DPYD genotyping and 5-fluoropyrimidine toxicity: An overview of systematic reviews protocol. / [Artículo traducido] Genotipado del gen DPYD y toxicidad de las 5-fluoropirimidinas: protocolo de un resumen de revisiones sistemáticas.

INTRODUCTION: The increased risk of severe and life-threatening toxicity in patients with dihydropyridine dehydrogenase deficiency, under treatment with fluoropyrimidines, has been widely studied. An up-to-date overview of systematic reviews summarizing existing literature can add value by highlighting most relevant information and supports decision-making regarding treatment in dihydropyridine dehydrogenase deficient patients. The main objective of this overview is to identify published systematic reviews on the association between germline variations in the DPYD gene and fluoropyrimidine toxicity. METHODS AND ANALYSIS: This protocol was developed following the Preferred Reported Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) checklist, and the overview of systematic reviews will be reported in accordance with the PRISMA statement. PubMed, Embase, Scopus and the Cochrane Library will be searched from inception to 2023. Systematic reviews irrespective of study designs that analyze the association between germline variations in the DPYD and fluoropyrimidine toxicity will be considered. Methodological quality will be assessed using AMSTAR2 checklist (Measurement Tool to Assess Systematic Reviews 2). Two independent investigators will perform the study selection, quality assessment and data collection. Discrepancies will be solved by a third investigator.

DPYD genotyping and 5-fluoropyrimidine toxicity: An overview of systematic reviews protocol.

INTRODUCTION: The increased risk of severe and life-threatening toxicity in patients with dihydropyridine dehydrogenase (DPD) deficiency, under treatment with fluoropyrimidines, has been widely studied. An up-to-date overview of systematic reviews summarizing existing literature can add value by highlighting most relevant information and supports decision-making regarding treatment in DPD deficient patients. The main objective of this overview of systematic reviews is to identify published systematic reviews on the association between germline variations in the DPYD gene and fluoropyrimidine toxicity. METHODS AND ANALYSIS: This protocol was developed following the Preferred Reported Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) checklist, and the overview of systematic reviews will be reported in accordance with the PRISMA statement. PubMed, Embase, Scopus, and the Cochrane Library will be searched from inception to 2023. Systematic reviews irrespective of study designs that analyze the association between germline variations in the DPYD and fluoropyrimidine toxicity will be considered. Methodological quality will be assessed using AMSTAR2 checklist (Measurement Tool to Assess Systematic Reviews 2). Two independent investigators will perform the study selection, quality assessment, and data collection. Discrepancies will be solved by a third investigator. REGISTRATION DETAILS: Registration number in PROSPERO: CRD42023401226.

Comparative pilot study about HPV test with partial genotyping in primary screening versus other strategies for cervical cancer population screening, CRYGEN 16/18 study.

INTRODUCTION: The early detection of cervical cancer requires the implementation of molecular screening programmes for human papillomavirus (HPV). However, there are discrepancies in the optimization of screening protocols. The performance of 10 primary screening strategies based on molecular, cytological or combined techniques is now evaluated. MATERIAL AND METHODS: A blind, prospective, and interventional study was designed in 1.977 35-year-old women. The molecular determination was carried out by the Cobas 4800 HPV platform. Cytological analysis were performed on the same samples without knowledge of the result of the molecular assay. All women in whom HPV-16/HPV-18 was detected or presented cytological alteration together with detection of other high-risk genotypes (HPVhr) were referred to colposcopy. RESULTS: The molecular assay detected the presence of HPVhr genotypes in 12.5% of the women, while only 8.1% of the cytologies were pathological. Among the patients referred to colposcopy, in 19.5% high-grade lesions were observed, being HPV-16 present in 65.3% of them. In six of these high-grade lesions (associated with HPV-16 in all cases), cytology was reported as normal. The follow-up one year later, of women with normal cytology and HPVhr detection a HSIL/CIN2+ lesion was detected (associated to HPV-33). In the comparative study with other strategies, the protocol called CRYGEN 16/18 yielded the best balance of sensitivity and specificity with the least referral to colposcopy. CONCLUSIONS: Performing molecular detection of HPVhr with partial first-line genotyping of at least HPV-16, with direct referral to colposcopy, increases the detection rate of HSIL/CIN2+ lesions.

