eficiente, designada para identificar e anotar pseudogenes processados não fixados. Por fim, vale destacar que o sideRETRO preenche uma lacuna metodológica e possibilita novas hipóteses e investigações sistemáticas no campo de chamada de variantes estruturais

The methodological and instrumental advances resulting from the Human Genome Project have created the necessary framework to the emergence of Next Generation DNA sequencing technologies, which are characterized by a reduced cost, low operational demand and the generation of a large volume of data per experiment. Concomitantly with this, the increase in computational processing power has driven the development of large-scale genetic analyses, which allowed us to study individualized genomic traits little or never explored before. Among these characteristics, those related to structural variations in genomes have received much attention. Processed pseudogenes, or retrocopies, are structural variations caused by the duplication of coding genes through the transposition of their mature messenger RNA by the LINE-1 enzymatic machinery. Retrocopies can be fixed (i.e., present in all genomes of a given species and included into the assembly of the reference genome) or unfixed, being polymorphic, germinal or somatic. However, knowledge about unfixed retrocopies is still limited due to the lack of bioinformatics tools dedicated to their identification and annotation in DNA sequencing data. Therefore, this work presents sideRETRO a computer program specialized in the detection of processed pseudogenes absent from the reference genome, but present in whole genome and exome sequencing data from other individuals. In addition to pointing out the presence of unfixed retrocopies, sideRETRO is able to annotate several other characteristics related to these events, such as: the genomic coordinate of the processed pseudogene insetion, which constitutes the chromosome, the insertion point and the DNA strand (leader or retard); the genomic context of the event (exonic, intronic or intergenic); genotyping (present or absent) and haplotyping (homozygous or heterozygous). To certify the sideRETRO efficiency, it was run on simulated data and on real data experimentally validated by an independent group. Therefore, in summary, this thesis describes the development and use of sideRETRO a robust and efficient computational tool, designed to identify and annotate unfixed processed pseudogenes. Finally, it is worth noting that sideRETRO fills a methodological gap and allows new hypotheses and systematic investigations in the field of structural variant calling

Importancia del uso de la genómica en el diagnóstico precoz de la esclerosis tuberosa, reporte de caso / The importance of the use of genomics in early diagnosis of tuberous sclerosis: case report

Introduccion: La esclerosis tuberosa en un trastorno raro con manifestaciones clínicas multisistémicas que puede comprometer órganos vitales como riñón pulmón y corazón por lo que requiere un diagnóstico precoz para brindar un tratamiento oportuno y dirigido mejorando el pronóstico y disminuyendo la morbimortalidad atribuida a esta patología. Objetivo: Establecer la importancia del uso de la genómica y la correlación fenotipo-genotipo para el diagnóstico, tratamiento, seguimiento, pronóstico, asesoramiento genético de la esclerosis tuberosa. Materiales y métodos: Reporte de caso de paciente 15 años con angiofibromas corporales, hamartoma retiniano, angiomiolipoma derecho y alteraciones de estudios de neuroimagen sin convulsiones ni trastornos neuroconductuales, se sospecho clínicamente de esclerosis tuberosa con confirmación genética al tener una variante patogénica en estado de heterocigosis en el gen TSC2. Resultados: Se encontró una deleción heterocigota patogénica que cambia una citosina en la posición 2.539 del ADNc del gen TSC2 (c.2539delC), que lleva a un codón de parada prematuro en el aminoácido 893 (p. Leu847Cysfs*47) en una proteína de 1.807 aminoácidos con significado clínico patogénico. Conclusiones: El complejo esclerosis tuberosa constituye una enfermedad huérfana para Colombia dada la baja prevalencia poblacional, con una alta carga en morbilidad y mortalidad debido al compromiso multisistémico. Su confirmación se realiza mediante métodos moleculares ­ genómicos que permiten establecer correlación fenotipo-genotipo dada la variabilidad en las variantes reportadas en este gen y los diferentes grados de expresión fenotípicos en los individuos, lo cual nos orienta a buscar signos y síntomas de compromiso de órganos o sistemas posiblemente afectados acercándonos a una medicina personalizada y de precisión.

