Hallazgos incidentales en medicina genómica / Incidental Findings in Genomic Medicine

Las técnicas de Biología Molecular de última generación, como es la secuenciación masiva en paralelo o NGS (Next Generation Sequencing), permite obtener gran cantidad de información genómica, la cual muchas veces va más allá de la detección de una variante patogénica en un gen que explique la patología (hallazgo primario). Es así como surgió desde hace años la discusión internacional respecto a la decisión a tomar frente a los hallazgos secundarios accionables, es decir, aquellos hallazgos de variantes clasificadas como patogénicas o probablemente patogénicas que no están relacionadas con el fenotipo del paciente, pero que tiene alguna medida preventiva o tratamiento posible y, por lo tanto, podría ser de utilidad para la salud del paciente. Luego de revisar la bibliografía internacional y debatir entre los expertos del Hospital de Pediatría Garrahan, se logró establecer una política institucional y reforzar el hecho de que se trata de una disciplina multidisciplinaria. Así, fue posible definir que solo se atenderá las cuestiones relacionadas con la edad pediátrica, dejando para un tratamiento posterior aquellas variantes detectadas en genes que sean accionables en edad adulta. En el Hospital Garrahan, ha sido posible definir claramente cómo proceder frente a los hallazgos secundarios, al adaptar el consentimiento informado a esta necesidad, definiendo cuándo serán informados, y sabiendo que serán buscados intencionalmente en los genes clínicamente accionables enlistados en la última publicación del American College of Medical Genetics and Genomics, siempre y cuando el paciente/padre/tutor lo consienta (AU)

The latest generation of molecular biology techniques, including massive parallel sequencing or NGS (Next Generation Sequencing), allows us to obtain a whealth of genomic information, which often goes beyond the detection of a pathogenic variant in a gene that explains the pathology (primary finding). As a result, an international discussion has arisen over the years regarding the decision-making concerning actionable secondary findings, it means, those findings of variants classified as pathogenic or probably pathogenic that are not related to the patient's phenotype, but which have some possible preventive measure or treatment and, therefore, could be useful for the patient's health. After reviewing the international literature and discussing among the experts of the Hospital de Pediatría Garrahan, an institutional policy was established and the concept that this is a multidisciplinary discipline was reinforced. Consequently, it has been defined that only issues related to children will be addressed, reserving those variants detected in genes that are actionable in adulthood for later treatment. At Garrahan Hospital, we were able to clearly define how to proceed with secondary findings by adapting the informed consent to this need, defining when they will be reported, and knowing that they will be intentionally searched for in the clinically actionable genes listed in the latest publication of the American College of Medical Genetics and Genomics, as long as the patient/parent/guardian consents (AU)

Prevalence of Somatic BRCA1 and BRCA2 mutations in ovarian cancer among Filipinos using next generation sequencing

INTRODUCTION@#Ovarian cancer is one of the leading causes of mortality in women. In 2020, 5,395 (6.2%) of diagnosed malignancies in females were ovarian in origin. It also ranked second among gynecologic malignancies after cervical cancer. The prevalence in Asian /Pacific women is 9.2 per 100,000 population. Increased mortality and poor prognosis in ovarian cancer are caused by asymptomatic growth and delayed or absent symptoms for which about 70% of women have an advanced stage (III/IV) by the time of diagnosis. The most associated gene mutations are Breast Cancer gene 1 (BRCA1) which is identified in chromosome 17q21 and Breast Cancer gene 2 (BRCA2) identified in chromosome 13. Both proteins function in the double-strand DNA break repair pathway especially in the large framework repair molecules. Olaparib is a first-line drug used in the management of ovarian cancer. It targets affected cells by inhibition of poly (ADP-ribose) polymerase (PARP) activity which induces synthetic lethality in mutated BRCA1/2 cancers by selectively targeting tumor cells that fail to repair DNA double-strand breaks (DSBs).@*OBJECTIVE@#The study aims to determine the prevalence of pathogenic somatic mutations in BRCA1 and BRCA2 among patients diagnosed of having ovarian cancer, to characterize the identified variants into benign/ no pathogenic variant identified, variant of uncertain significance (VUS), and pathogenic, and to determine the relationship of specific mutations detected with histomorphologic findings and clinical attributes.@*METHODOLOGY@#Ovarian cancer tissues available at the St. Luke’s Medical Center Human Cancer Biobank and formalin-fixed paraffin-embedded (FFPE) tissue blocks diagnosed as ovarian cancer from the year 2016 to 2020 were included. Determination of the prevalence of somatic BRCA1 and BRCA2 mutations using Next Generation Sequencing (NGS).@*RESULTS@#A total of 60 samples were processed, and three samples were excluded from the analysis due to an inadequate number of cells. In the remaining 57 samples diagnosed ovarian tumors, pathogenic BRCA1/2 variants were identified in 10 (17.5%) samples. Among the BRCA1/2 positive samples, 3 (5.3%) BRCA1 and 7 (12.3%) BRCA2 somatic mutations were identified.@*CONCLUSION@#Identification of specific BRCA1/2 mutations in FFPE samples with NGS plays a big role in the management of ovarian cancer, particularly with the use of targeted therapies such as Olaparib. The use of this drug could provide a longer disease-free survival for these patients. Furthermore, we recommend that women diagnosed with ovarian cancer should be subjected to genetic testing regardless of the histologic subtypes or clinical features. Lastly, genetic testing should be done along with proper genetic counseling, especially for patients who are susceptible to these mutations.

