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)

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.

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

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-."

Genomic and transcriptomic characterization of the human glioblastoma cell line AHOL1

Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.

Genomics and functional genomics in Leishmania and Trypanosoma cruzi: statuses, challenges and perspectives

The availability of Trypanosomatid genomic data in public databases has opened myriad experimental possibilities that have contributed to a more comprehensive understanding of the biology of these parasites and their interactions with hosts. In this review, after brief remarks on the history of the Trypanosoma cruzi and Leishmania genome initiatives, we present an overview of the relevant contributions of genomics, transcriptomics and functional genomics, discussing the primary obstacles, challenges, relevant achievements and future perspectives of these technologies.

Identification of Proteins Associated with the Formation of Oral Biofilms

ABSTRACT Objective: To identify proteins associated with the formation of Streptococcus gordonii and Fusobacterium nucleatum biofilms. Material and Methods: Biofilms composed of two bacterial species, S. gordonii and F. nucleatum, were cultured for 1, 4, 7, and 10 days. The presence of both species was confirmed via amplification of the srtA and radD genes using real-time PCR. The concentrations of proteins associated with the biofilms and individual species were quantified using Western blotting. Results: The protein profiles of S. gordonii and F. nucleatum from individual cultures determined using one-dimensional electrophoresis revealed proteins found in S. gordonii and in F. nucleatum. Ct and reciprocal Ct values were determined for the exposed S. gordonii and F. nucleatum biofilms. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein was detected in biofilms and F. nucleatum, whereas HSP40 protein was present only in biofilms after 7 and 10 days of formation. Conclusion: HSP40 was detected only in the formed biofilms; thus, HSP40 is an essential proteins for adhesion.

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)

Genomic analysis on Brazilian strains of Anaplasma marginale / Análise genômica de cepas Brasileiras de Anaplasma marginale

Abstract Anaplasma marginale is a vector-borne pathogen that causes a disease known as anaplasmosis. No sequenced genomes of Brazilian strains are yet available. The aim of this work was to compare whole genomes of Brazilian strains of A. marginale (Palmeira and Jaboticabal) with genomes of strains from other regions (USA and Australia strains). Genome sequencing of Brazilian strains was performed by means of next-generation sequencing. Reads were mapped using the genome of the Florida strain of A. marginale as a reference sequence. Single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) were identified. The data showed that two Brazilian strains grouped together in one particular clade, which grouped in a larger American group together with North American strains. Moreover, some important differences in surface proteins between the two Brazilian isolates can be discerned. These results shed light on the evolutionary history of A. marginale and provide the first genome information on South American isolates. Assessing the genome sequences of strains from different regions is essential for increasing knowledge of the pan-genome of this bacteria.

Resumo Anaplasma marginale é um patógeno transmitido por vetores que causam uma doença conhecida como anaplasmose. Até a presente data, não há genomas sequenciados de cepas brasileiras. O objetivo deste estudo foi comparar o genoma completo das cepas brasileiras de A. marginale (Palmeira e Jaboticabal) com os genomas de cepas de outras regiões (cepas dos EUA e Austrália). As sequências dos genomas das cepas brasileiras foram obtidas mediante sequenciamento de nova geração. As "reads" foram mapeadas usando-se como referência o genoma de A. marginale da cepa Florida. Foram identificados polimorfismos de nucleotídeo único (SNPs) e analisadas inserções/deleções (INDELs). As duas linhagens brasileiras se agruparam em um clado particular que, por sua vez, agrupou-se em um grupo maior junto com as linhagens norte-americanas. Além disso, foram identificadas diferenças significativas nas proteínas de superfície entre os dois isolados brasileiros. Esses resultados lançam luz sobre a história evolutiva de A. marginale e fornecem as primeiras informações de genomas de isolados sul-americanos. Avaliar as sequências de genomas de cepas de diferentes regiões é essencial para aumentar o conhecimento do pan-genoma dessa bactéria.