Introduction: Tuberous sclerosis is a rare disorder with multisystemic clinical manifestations that can compromise vital organs such as the kidney, lung and heart, which requires early diagnosis to provide timely and targeted treatment, improving the prognosis and reducing the morbidity and mortality attributed to these pathologies. Objective: To establish the importance of the use of genomics and the phenotype-genotype correlation for the diagnosis, treatment, follow-up, prognosis, genetic counseling of tuberous sclerosis. Materials and methods : Case report of a 15 year old patient with body angiofibromas, retinal hamartoma, right angiomyolipoma and alterations in neuroimaging studies without seizures or neurobehavioral disorders, clinically suspected of tuberous sclerosis with genetic confirmation by having a pathogenic variant in heterozygosity in the TSC2 gene. Results: A pathogenic heterozygous deletion was found in which a cytosine is changed at position 2539 of the TSC2 gene cDNA (c.2539delC), leading to a premature stop codon at amino acid 893 ( p.Leu847Cysfs*47) into a protein of 1,807 amino acids with pathogenic clinical significance. Conclusions: Tuberous sclerosis complex is an orphan disease for Colombia given the low population prevalence, with a high burden of morbidity and mortality due to multisystem involvement. Its confirmation is performed by molecular-genomic methods that allow establishing phenotype-genotype correlation given the variability in the variants reported in this gene and the different degree of phenotypic expression in individuals, which guides us to look for signs and symptoms of involvement of organs or systems possibly affected, approaching a personalized and precision medicine.

Heritable genomic diversity in breast cancer driver genes and associations with risk in a Chilean population

BACKGROUND: Driver mutations are the genetic components responsible for tumor initiation and progression. These variants, which may be inherited, influence cancer risk and therefore underlie many familial cancers. The present study examines the potential association between SNPs in driver genes SF3B1 (rs4685), TBX3 (rs12366395, rs8853, and rs1061651) and MAP3K1 (rs72758040) and BC in BRCA1/2-negative Chilean families. METHODS: The SNPs were genotyped in 486 BC cases and 1258 controls by TaqMan Assay. RESULTS: Our data do not support an association between rs4685:C > T, rs8853:T > C, or rs1061651:T > C and BC risk. However, the rs12366395-G allele (A/G + G/G) was associated with risk in families with a strong history of BC (OR = 1.2 [95% CI 1.0-1.6] p = 0.02 and OR = 1.5 [95% CI 1.0-2.2] p = 0.02, respectively). Moreover, rs72758040-C was associated with increased risk in cases with a moderate-to-strong family history of BC (OR = 1.3 [95% CI 1.0-1.7] p = 0.02 and OR = 1.3 [95% CI 1.0-1.8] p = 0.03 respectively). Finally, risk was significantly higher in homozygous C/C cases from families with a moderate-to-strong BC history (OR = 1.8 [95% CI 1.0-3.1] p = 0.03 and OR = 1.9 [95% CI 1.1-3.4] p = 0.01, respectively). We also evaluated the combined impact of rs12366395-G and rs72758040-C. Familial BC risk increased in a dose-dependent manner with risk allele count, reflecting an additive effect (p-trend = 0.0002). CONCLUSIONS: Our study suggests that germline variants in driver genes TBX3 (rs12366395) and MAP3K1 (rs72758040) may influence BC risk in BRCA1/2-negative Chilean families. Moreover, the presence of rs12366395-G and rs72758040-C could increase BC risk in a Chilean population.

El asesoramiento genético: evolución, actualidad y retos en la era genómica / Genetic counseling: evolution, current affairs and challenges in the genomic era

Introducción: El asesoramiento genético es un proceso de comunicación centrado en el paciente/cliente, con el objetivo de ayudarlo a entender, adaptarse y ajustarse a las consecuencias médicas y psicosociales de las contribuciones genéticas a la enfermedad. Objetivo: Describir la evolución del concepto, modelos de asesoramiento genético y de la profesión de asesor genético, desde su inicio hasta la etapa actual, denominada era genómica con sus nuevos retos. Material y Métodos: Se llevó a cabo una sistematización a partir de la lectura reflexiva y crítica sobre el tema, en publicaciones sin límite de tiempo anterior y hasta el 2020; se contó también con la experiencia individual en la docencia, la asistencia médica y la investigación sobre el tema. Desarrollo: Se hace un recorrido y valoraciones acerca de los nuevos conceptos y modelos prácticos de asesoramiento genético, la profesión de asesor genético y los servicios, el asesoramiento genético en la era genómica y aspectos éticos. Conclusiones: El asesoramiento genético, en más de medio siglo de práctica formal influenciada por una variedad de factores sociales, culturales, históricos, locales - regionales y técnicos, ha evolucionado en sus objetivos y alcance. Los nuevos asesores (genómicos) tendrán que enfrentar nuevos dilemas éticos como: la decisión de comunicar hallazgos secundarios, el potencial de incertidumbre a partir de la gran cantidad de datos generados por las tecnologías genómicas; así como la posible vulneración de la privacidad, la discriminación, la estigmatización y el abuso, basados en el uso de la información genómica(AU)