Muerte súbita y secuenciación de siguiente generación. Revisión bibliográfica / Sudden death and next generation sequencing. A review

Introducción: la muerte súbita se trata de un evento fatal e imprevisible. Realizada la autopsia y estudios complementarios, en ausencia de otros hallazgos que expliquen la causa de muerte, se clasifica como muerte súbita inexplicada. Siendo recomendable en estos casos realizar análisis genéticos, especialmente con metodologías de secuenciación de siguiente generación, las que permiten explicar un porcentaje importante de estos casos. Objetivo: analizar las publicaciones más relevantes sobre secuenciación de siguiente generación, aplicada a la autopsia molecular, para determinar aquellas muertes súbitas inexplicables relacionadas a cardiomiopatías y canalopatías. Metodología: se realizó la búsqueda en PubMed del Instituto Nacional de Salud usando palabras clave en inglés y español: NGS, muerte súbita, autopsia molecular y sus combinaciones. Además, se realizaron búsquedas en OMIN y ClinVar relacionada a las diferentes afecciones cardiacas relacionadas a muerte súbita. Los criterios de inclusión: artículos completos en español e inglés de libre acceso, con antigüedad máxima de diez años, realizados en cualquier área geográfica y que trataran sobre la temática. Resultados: para secuenciación de siguiente generación, muerte súbita se encontraron más de 22000 y 65000 publicaciones, respectivamente. En cambio, al combinar las palabras clave se recuperaron 74 trabajos, según los criterios de inclusión y objetivo del trabajo se revisaron 67 artículos. La aplicación de las plataformas de secuenciación en la investigación de casos de muerte súbita tomo auge en el 2014 y en poco tiempo, demostraron su versatilidad para el análisis de una gran cantidad de genes simultáneamente, de forma rápida y a bajo costo. Conclusiones: las patologías asociadas a muerte súbita son múltiples, complejas y pueden generar fenotipos variables que dificultan el análisis genético de las mismas. Las plataformas de secuenciación de siguiente generación son sumamente útiles en los casos de muerte súbita inexplicada, además permiten la identificación de variantes genéticas en familiares para la implementación de medidas preventivas...(AU)

Clinical and genetic study of developmental and epileptic encephalopathy in argentinean pediatric patients / Estudio clínico y genético de encefalopatía epiléptica y del desarrollo en pacientes pediátricos argentinos

Abstract Introduction: The aim of this study was to extend our knowledge of the genetic background of Argentinean pediatric patients with developmental and epileptic encephalopathy (DEE) applying a next generation sequencing (NGS) panel. Methods: Thirty one patients with DEE were studied, including these phenotypes: Dravet syndrome (n:7), Dravet like syndrome (n:3), West syndrome (WS) (n:6), WS that evolved to Lennox-Gastaut syndrome (LGS) (n:4), epilepsy of infancy with migrating focal seizures (n:2), continuous spikes and waves during slow sleep evolving to LGS (n:1), LGS (n:1), myoclonic status in non-progressive encephalopathy (n:1), myoclonic atonic epilepsy (n:1), epileptic encephalopathy with multifocal spikes (n:1) and unclassified epileptic encephalopathy (n:4). Fifty-two genes frequently associated with DEE were studied by NGS in genomic DNA from peripheral blood. Results: Relevant variants were detected in 12 cases; 6 novel pathogenic or likely pathogenic variants, 6 previously reported as pathogenic and 1 variant of unknown sig nificance. Single-nucleotide heterozygous variants were identified in the SCN1A (5), GABRG2 (1), STXBP1 (2) genes, a mosaic variant in SCN2A (1) and a homozygous variant in SCN1B (1). Additionally, a heterozygous deletion involving the SCN1A, SCN2A and SCN3A genes (1), and the most frequent triplet repeat expansion in the ARX gene (1) were detected. Discussion: Genetic diagnosis was made in 39% of patients. We emphasize the importance of considering mosaic variants, copy number variants and hereditary forms when designing and interpreting molecular studies, to optimize diagnosis and management of patients. Approximately 42% of the de tected variants were novel, expanding the knowledge of the molecular basis of DEEs in Latin-American patients.