COMPARACIÓN MORFO-AGRONÓMICA Y MOLECULAR DE CATORCE VARIEDADES DE ARROZ (Oryza sativa) CON LAS LÍNEAS QUE DIERON SU ORIGEN / Morpho-agronomic and molecular comparison of fourteen varieties of rice (Oryza sativa) with the lines that gave them the origin

RESUMEN Con el objetivo de determinar las diferencias morfo-agronómicas y de calidad, y la diversidad genética entre 14 variedades de arroz de América Latina con sus respectivas líneas de origen, se estableció un estudio (Bloques completos al azar, con 28 genotipos, tres repeticiones y dos siembras en el tiempo), en el cual se midieron 25 variables morfo-agronómicas y de calidad de grano. El análisis molecular se hizo mediante un arreglo de 96 marcadores tipo SNP de alta capacidad de discriminación para arroces Indica. El análisis estadístico se hizo combinando los datos de las dos siembras porque no hubo diferencias estadísticas entre ellas. Además, se analizaron en conjunto los datos moleculares con los morfo-agronómicos y de calidad, usando el índice de Gower para generar una matriz de similitud. Mediante el programa SAS se analizaron los datos agronómicos y moleculares tanto en forma independiente como en conjunto. Los resultados mostraron que, de las 14 variedades, ocho se agruparon con su línea de origen y hubo una variedad que se agrupó con una línea hermana de su ancestro. Los resultados fueron consistentes cuando el análisis de datos se hizo independientemente o combinado. Dada la amplia diversidad encontrada dentro de las variedades y que ninguna fue homocigota al 100 % no se pudieron establecer los perfiles genéticos distintivos de ellas, por lo que se debe hacer la purificación de las variedades para establecer su huella genética.

ABSTRACT This research aimed to determine the morpho-agronomic, grain quality, and molecular differences between 14 rice varieties and their ancestors. These rice varieties from Latin America were tested for 25 variables in a randomized complete block design with 28 genotypes, two planting dates, and three replications. The molecular analysis was done using an array of 96 SNP markers with a high discrimination capacity for Indica rice. A combined statistical analysis was done because there were no statistical differences between the planting dates. Also, molecular, morpho-agronomic, and grain quality data were analyzed together, using the Gower index to generate a similarity matrix. Agronomic and molecular data were analyzed both, together and independently, through the SAS program. Results showed that eight varieties were grouped with their respective ancestor, and one variety was grouped with a sibling of their ancestor and was consistent in all the analyses. However, given the wide heterozygosity found within the varieties, distinctive genetic profiles could not be established; the varieties must be purified to establish their genetic footprint.

Diversidad genética de Mycobacterium tuberculosis circulando en la jurisdicción V de Jalapa, Veracruz, México / Genetic diversity of Mycobacterium tuberculosis circulating in the jurisdiction V from Jalapa, Veracruz, Mexico

ANTECEDENTES: El estado de Veracruz se ubica en el sureste de México y presenta una alta prevalencia de tuberculosis (TBC) y drogo resistencia. Sin embargo, la composición de los genotipos circulantes es poco conocida. OBJETIVO: Caracterizar la diversidad genética de la TBC en la jurisdicción sanitaria V del estado de Veracruz. MÉTODOS: Estudio transversal realizado en aislados clínicos de pacientes con TBC residentes de la jurisdicción V. Se determinó la sensibilidad a medicamentos de primera línea. La genotipificación se realizó mediante espoligotipificación y MIRU-VNTR 15 loci. RESULTADOS: Entre los 74 aislados analizados se observó resistencia a un fármaco en 44 (59%) aislados. Linaje L4 (EuroAmericano) se presentó en 73 aislados. Se identificaron cinco sublinajes; H (40%), T (22%), LAM (16%), X (13%) y U (7%). El 32% de los aislados se agrupó mediante su espoligotipo y 40% en 10 complejos clonales. CONCLUSIONES: Es la primera descripción sobre la estructura genética de TBC en la región central de Veracruz. La diversidad de genotipos podría contribuir a su dispersión en la región. Esta información será útil para el desarrollo de intervenciones y reducir el impacto de TBC en la población.