Introduction: Genetic counseling is a patient/client centered communication process with the aim of helping them understand, adapt and adjust to the medical and psychosocial consequences of genetic contributions to the disease. Objective: To describe the evolution of the concept, models of genetic counseling and the profession of the genetic counselor from its inception to the current stage called the "genomic era" and its new challenges. Material and Methods: A systematization was carried out on the basis of reflective and critical reading on the subject. Publications without previous time limit and until 2020 were selected. Individual experience in teaching, medical assistance and research on the subject was also taken into account. Development: Analyses and assessments are made in relation to new concepts and practical models of genetic counseling, the profession of genetic counselor and services, genetic counseling in the genomic era and ethical aspects. Conclusions: Genetic counseling, in more than half a century of formal practice influenced by a variety of social, cultural, historical, local - regional and technical factors has evolved in its objectives and scope. The new (genomic) counselors will have to face new ethical dilemmas such as: the decision to communicate secondary findings; the potential for uncertainty from the large amount of data generated by genomic technologies; and the possible violation of privacy, discrimination, stigmatization and abuse based on the use of genomic information(AU)

Evaluation of eight protocols for genomic DNA extraction of Hypostomus commersoni Valenciennes, 1836 (Loricariidae: Siluriformes) / Avaliação de oito protocolos na extração de DNA genômico de Hypostomus commersoni Valenciennes, 1836 (Loricariidae: Siluriformes)

Abstract The principle and the techniques applied in DNA extraction play a pivotal role in the obtention of a purified genetic material. The present study investigates the efficiency of eight protocols in the DNA extraction of Hypostomus commersoni, an essential component of South American freshwater ichthyofauna. The quality of samples was assessed through spectrophotometry, gel electrophoresis, and PCR-RAPD markers amplification. The efficiency of DNA extraction was influenced both by the method applied and the target-tissue of choice. Higher concentrations and yield of DNA were obtained from ocular tissue, with a positive spectrum of incubation in lysis buffer for up to 36 hours after sample collection, using fresh tissues and in the presence of a high concentration of Proteinase K (20 mg.ml-1). In these conditions, samples were successfully amplified. To date, there is no record of description for the parameters analyzed in this work, neither the description of RAPD markers for the species H. commersoni.

Resumo Os princípios e as técnicas aplicadas na extração de DNA desempenham um papel crucial na obtenção de material genético purificado. O presente estudo investiga a eficiência de oito protocolos na extração de DNA de Hypostomus commersoni, um importante componente ictiofaunístico de riachos da América do Sul. A qualidade das amostras foi avaliada por espectrofotometria, eletroforese em gel e amplificação por marcadores de PCR-RAPD. A eficiência da extração de DNA foi influenciada tanto pelo método aplicado quanto pelo tecido-alvo de escolha. Maiores concentrações e rendimento de DNA foram obtidos a partir do tecido ocular, com um espectro positivo de incubação em tampão de lise por até 36 horas após a coleta da amostra, utilizando tecidos frescos e na presença de alta concentração de proteinase K (20 mg.ml-1). Nestas condições, as amostras foram amplificadas com sucesso. Até o momento, não há registro de descrição para os parâmetros analisados neste trabalho, nem a descrição de marcadores RAPD para a espécie H. commersoni.