Resumen Introducción: El objetivo del estudio fue ampliar el conocimiento de las bases moleculares de las encefalopatías epilépticas y del desarrollo (EED) en pacientes pediátricos argentinos aplicando un panel de secuenciación de nueva generación (NGS). Métodos: Se analizaron 31 pacientes con los fenotipos clínicos de síndrome de Dra vet (n:7), síndrome símil Dravet (n:3), síndrome de West (SW) (n:6), SW que evoluciona a síndrome de Lennox Gastaut (SLG)(N:4), epilepsia de la infancia con crisis focales migratorias (n:2), actividad de punta onda continua durante el sueño que evolucionan a SLG (n:1), SLG (n:1), encefalopatía no progresiva con estatus mioclónico (n:1), epilepsia mioclónica atónica (n:1), encefalopatía epiléptica con espigas multifocales (n:1) y encefalopatía epiléptica indeterminada (n:4). Se estudiaron los 52 genes más frecuentemente asociados a EED a través de NGS, en ADN extraído de sangre periférica. Resultados: Se identificaron variantes relevantes en 12 casos, de las cuales 5 fueron nuevas y 6 previamente reportadas como patogénicas o posiblemente patogénicas, mien tras que una variante fue clasificada como de significado incierto. Variantes heterocigotas, de nucleótido único, se identificaron en los genes SCN1A (5), GABRG2 (1), STXBP1 (2), una variante en mosaico en SCN2A (1) y otra homocigota en SCN1B (1). Además, se detectó una deleción que involucra a los genes SCN1A, SCN2A y SCN3A (1) y la expansión de repeticiones de tripletes más frecuente en el gen ARX (1). Discusión: Se alcanzó el diagnóstico molecular en el 39% de los pacientes. Remarcamos la importancia de considerar variantes en mosaico, variantes en el número de copias y formas heredadas al momento de diseñar e interpretar los estudios moleculares, de tal forma de optimizar el diagnóstico y seguimiento de los pacientes con EED. Cabe destacar, que el 42% de las variantes detectadas fueron nuevas, ampliando nuestro conocimiento sobre las bases mole culares de las EED en población latino americana.

Identificación de variantes del gen BRCA 1 Y BRCA 2 en pacientes con cáncer de próstata resistente a la castración del Hospital Central Militar / Identification of BRCA 1 AND BRCA 2 gene variants in patients with castration-resistant prostate cancer at the Hospital Central Militar

Resumen El cáncer de próstata metastásico resistente a la castración (CPRC) es una neoplasia heterogénea letal entre los hombres. 30% de los tumores acumulan errores deletéreos en genes implicados en la respuesta al daño del ADN (DNA damage response en inglés, DDR). Algunos de estos genes asociados a cáncer son BRCA 1 y BRCA 2. Mutaciones en estos genes favorecen la pérdida o la modificación de la función provocando un cambio permanente y transmisible, lo que conduce al desarrollo de cáncer de próstata agresivo. El objetivo del estudio fue identificar mediante secuenciación dirigida (Next-generation sequencing; NGS) variantes génicas de BRCA 1 y BRCA 2 en el genoma de pacientes con CPRC del Hospital Central Militar. Es importante destacar que los resultados demostraron una serie de alteraciones clínicas, así como una pérdida de la función de las proteínas relacionadas con mecanismos de reparación del ADN. Curiosamente, algunas de las variantes en el gen BRCA, de las que se informa aquí, son de significado incierto, lo que nos ha sido comunicado por primera vez.

Abstract Metastatic castration-resistant prostate cancer (CRPC) is a heterogeneous lethal neoplasm among men. 30% of tumors harbor deleterious errors in genes involved in the DNA damage response (DDR). Some of these cancer-associated genes are BRCA 1 and BRCA 2. Mutations to these genes favor loss or modification of function causing a permanent and transmissible change, leading to the development of aggressive prostate cancer. The aim of the study was to identify by Next-generation sequencing (NGS) BRCA 1 and BRCA 2 gene variants in peripheral blood of patients with CRPC at the Hospital Central Militar. Importantly, the results demonstrated a number of clinical alterations, as well as a loss of function of proteins related to DNA repair mechanisms. Interestingly, some of the variants in the BRCA gene, reported here, are of uncertain significance, which has been reported to us for the first time.

CONCORDANCE: A real?world evidence study to evaluate the concordance of detecting epidermal growth factor receptor (EGFR) mutation by circulating tumor DNA* versus tissue biopsy in patients with metastatic non?small cell lung cancer

Background: Molecular tissue testing in non?small cell lung cancer (NSCLC) is done for the assessment of epidermal growth factor receptor (EGFR) mutation. EGFR mutation status is the basis for deciding the targeted treatment option for patients with metastatic NSCLC. The nonavailability of tissue samples and contraindications for biopsy pose a significant challenge. Hence circulating tumor DNA (ctDNA) by liquid biopsy can be a viable alternative for NSCLC patients. Methods: This study was conducted at 15 sites across India. EGFR mutation testing from plasma was done as part of the study at the central laboratory by the next?generation sequencing (NGS) method and EGFR mutation test results from tissue samples (done as part of routine practice) were recorded for all the patients. Results: Out of the total patients enrolled (N = 245) the majority (64.5% n = 158) were men. The median age of patients was 58.0 (range: 26�) years. The concordance between plasma and tissue testing was found to be 82.9% (95% confidence interval [CI]: 77.55 87.45). The sensitivity and specificity of NGS were 68.4% (95% CI: 56.92 78.37) and 90.1% [95% CI: 84.36 94.21) respectively. Plasma testing detected 1.2% (n = 3) and tissue sample testing detected 2.4% (n = 6) positive status of exon 20 T790M EGFR mutation. Out of the total number of patients enrolled 25 were tissue positive and plasma negative while 16 were plasma positive and tissue negative. Conclusions: This real?world study in Indian patients suggests that plasma testing for EGFR mutation analysis is a viable diagnostic option in newly diagnosed advanced/metastatic NSCLC patients. The noninvasive plasma procedure in patients without available/evaluable tumor sample may enable more patients to receive appropriate targeted therapies by providing clinicians with valuable insights into the patient抯 tumor mutation status. ClinicalTrials.gov Identifier: NCT03562819