BACKGROUND: The state of Veracruz is placed in southeastern Mexico and has a high prevalence of tuberculosis (TB) and drug resistance. Nevertheless, the composition of circulating genotypes in the central region of the state is partially known. AIM: To characterize the genetic diversity of TB in the sanitary jurisdiction V of the state of Veracruz. METHODS: A cross-sectional study was conducted among clinical isolates from patients with TB living in the jurisdiction V, in Jalapa Ver., Mexico. Sensitivity to first-line drugs was determined, and genotyping was performed by spoligotyping and MIRU-VNTR 15 loci. RESULTS: Among the 74 isolates analyzed, resistance to one drug was observed in 44 isolates. L4 (EuroAmerican) was the major lineage identified. Five sublineages were the most abundant; H (40%), T (22%), LAM (16%), X (13%) and U (7%). Only 32% of the isolates were clustered by spoligotype and 40% were placed in ten clonal complexes. CONCLUSIONS: This is the first description of the genetic structure of TB in the central region of Veracruz. The diversity of genotypes could contribute to its dispersion. This information will be useful for the development of interventions to reduce the impact of TB in the population.

Comparative pilot study about HPV test with partial genotyping in primary screening versus other strategies for cervical cancer population screening, CRYGEN 16/18 study. / Estudio piloto comparativo del test VPH con genotipado parcial en primera línea frente a otras estrategias de cribado poblacional del cáncer de cérvix. Estudio CRYGEN 16/18.

INTRODUCTION: The early detection of cervical cancer requires the implementation of molecular screening programs for human papillomavirus (HPV). However, there are discrepancies in the optimization of screening protocols. The performance of 10 primary screening strategies based on molecular, cytological or combined techniques is now evaluated. MATERIAL AND METHODS: A blind, prospective, and interventional study was designed in 1977 35-year-old women. The molecular determination was carried out by the Cobas 4800 HPV platform. Cytological analysis was performed on the same samples without knowledge of the result of the molecular assay. All women in whom HPV-16/HPV-18 was detected or presented cytological alteration together with detection of other high-risk genotypes (HPVhr) were referred to colposcopy. RESULTS: The molecular assay detected the presence of HPVhr genotypes in 12.5% of the women, while only 8.1% of the cytologies were pathological. Among the patients referred to colposcopy, in 19.5% high-grade lesions were observed, being HPV-16 present in 65.3% of them. In six of these high-grade lesions (associated with HPV-16 in all cases), cytology was reported as normal. The follow-up one year later, of women with normal cytology and HPVhr detection a HSIL/CIN2+ lesion was detected (associated to HPV-33). In the comparative study with other strategies, the protocol called CRYGEN 16/18 yielded the best balance of sensitivity and specificity with the least referral to colposcopy. CONCLUSIONS: Performing molecular detection of HPVhr with partial first-line genotyping of at least HPV-16, with direct referral to colposcopy, increases the detection rate of HSIL/CIN2+ lesions.