Genetics of COVID-19

Abstract Objective This narrative, non-systematic review provides an update on the genetic aspects of the SARS-CoV-2 virus and its interactions with the human genome within the context of COVID-19. Although the main focus is on the etiology of this new disease, the genetics of SARS-CoV-2 impacts prevention, diagnosis, prognosis, and the development of therapies. Data source A literature search was conducted on MEDLINE, BioRxiv, and SciELO, as well as a manual search on the internet (mainly in 2019 and 2020) using the keywords "COVID-19," "SARS-CoV-2," "coronavirus," "genetics," "molecular," "mutation," "vaccine," "Brazil," "Brasil," and combinations of these terms. The keywords "Brazil" and "Brasil" were used to find publications that were specific to the Brazilian population's molecular epidemiology data. Articles most relevant to the scope were selected non-systematically. Data synthesis A number of publications illustrate an expanding knowledge on the genetics and genomics of SARS-CoV-2 and its implications for understanding COVID-19. Conclusions Knowledge of the SARS-CoV-2 genome sequence permits an in-depth investigation of the role its proteins play in the pathophysiology of COVID-19, which in turn will be enormously valuable for understanding the evolutionary, clinical, and epidemiological aspects of this disease and focusing on prevention and treatment.

Identification of genomic imbalances in oral clefts

Abstract Objective This article presents a clinical and cytogenomic approach that focuses on the diagnosis of syndromic oral clefts (OCs). Methods The inclusion criteria were individuals with OC presenting four or more minor signs and no major defects (non-syndromic oral clefts [NSOCs]) as well as individuals with OC presenting at least another major defect, regardless of the number of minor signs (syndromic oral clefts [SOCs]). The exclusion criteria included NSOC with less than four minor signs, SOC with known etiology, as well as atypical oral clefts. Results Of 1647 individuals with OC recorded in the Brazilian Database of Craniofacial Anomalies, 100 individuals were selected for chromosome microarray analysis (CMA). Among these, 44 individuals were clinically classified as NSOC and 56 as SOC. CMA was performed for both groups, and abnormal CMA was identified in 9%, all previously classified as SCO. The clinical and CMA data analyses showed a significant predominance of abnormal CMA in individuals classified as SOC (p = 0.0044); prematurity, weight, length, and head circumference at birth were significantly lower in the group with abnormal CMA. Besides, minor signs were significantly higher in this group (p = 0.0090). Conclusion The rigorous selection of cases indicates that the significant variables could help in early recognition of SOC. This study reinforces the importance of applying the CMA technique to establish the diagnosis of SOC. This is an important and universal issue in clinical practice for intervention, care, and genetic counseling.

Global publication trends in ophthalmic genetics and gene therapy research: A Scientometric analysis / Tendências globais de publicação de pesquisas sobre genética oftálmica e terapia genética: uma análise cientométrica

ABSTRACT Objective: A scientometric analysis produced in ophthalmic genetics and gene therapy research is lacking. The purpose of this study is to present a holistic analysis of ophthalmic genetics literature. Methods: The data used in this study were obtained from the Web of Science (WoS) Core Collection. All published documents between 1975-2019 were included. The data exported from WoS enabled the extensive details of ophthalmic genetics related literature including countries, institutions, authors, citations and keywords. Scientometric network maps of keywords and also country and institution co-authorships were created with free software. Global contributions of the countries to the ophthalmic genetics literature were shown by a graphic. Results: The search query revealed a total of 2322 documents. Most of the documents were original articles (75.75%). USA was the leading country by producing 45.39% of all documents in ophthalmic genetics research followed by UK, Germany, China and France. Pennsylvania University was the most contributing institution in the literature (5.25%) followed by University College London and Moorfields Eye Hospital. The average citations per item was 29.4. The most used keywords over a 40-year period were 'family', 'cell', 'photoreceptor' and 'expression'. Conclusions: USA and UK dominated the ophthalmic genetics research. A substantial increase in the number of published documents in this field were observed after 2010.

RESUMO Objetivo: A literatura carece de análise cienciométrica produzida em genética oftálmica e de pesquisa em terapia genética. O objetivo deste estudo é apresentar uma análise holística da literatura genética oftálmica. Métodos: Os dados utilizados neste estudo foram obtidos na base de dados Web of Science (WoS) Core Collection. Todos os documentos publicados entre 1975 e 2019 foram incluídos na análise. Os dados exportados da WoS viabilizaram acesso a amplos detalhes da literatura relacionada à genética oftálmica, incluindo países, instituições, autores, citações e palavras-chave. Mapas de rede cienciométrica foram criados por meio de software gratuito, com base em palavras-chave e em coautorias de países e instituições. As contribuições globais dos países para a literatura sobre genética oftálmica foram apresentadas em gráfico. Resultados: a busca por pesquisas revelou um total de 2.322 documentos cuja maioria eram artigos originais (75,75%). Os EUA foram o país que mais produziu artigos sobre o tema, com 45,39% de todos os documentos em pesquisa genética oftálmica; ele foi seguido pelo Reino Unido, Alemanha, China e França. A Universidade da Pensilvânia foi a instituição que mais contribuiu para a literatura (5,25%), e foi seguida pela University College London e pelo Moorfields Eye Hospital. A média de citações por item foi de 29,4. As palavras-chave mais usadas em um período de 40 anos foram 'família', 'célula', 'fotorreceptor' e 'expressão'. Conclusões: Os EUA e o Reino Unido dominaram a pesquisa em genética oftálmica. Após 2010, observou-se um aumento substancial no número de documentos publicados nessa área.