Technical specification for clinical diagnosis and treatment of human parvovirus B19 infection in kidney transplant recipients (2022 edition) / 器官移植

Long-term use of immunosuppressant in kidney transplant recipients leads to poor immune function and infection with various pathogens. In recent years, along with the advancement of detection technique of human parvovirus B19 (HPV-B19) infection and the increasing quantity of kidney transplantation, the infection rate of HPV-B19 after kidney transplantation has been elevated year by year, becoming one of the major causes of pure red cell aplasia (PRCA), affecting the recovery of renal allograft function, and even leading to the injury or poor prognosis of renal allograft. To further standardize the diagnosis and treatment of HPV-B19 infection in kidney transplant recipients, Branch of Organ Transplantation of Chinese Medical Association and National Kidney Transplantation Quality Control Center jointly organized experts to formulate the clinical diagnosis and treatment specification for HPV-B19 infection after kidney transplantation from the perspectives of etiology, epidemiological characteristics, clinical manifestations, diagnosis, prevention, treatment, existing problems and prospects of HPV-B19, aiming to provide guidance for standardized prevention and treatment of HPV-B19 infection post-kidney transplantation in China.

Avances de la bioinformática en Costa Rica: vista retrospectiva y perspectivas / Bioinformatics advances in Costa Rica: retrospective view and perspectives

Resumen Introducción: La disciplina científica de la bioinformática tiene el potencial de generar aplicaciones innovadoras para las sociedades humanas. Costa Rica, pequeña en tamaño y población en comparación con otros países de América Latina, ha ido adoptando la disciplina de manera progresiva. El reconocer los avances permite determinar hacia dónde puede dirigirse el país en este campo, así como su contribución a la región latinoamericana. Objetivo: En este manuscrito se reporta evidencia de la evolución de la bioinformática en Costa Rica, para identificar debilidades y fortalezas que permitan definir acciones a futuro. Métodos: Se realizaron búsquedas en bases de datos de publicaciones científicas y repositorios de secuencias, así como información de actividades de capacitación, redes, infraestructura, páginas web y fuentes de financiamiento. Resultados: Se observan avances importantes desde el 2010, incluyendo un aumento en oportunidades de entrenamiento y número de publicaciones, aportes significativos a las bases de datos de secuencias y conexiones por medio de redes. Sin embargo, ciertas áreas, como la masa crítica y la financiación requieren más desarrollo. La comunidad científica y sus patrocinadores deben promover la investigación basada en bioinformática, invertir en la formación de estudiantes de posgrado, aumentar la formación de profesionales, crear oportunidades laborales para carreras en bioinformática y promover colaboraciones internacionales a través de redes. Conclusiones: Se sugiere que para experimentar los beneficios de las aplicaciones de la bioinformática se deben fortalecer tres aspectos clave: la comunidad científica, la infraestructura de investigación y las oportunidades de financiamiento. El impacto de tal inversión sería el desarrollo de proyectos ambiciosos pero factibles y colaboraciones extendidas dentro de la región latinoamericana. Esto permitiría realizar contribuciones significativas para abordar los desafíos globales y la aplicación de nuevos enfoques de investigación, innovación y transferencia de conocimiento para el desarrollo de la economía, dentro de un marco de ética de la investigación.

Abstract Introduction: The scientific discipline of bioinformatics has the potential to generate innovative applications for human societies. Costa Rica, small in size and population compared to other Latin American countries, has been progressively adopting the discipline. Recognizing progress makes it possible to determine where the country can go in this field, as well as its contribution to the Latin American region. Objective: This manuscript reports evidence of the evolution of bioinformatics in Costa Rica, to identify weaknesses and strengths allowing future actions plans. Methods: We searched databases of scientific publications and sequence repositories, as well as information on training activities, networks, infrastructure, web pages and funding sources. Results: Important advances have been observed since 2010, such as increases in training opportunities and the number of publications, significant contributions to the sequence databases and connections through networks. However, areas such as critical mass and financing require further development. The scientific community and its sponsors should promote bioinformatics-based research, invest in graduate student training, increase professional training, create career opportunities in bioinformatics, and promote international collaborations through networks. Conclusions: It is suggested that in order to experience the benefits of bioinformatics applications, three key aspects must be strengthened: the scientific community, the research infrastructure, and funding opportunities. The impact of such investment would be the development of ambitious but feasible projects and extended collaborations within the Latin American region and abroad. This would allow significant contributions to address global challenges and the implementation of new approaches to research, innovation and knowledge transfer for the development of the economy, within an ethics of research framework.