Conhecimento de enfermeiros sobre genética e genômica aplicado ao câncer de mama / Conocimiento de enfermeros sobre genética y genomas aplicados al cáncer de mama / Nurse's knowledge about genetics and genomics applied to breast cancer

RESUMO Objetivo: identificar o conhecimento de enfermeiros em genética e genômica aplicado ao câncer de mama. Método: estudo transversal com a aplicação de um questionário desenvolvido pelos autores a enfermeiros assistenciais, maiores de 18 anos, atuantes na atenção secundária e terciária, no município de Belém do Pará, região Norte do Brasil. Realizada técnica de amostragem por conveniência em relação aos locais de coleta e amostragem aleatória simples para o número amostral mínimo de 71 participantes. Resultados: foram abordados 80 enfermeiros com idade média de 42 anos, sendo a maior parte de especialistas. Verificaram-se diferenças entre o nível da atenção em que os enfermeiros atuam e o primeiro contato com genética e/ou genômica (p<0,001); entre o conceito de DNA (p<0,0001); o conhecimento sobre o heredograma (p=0,004); conhecimento sobre a faixa etária do rastreamento mamográfico com risco familiar (p=0,027); o exame clínico realizado por um médico ou enfermeira treinados, anualmente, a partir de 40 anos (p=0,005). A maioria dos casos de CA de mama ocorre devido a alterações genéticas hereditárias (p=0,0004) e da menarca precoce, menopausa tardia, nuliparidade, alterações hormonais, sedentarismo, sobrepeso, tabagismo e terapia hormonal, que são os principais fatores de risco para o câncer de mama esporádico (p=0,0039). Conclusão: identificou-se uma lacuna de conhecimento sobre os conceitos de genética e genômica aplicados ao câncer de mama entre os dois grupos.

RESUMEN Objetivo: identificar los conocimientos de enfermeros en genética y genómica aplicadas al cáncer de mama. Método: estudio transversal con la aplicación de un cuestionario desarrollado por los autores a enfermeros asistenciales, mayores de 18 años, que trabajan en la atención secundaria y terciaria, en la ciudad de Belém do Pará, región norte de Brasil. Se realizó una técnica de muestreo por conveniencia con relación a los sitios de recolección y muestreo aleatorio simple para una muestra mínima de 71 participantes. Resultados: se abordó a 80 enfermeros con una edad promedio de 42 años, la mayoría especialistas. Hubo diferencias entre el nivel de atención en el que trabajan los enfermeros y el primer contacto con la genética y / o genómica (p <0,001); entre el concepto de ADN (p <0,0001); conocimiento sobre el árbol genealógica (p = 0,004); conocimiento sobre el grupo de edad de cribado mamográfico con riesgo familiar (p = 0,027); el examen clínico realizado por un médico o enfermero capacitado, anualmente, a partir de los 40 años (p = 0,005). La mayoría de los casos de CA de mama se producen por alteraciones genéticas hereditarias (p = 0,0004) y menarquia precoz, menopausia tardía, mujeres que nunca han parido, cambios hormonales, sedentarismo, sobrepeso, tabaquismo y terapia hormonal, que son los principales factores de riesgo de cáncer de mama esporádico (p = 0,0039). Conclusión: entre los dos grupos se identificó una brecha de conocimiento sobre los conceptos de genética y genómica aplicados al cáncer de mama.

ABSTRACT Objective: to identify nurse's knowledge in genetics and genomics applied to breast cancer. Method: a cross-sectional study with the application of a questionnaire developed by the authors to clinical nurses, over 18 years old, working in secondary and tertiary care, in the city of Belém do Pará, the northern region of Brazil. Convenience sampling technique was performed in the collection places and simple random sampling for a minimum sample number of 71 participants. Results: Eighty nurses with an average age of 42 years old were approached, most of the experts. There were differences between the level of care in which nurses work and the first contact with genetics and/or genomics (p<0.001); between the concept of DNA (p<0.0001); knowledge about the genogram (p=0.004); knowledge about the age group of mammographic screening with familial risk (p=0.027); the clinical examination performed by a trained physician or nurse, annually, from 40 years old (p=0.005). Most cases of breast cancer occur due to hereditary genetic changes (p=0.0004) and early menarche, late menopause, nulliparity, hormonal changes, sedentary lifestyle, overweight, smoking, and hormonal therapy, which are the main risks factors for sporadic breast cancer (p=0.0039). Conclusion: a knowledge gap about the concepts of genetics and genomics applied to breast cancer was identified between the two groups.