Lineamientos para el abordaje de casos positivos para secuenciación de SARS-CoV-2 para pacientes que asisten a hospitales privados, públicos y al Instituto Guatemalteco de Seguridad Social ­IGSS- / Guidelines for addressing positive cases for SARS-CoV-2 sequencing for patients attending private and public hospitals and the Guatemalan Social Security Institute -IGSS-

En los antecedentes se presentan estadísticas del COVID-19 a la fecha en la que se elaboró el documento (enero 2021) y aborda las tres mutaciones del virus conocidas hasta la fecha del documento. "La caracterización genética de patógenos virales es la base para el desarrollo de protocolos de diagnóstico, vacunas y medicamentos antivirales. Esta estrategia también es una herramienta útil en salud pública para el seguimiento a brotes y control de enfermedades mediante estudios de epidemiología molecular." "…la secuenciación genómica del SARS-CoV-2 y la liberación oportuna de la información no solo permitió la caracterización del agente etiológico involucrado en el brote inicial, sino también el desarrollo oportuno de protocolos de diagnóstico y seguimiento a la evolución de la pandemia de COVID-19. Así, la secuenciación genómica se ha convertido en una herramienta esencial para generar datos virológicos de SARS-CoV-2, para impulsar la respuesta de laboratorio, y entender mejor los patrones de dispersión y evolución de SARS-CoV-2" De manera que el objetivo del documento es: "Generar información genética mediante la vigilancia genómica de casos confirmados de COVID-19 de pacientes que asisten a los servicios de salud públicos y privados del país, así como del Instituto Guatemalteco de Seguridad Social ­IGSS-."

Avaliação do Conhecimento dos Acadêmicos de Enfermagem em Genética/Genômica sobre o Câncer de Mama / Assessment of the Knowledge of Nursing Academics in Genetics/Genomics about Breast Cancer / Evaluación del Conocimiento de Academias de Enfermería en Genética/Genómica sobre el Cáncer de Mama

Introdução: As universidades de enfermagem não têm acompanhado as demandas relativas às disciplinas de genética, genômica ou oncologia para aperfeiçoar o conhecimento dos acadêmicos no manejo do câncer de mama, que é o mais comum entre as mulheres brasileiras, exigindo maior eficácia das políticas de detecção precoce, tratamento oportuno e aconselhamento genético. Isso se deve em parte à não obrigatoriedade de oferecer essas disciplinas na grade curricular, o que pode levar a um déficit de conhecimento e possível prejuízo da futura qualidade desses profissionais. Objetivo: Analisar se o conhecimento dos acadêmicos de enfermagem sobre os conceitos de genética e genômica aplicados ao câncer de mama está associado à grade curricular das instituições onde estudam. Método: Estudo multicêntrico, transversal, norteado pela ferramenta STROBE, realizado entre agosto/outubro de 2018. Resultados: Acadêmicos de instituições públicas apresentaram correlação entre a ausência das disciplinas genética/genômica (p=0,0001) e pouco conhecimento dos respectivos conceitos (p=0,0045). Alternativamente, os de instituições privadas mostraram maiores erros em relação ao exame clínico de mama anual a partir dos 40 anos (p=0,0009) e à periodicidade do rastreio mamográfico na população sob risco geral (p=0,0021). Os dois grupos convergiram na recomendação da mamografia à população sob risco familiar entre 35-69 anos. Conclusão: Os acadêmicos das instituições de ensino superior privadas apresentaram maiores acertos sobre conceitos de genética/genômica, pois continham a disciplina genética na grade curricular, enquanto os das instituições públicas se destacaram nos acertos relacionados ao câncer de mama sobre políticas de saúde, em razão da maior vivência prática no estágio curricular