The utilization of biotinylated RNA baits on captured sequencing of cancer marker genes functional regions / Монголын Анагаах Ухаан

Background@#Nucleic acid sequencing is a multi-step process taken place in medical research or diagnostic laboratories. Since the emerge of second generation sequencing technology generally referred as next generation sequencing (NGS), the mass parallel reads covering human genome or transcriptome is achieved by cost cut down over thousand folds. Though the technology made tremendous push forward to various applications, its data analysis time and effort still takes worrisome time and human effort, bringing the emerge of next-step demand: targeted mass sequencing of only desired part from human genome or transcriptome with lower material cost and labor. By targeted sequencing, both run cost and data analysis process can be further cut down, and the read results are more reliable on changes such as determining varied number of repeats, heterozygote alleles, deletions, chromosomal scale abnormality and more. @*Objective@#In this study, we explored the utilization of biotinylated RNA baits on captured sequencing of cancer marker genes functional regions.@*Method@#Targeted NGS was achieved by capturing desired genomic regions using preparatory nucleic acid probes. RNA bait capturing of desired genomic regions has shown to have high specificity and quality. </br> The study was carried out with informed consent obtained from patients, with the approval №53 in 2018.03.15 by Medical Ethics committee, Ministry of Health, Mongolia.@*Result@#By preparing library of biotinylated RNA baits with 75000 unique sequences, we achieved mass parallel sequencing of human 410 cancer-marker-genes’ exons and UTRs with average read depth ~760, and covered thousands of SNPs on 5 genomic DNA samples. Tissue samples derived from breast cancer and ovary cancer had SNP and deletion on 7 marker genes (BRCA1, BRCA2, ATM, BRIP1, PTEN, TP53, RAD51C) not registered in database.@*Conclusion@#Experiments showed RNA baits with up to 117 nucleotide length, produced from ssDNA oligonucleotide stock, can be utilized to capture desired regions of human genome, and bring the cost of captured mass sequencing to 1500 USD, with 93.14-93.33% of Q30 read quality.

Genomic mutations in patients with advanced non-small cell lung cancer in Yunan and its clinical significance / 中国肿瘤生物治疗杂志

@#[Abstract] Objective: To investigate the lung cancer-associated driver gene mutations in peripheral blood of patients with advanced non-small cell lung cancer (NSCLC) in Yunnan area, and to explore their association with clinical pathological features. Methods: Peripheral blood of 304 patients with stage Ⅳ NSCLC were collected from Molecular Diagnostic Center of Yunnan Cancer Hospital during January 2019 to December 2019. Next generation sequencing (NGS) technique was used to detect the mutation of NSCLC related driver genes, chi-square test was used to analyze the relationship between the major mutant genes and the clinicopathological features of patients, and Logistic regression was used to analyze the independent risk factors. Results: In the peripheral blood of 304 patients with stage Ⅳ NSCLC, there were 120 (39.47%) cases with EGFR mutations, 12 (3.95%) cases with ALK fusion, 36 (11.84%) case with other mutations such as KRAS, BRAF and RET. The main EGFR mutations were 19del and L858R (69.17%). The mutation rate of EGFR was higher in female, young, non-smoking, non-chemotherapy and lung adenocarcinoma patients (49.26% vs 31.55%, 45.39% vs 33.56%, 45.92% vs 27.78%, 45.07% vs 26.37%, 42.39% vs 10.71%, all P<0.05). Multivariate analysis showed that female, no history of chemotherapy and lung adenocarcinoma were independent risk factors for EGFR mutations (all P<0.05). Conclusion: Using NGS technology to detect the driver genes in peripheral blood of patients with advanced NSCLC in Yunnan area showed that the mutation rate of EGFR was higher in women and lung adenocarcinoma patients without chemotherapy history.

Diagnostic criteria and research progress on heart allograft pathology / 器官移植

With the improvement of surgical technique of heart transplantation and clinical application of potent immunosuppressant, the quantity of heart transplantation and the survival time of heart allograft have been significantly improved. However, a series of complications, such as right ventricular failure, ischemia-reperfusion injury, acute rejection, "Quilty lesion", infection and chronic rejection characterized by transplant coronary artery disease (TCAD) may still occur at different stages after heart transplantation. The application of endomyocardial biopsy (EMB) makes it possible to observe and understand the pathological features of multiple complications of heart allograft including rejection, which has become the most accurate diagnostic tool for postoperative complications. In this article, the brief history of heart allograft pathology, main postoperative complications and pathological diagnostic criteria, and cutting edge research progress on diagnostic criteria of rejection were illustrated, aiming to bring clinical benefits to more recipients undergoing heart transplantation.

Analysis of bacterial diversity associated with polyketide synthase (PKS) gene in brackish metagenome of TsoKar Lake of Ladakh, India

Aim: To explore bacterial diversity associated to polyketide synthase (PKS) genes in the TsoKar brackish metagenome.Methodology: The metagenomic DNA of TsoKar water and sediment samples were isolated and amplified using pks specific degenerate primers. PCR amplified products were analysed using Ion Torrent PGM platform and revealed a total of 2,11,030 reads with 534 contigs and 55% of G+C content. The results of BLASTx was further analyzed for species diversity using MEGAN5 software. Results: Halomonas was found to be the dominant phyla followed by Cyanobium, Acinetobacter and Burkholderia, respectively, along with majority of uncultured microorganisms present in TsoKar metagenome. Since TsoKar is a brackish water lake, and brackish aquatic ecosystems are a major hub of diverse microbes was also revealed in this study. TsoKar metagenomic sequence with accession number SRR8381943 was deposited in SRA database. Interpretation: TsoKar Lake is considered as one of the most important biosphere reserves. The results of this study confirm that this unique niche harbors good bacterial diversity associated with polyketide synthase genes, which justifies the idea of bioprospecting such niches for the discovery of novel metabolites like antimicrobial compounds using next-generation sequencing approach

Aplicación de la secuenciación masiva y la bioinformática al diagnóstico microbiológico clínico / Bioinformatics of next generation sequencing in clinical microbiology diagnosis

Resumen La aparición de secuenciadores masivos que permiten leer en paralelo de millones a miles de millones de secuencias o fragmentos del ADN (reads) ha revolucionado la microbiología, la cual ha pasado de un ámbito exclusivamente laboratorial a uno computacional, con la aplicación ineludible de la bioinformática. La posibilidad de efectuar estudios de la microbiota, el microbioma y el metagenoma de una muestra clínica de manera rápida y a un coste reducido permite avanzar más rápidamente en el diagnóstico de enfermedades, en el conocimiento de la taxonomía y la epidemiología de los agentes involucrados, así como de su virulencia. También posibilita la realización de estudios de genómica comparada y el descubrimiento de genes o variantes de interés, lo que puede llevar a que enfermedades tradicionalmente consideradas como de carácter no microbiano sean asociadas a la presencia de microrganismos. En esta revisión se aclara la terminología usada en este campo, y se describen las principales tecnologías de secuenciación y su utilidad en el análisis microbiano. Asimismo, se señalan diversos programas de código libre, pipelines de análisis, bases de datos y plataformas web que permiten que la bioinformática se integre exitosamente al ámbito de la microbiología clínica y al estudio de las enfermedades infecciosas.

Abstract Massive parallel sequencing (High-Throughput Sequencing [HTS]) allows to read millions or billions of DNA sequences or fragments (reads) in parallel and is revolutionizing microbiology research, moving from laboratory methods to computed-assisted analyses, with the compelling use of Bioinformatics. The time and cost reduction in studies on the microbiota, microbiome and metagenome, allows to rapidly progress in diagnosis, taxonomy, epidemiology, comparative genomics, virulence, discovery of genes or variants of interest and the association of microorganisms with traditionally considered non-microbial diseases. In this review, the terminology, the sequencing technologies and their applications are described for microbial analysis using open-source bioinformatics software, analysis pipelines, databases and web platforms that allow a user-friendly bioinformatics approach affordable by the clinical microbiologist and infectious disease practitioners.

Genomics and animal production / Genómica y producción animal

Abstract Developing countries have the challenge of achieving food security in a world context that is affected by climate change and global population growth. Molecular Genetics and genomics are proposed as technologies that will help to achieve sustainable food security. Technologies that have been developed in the last decade such as the development of genetic markers, genetic maps, genomic selection, next-generation sequencing, and DNA editing systems are discussed. Examples of some discoveries and achievements are provided.

Resumen Los países en vías de desarrollo tienen el reto de alcanzar seguridad alimentaria en un contexto mundial afectado por el cambio climático y crecimiento poblacional global. La genética molecular y la genómica son propuestas como tecnologías que ayudarán a alzanzar una seguridad alimentaria sostenible. Tecnologías que han sido desarrolladas en la última década como el desarrollo de marcadores moleculares, mapeo genético, selección genómica, secuenciamiento de próxima generación y sistemas de edición de ADN son discutidos. Se proveen ejemplos de algunos descubrimientos y logros.

Microbial communities from arid environments on a global scale: a systematic review

Abstract Arid environments are defined by the lack of water availability, which is directly related to the mean annual precipitation (MAP), and high values of solar irradiation, which impacts the community composition of animals, plants, and the microbial structure of the soil. Recent advances in NGS technologies have expanded our ability to characterize micro- biomes, allowing environmental microbiologists to explore the complete microbial structure. Intending to identify and describe the state-of-the-art of bacterial communities in arid soils at a global scale, and to address the effect that some environmental features may have on them, we performed a systematic review based on the PRISMA guideline. Using a combination of keywords, we identified a collection of 66 studies, including 327 sampled sites, reporting the arid soil bacterial community composition by 16S rDNA gene high-throughput sequencing. To identify factors that can modulate bacterial communities, we extracted the geographical, environmental, and physicochemical data. The results indicate that even though each sampled site was catalogued as arid, they show wide variability in altitude, mean annual temperature (MAT), soil pH and electric conductivity, within and between arid environments. We show that arid soils display a higher abundance of Actinobacteria and lower abundance of Proteobacteria, Cyanobacteria, and Planctomycetes, compared with non-arid soil microbiomes, revealing that microbial structure seems to be strongly modulated by MAP and MAT and not by pH in arid soils. We observed that environmental and physicochemical features were scarcely described among studies, hence, we propose a reporting guideline for further analysis, which will allow deepening the knowledge of the relationship between the microbiome and abiotic factors in arid soil. Finally, to understand the academic collaborations landscape, we developed an analysis of the author's network, corroborating a low degree of connectivity and collaborations in this research topic. Considering that it is crucial to understand how microbial processes develop and change in arid soils, our analysis emphasizes the need to increase collaborations between research groups worldwide.