Introduction: Nursing universities have not kept up with the demands related to the disciplines of genetics, genomics, or oncology to improve the knowledge of students in managing breast cancer, which is the most common among Brazilian women, demanding greater effectiveness of policies for early detection, timely treatment, and genetic counseling. This is partly due to the fact that it is not mandatory to offer these subjects in the curriculum, which can lead to a deficit of knowledge potentially harmful to the future quality of these professionals. Objective: To analyze whether the knowledge of nursing students about the concepts of genetics and genomics applied to breast cancer is associated with the curriculum of the institutions where they study. Method: Multicenter, cross-sectional study, guided by the STROBE tool, carried out between August-October 2018. Results: Students from public institutions showed correlation between the absence of genetics/genomics disciplines (p=0.0001) and poor knowledge of the respective concepts (p=0.0045). Alternatively, those from private institutions showed more errors in relation to the annual clinical breast exam from the age of 40 (p=0.0009) and the frequency of mammographic screening in the population at general risk (p=0.0021). The two groups concurred in recommending mammography to the population at risk between 35 and 69 years of age. Conclusion: Students from private universities where genetics is included in the disciplines were more cognizant about concepts of genetics and genomics, while those from public institutions stood out regarding correct responses on breast cancer related health policies because of their internship practice

Introducción: Las universidades de enfermería no se han mantenido al día con las demandas relacionadas con las disciplinas de genética, genómica u oncología para mejorar el conocimiento de los académicos en el manejo del cáncer de mama, que es el más común entre las mujeres brasileñas, exigiendo una mayor efectividad de las políticas de detección precoz. tratamiento oportuno y asesoramiento genético. Esto se debe en parte a que no es obligatorio ofrecer estas asignaturas en el plan de estudios, lo que puede conllevar un desconocimiento y posibles daños a la calidad futura de estos profesionales. Objetivo: Analizar si el conocimiento de los estudiantes de enfermería sobre los conceptos de genética y genómica aplicados al cáncer de mama está asociado al currículo de las instituciones donde cursan estudios. Método: Estudio multicéntrico, transversal, guiado por la herramienta STROBE, realizado entre agosto y octubre de 2018. Resultados: Los académicos de las instituciones públicas mostraron una correlación entre la ausencia de disciplinas de genética/ genómica (p=0,0001) y el escaso conocimiento de los conceptos respectivos (p=0,0045). Alternativamente, las de instituciones privadas mostraron mayores errores en relación al examen clínico de mama anual a partir de los 40 años (p=0,0009) y la frecuencia de cribado mamográfico en la población de riesgo general (p=0,0021). Los dos grupos convergieron en la recomendación de la mamografía a la población de riesgo entre los 35 y los 69 años. Conclusión: Los académicos de las instituciones privadas de educación superior fueron más correctos sobre los conceptos de genética y genómica, ya que incluyeron la disciplina genética en el plan de estudios, mientras que los de las instituciones públicas se destacaron en las respuestas correctas relacionadas con el cáncer de mama en las políticas de salud, debido a la mayor experiencia práctica en la pasantía curricular

Biomarcadores na bexiga hiperativa: artigo de revisão / Biomarkers in overactive bladder: review article

A bexiga hiperativa caracteriza-se pela urgência miccional, geralmente acompa- nhada de noctúria e aumento da frequência urinária. Trata-se de afecção preva- lente, com enorme comprometimento da qualidade de vida, em todos os seus as- pectos. Diversos biomarcadores vêm sendo estudados para melhor caracterização dos diferentes fenótipos da afecção, entre eles as neurotrofinas urinárias, o ATP, a genômica e a microbiota urinária. Acredita-se que tal caracterização poderá ter implicações para prevenção, fisiopatologia e individualização do tratamento.(AU)

The overactive bladder is characterized by urinary urgency, usually accompanied by nocturia and increased urinary frequency. It is a prevalent condition, with enormous impairment of quality of life, in all its aspects. Several biomarkers have been studied to better characterize the different phenotypes of the condition, including urinary neurotrophins, ATP, genomics and urinary microbiota. It is believed that such charac- terization may have implications for prevention, pathophysiology and individualiza- tion of treatment.(AU)