Detection of high-frequency mutant genes in extranodal NK/T cell lymphoma by next-generation sequencing technology and its clinical significance / 中国肿瘤生物治疗杂志

@# Objective: To analyze the mutation of target genes in extranodal natural killer/T-cell lymphoma (ENKTL) by using nextgeneration sequencing, and to explore its relationship with prognosis and clinical characteristics, as to provide evidence for the pathogenesis, clinical diagnosis and targeted therapy of ENKTL. Methods: According to previous literature reports, the genes whose mutations can affect the development of lymphoma were selected as the target genes for this study. 29 patients with ENKTL, who were newly diagnosed at the Fourth Hospital of Hebei Medical University from August 2010 to October 2018, were selected for this study. The mutation of 9 target genes in the specimen was detected by thenext-generationsequencingtechnology.Therelationshipsamongclinicalfeatures,diseaseprognosisandmutationofthetargetgeneswereanalyzedbySPSS21.0statisticalsoftware.Results： ：Ninetargetgenes were were screened. AT-rich interactive-domain 1A(ARID1A) gene showed the highest mutation rate in ENKTL (10 cases, 34.48%) followedbylysinemethyltransferase2D(KMT2D)gene(31.03%)andtumorprotein P53 (TP53) gene (24.13%). Kaplan-Meier survival analysis showed that the overall survival of ENKTL patients with KMT2D gene wild type was significantly better than patients with KMT2D gene mutation (P=0.006). The KMT2D gene mutation was found to besignificantlyrelatedtoclinicalstage,CRP,albumin,lymphocyte count and Ki67 expression in ENKTL patients (all P<0.05). COX regression analysis showed that KMT2D gene mutation was an independent adverse prognostic factor (P<0.05). Conclusion: The KMT2D gene has a high mutant frequency in ENKTL and is associated with patients’prognosis, suggesting that KMT2D gene plays an important role in the initiation and development of ENKTL. It could be used as a clinical therapeutic target for ENKTL.

Development status and clinical applications of precision detection technology in the times of precision oncology / 中国肿瘤生物治疗杂志

@#Precision detection techniques have promoted the development of individualized diagnosis and treatment of tumors in the era of precision medicine. At the same time, clinical demands of precision treatments have further driven the development and application of precision detection techniques. In recent years, precision medical detection techniques realized rapid transformations from low-throughput to high-throughput genomic sequencing, from tissue biopsies to liquid biopsies, and from multicell promiscuous detection to single cell precision sequencing. All these changes have promoted the emergence and development of new technologies, new targets, and new drugs in the era of precision oncology medicine. In the future, multi-dimensional combined detection could help to improve the accuracy of precision medicine; ctDNA methylation detection analysis could broaden the research field of precision medicine; and the transformation of clinical trial design could also contribute to promote the in-depth development of precision medicine.

Bioinformatics analysis of HLA-A2 restricted neoantigen epitopes in breast cancer / 中国肿瘤生物治疗杂志

@#[Abstract] Objective: To screen candidate epitopes of breast cancer HLA-A2 restrictive neoantigen and to identify high frequency mutation sites in breast cancer neoantigen by using bioinformatics method. Methods: NCBI and GDC databases were used to search missense mutation sites formed by single nucleotide mutation in breast cancer among reported literatures and sequencing data. The new antigen epitopes were predicted by HLA-A2 antigen epitope prediction website BIMAS, SYFPEITHI and artificial neural networkbased NetMHC4.0, and the epitopes with TAP binding power less than Intermediate were eliminated. The candidate epitopes were prioritized by mutation frequency and prediction results. Results: A total of 17 high-frequency mutation genes, including BTLA, ERBB2 and NBPF12 etc, were screened by the above-mentioned methods, and a total of 26 neoantigen epitopes were identified. The binding power of epitopes predicted using BIMAS and SYFPEITHI showed great difference (P<0.05), epitopes in high priority as GSTP1 (A114V , mutation frequency of 5.94%) and BRCA2 (N991H, mutation frequency of 5.40%) etc, were expected to be candidate neo-antigen epitopes; however, their mutation frequency was relatively too low to achieve“universal use” . The possibility of these epitopes used as general breast cancer neo-antigen epitopes is less likely. Conclusion: The common mutation frequency of breast cancer is lower than that of other tumors; it ’s difficult to find“universal”new antigen epitopes of breast cancer; the individualized neoantigen vaccine may be of more promise, which needs further research.

Plataformas de secuenciación de nueva generación y proteómica aplicadas a la virología vegetal: ¿Cómo ha avanzado Colombia? / Next generation sequencing and proteomics in plant virology: how is colombia doing?

ABSTRACT Crop production and trade are two of the most economically important activities in Colombia, and viral diseases cause a high negative impact to agricultural sector. Therefore, the detection, diagnosis, control, and management of viral diseases are crucial. Currently, Next-Generation Sequencing (NGS) and 'Omic' technologies constitute a right-hand tool for the discovery of novel viruses and for studying virus-plant interactions. This knowledge allows the development of new viral diagnostic methods and the discovery of key components of infectious processes, which could be used to generate plants resistant to viral infections. Globally, crop sciences are advancing in this direction. In this review, advancements in 'omic' technologies and their different applications in plant virology in Colombia are discussed. In addition, bioinformatics pipelines and resources for omics data analyses are presented. Due to their decreasing prices, NGS technologies are becoming an affordable and promising means to explore many phytopathologies affecting a wide variety of Colombian crops so as to improve their trade potential.

RESUMEN La producción y el comercio de cultivos es una de las actividades económicas más importantes para el país. Las enfermedades causadas por virus ocasionan graves pérdidas económicas en el sector, por lo tanto, la detección, diagnóstico y diseño de estrategias para su control y manejo es crucial. Las tecnologías de secuenciación masiva (NGS por sus siglas en ingles) y las ciencias Ómicas constituyen hoy, una herramienta para el descubrimiento de nuevos virus y para el estudio de la interacción entre los virus y su hospedero vegetal. Este conocimiento no solo permite el desarrollo de nuevos métodos de diagnóstico, sino también permite el descubrimiento de componentes claves en la infección, los cuales podrían usarse para obtener plantas resistentes a los virus. En el mundo, el manejo de cultivos se está trabajando con ese enfoque. Por lo tanto, en esta revisión se presentan las diferentes aplicaciones de las tecnologías ómicas en la virología de plantas y el avance que ha alcanzado Colombia. Adicionalmente, se muestran los diferentes recursos y programas usados para el análisis bioinformático de datos ómicos. Debido a su costo cada vez más reducido, las tecnologías NGS son una excelente oportunidad para explorar fitopatologías en una gran diversidad de productos agrícolas y para mejorar su potencial comercial.

COINFECCIÓN NATURAL DE VIRUS DE ARN EN CULTIVOS DE PAPA (Solanum tuberosum subsp. Andigena) EN ANTIOQUIA (COLOMBIA) / Natural coinfection of RNA viruses in potato (Solanum tuberosum subsp. Andigena) crops in Antioquia (Colombia)

RESUMEN Las enfermedades virales son uno de los principales problemas fitopatológicos de la papa. Con el fin de determinar los virus más prevalentes en cultivos de papa var. Diacol Capiro en el oriente Antioqueño (Colombia), se evaluó mediante RT-qPCR la presencia de diez virus de ARN (PVY, PVA, PVV, TaLMV, PVS, PLRV, PYVV, PVX, ToRSV y PMTV) en 36 muestras de tejido foliar. Los resultados indicaron la ocurrencia de cinco de los diez virus evaluados, con niveles de prevalencia de 88,9 %, 75 %, 75 %, 41,7 % y 25 % para PVY, PVX, PYVV, PLRV y PVS, respectivamente. Con fines comparativos, cuatro virus también se evaluaron mediante ELISA, siendo detectados PVS (80,5 %), PVY (55 %) y PLRV (5,5 %); mientras que PVX no fue encontrado con esta prueba. La comparación de estas técnicas mediante la razón de prevalencia (RP), indicó que la RT-qPCR ofrece niveles superiores de detección con valores de RP = 1,6 y RP = 7,5 para los virus PVY y PLRV; mientras que para PVS la ELISA detectó más muestras positivas que RT-qPCR (RP = 3,22), evidenciándose la necesidad de diseñar nuevos cebadores ajustados a la diversidad de este virus en Antioquia. La coinfección mixta más frecuente fue PVY-PYVV-PVX (22,2 %), mientras que los cinco virus se encontraron en el 11,1 % de las muestras. Finalmente, utilizando secuenciación Sanger de la cápside y NGS para los genomas completos, se confirmó la circulación de todos los virus detectados en los cultivos de papa del oriente Antioqueño. Estos resultados señalan la necesidad de fortalecer los programas de manejo integrado de enfermedades virales en Antioquia.

ABSTRACT Viral diseases are one of the main phytopathological problems affecting potato crops worldwide. To determine the most prevalent viruses in potato var. Diacol Capiro crops in Eastern Antioquia, 36 leaf samples were tested for the presence of PVY, PVA, PVV, TaLMV, PVS, PLRV, PYVV, PVX, ToRSV and PMTV using RT-qPCR. Detected viruses included PVY, PVX, PYVV, PLRV and PVS with prevalence levels of 88.9 %, 75.0 %, 75.0 %, 41.7 % and 25.0 %, respectively. PVS, PVY, PLRV and PVX were also tested by ELISA. PVS, PVY and PLRV tested positive in 80.5 %, 55.0 % and 5.5 % of samples; PVX was not detected. Prevalence Ratios (PR) suggests that detection is higher for PVY (PR = 1.6) and PLRV (PR = 7.5) using RT-qPCR. ELISA worked better for PVS with a PR of 3.2; this result suggests that the RT-qPCR primers used for PVS must be adjusted to reflect the genome diversity of virus in Antioquia. The most frequent coinfection was PVY-PYVV-PVX, which occurred in 22.2 % of samples; coinfection with PVY, PVX, PYVV, PLRV and PVS was present in 11.1 % of samples. The circulation of these viruses in Eastern Antioquia was further confirmed using Sanger and high-throughput sequence. This work highlights the need to strengthen integrated disease management programs of viruses in Antioquia.