Tipificación molecular de Mycobacterium avium subsp. paratuberculosis en lecherías de Antioquia, Colombia

RESUMEN Objetivo. Determinar la diversidad molecular de Mycobacterium avium subsp. paratuberculosis (MAP) en muestras ambientales de hatos lecheros colombianos. Materiales y métodos. Las muestras ambientales de 25 hatos lecheros positivos a MAP por IS900-qPCR se cultivaron por duplicado en medio de yema de huevo de Herrold con micobactina J para obtener aislamientos. Las colonias sospechosas fueron confirmadas para MAP por IS900-qPCR. El ADN positivo se subtipó utilizando técnicas de unidades micobacterialess repetitivas intercaladas - número variable de repeticiones en tándem (MIRU-VNTR) y técnicas de repeticiones de multilocus de secuencia corta (MLSSR) para analizar las diferencias genéticas entre los aislamientos. Resultados. El subtipado reveló dos genotipos diferentes por MIRU-VNTR (INMV 2 e INMV 36). La técnica de MLSSR se realizó para aumentar el poder discriminatorio de lo obtenido por MIRU-VNTR, pero no se observaron diferencias entre los aislamientos recuperados. Conclusiones. El presente estudio representa un enfoque importante para el conocimiento del estatus epidemiológico de MAP en la población de estudio.

ABSTRACT Objective. To determine Mycobacterium avium subsp. paratuberculosis (MAP) molecular diversity in environmental samples from Colombian dairy herds. Materials and methods. Environmental samples from 25 IS900-qPCR MAP-positive dairy herds were cultured by duplicate in Herrold's egg yolk medium with mycobactin J to obtain isolates. Suspicious colonies were confirmed by MAP-IS900-qPCR. Positive DNA was sub-typed using mycobacterial interspersed repetitive units-variable number of tandem repeat (MIRU-VNTR) and multilocus short sequence repeats (MLSSR) techniques to analyze the genetic differences between the isolates. Results. Sub-typing revealed two different genotypes by MIRU-VNTR (INMV 2 and INMV 36). MLSSR technique was carried out to increase the discriminatory power from what was obtained by MIRU-VNTR, but no differences were observed among the recovered isolates. Conclusions. The present study represents an important approach to the knowledge on MAP epidemiological status in the study population.

¿Permiten la citología, el genotipado y la anoscopia de alta resolución establecer un protocolo para la detección precoz del carcinoma epidermoide de canal anal en población de riesgo? / Do cytology, genotyping, and high resolution anoscopy allow to establish a protocol for early detection of squamous cell carcinoma of the anal canal in risk population?

Introducción: El cáncer anal ha experimentado un aumento de incidencia en los últimos años. Está mediado por el VPH y precedido de cambios precancerosos planteando la posibilidad de dirigir los esfuerzos preventivos hacia los grupos de alto riesgo. Sigue siendo controvertida la indicación de cribado y los métodos de detección ideales. Objetivo: Validar las pruebas de cribado implementadas en la actualidad comparadas con la biopsia como "gold standard". Material y Métodos: Estudio transversal con recogida de datos prospectiva, en una cohorte de hombres VIH+ que tienen sexo con hombres, pertenecientes al Hospital Gregorio Marañón e Infanta Leonor en un periodo de 2 años. Resultados: Se seleccionaron 179 pacientes con 286 visitas a la consulta de screening en las que se llevaron a cabo 3 pruebas de cribado en paralelo (citología anal, genotipado del VPH y anoscopia de alta resolución (AAR) con toma de biopsia dirigida sobre zona sospechosa o aleatoria). La sensibilidad y especificidad para la detección de displasia de alto grado y cáncer y su grado de concordancia con la biopsia fue la siguiente: citología 3,23%/94,43% (k: 0,03), genotipado de VPH de alto riesgo 90,32%/27,45% (k: 0,05), AAR 32,26%/87,45 (k: 0, 17) siendo el rendimiento diagnóstico de las tres pruebas muy bajo. Conclusión: La citología presenta un rendimiento diagnóstico muy bajo comparado con el genotipado que representa el mayor. A la luz de nuestros resultados, los protocolos clínicos tal y como vienen desarrollándose en la actualidad deberían de ser abandonados.

Introduction: The incidence of anal cancer has increased in recent years. It is mediated by HPV and preceded by precancerous changes, raising the possibility of directing preventive efforts towards high-risk groups. The indication of screening remains controversial and which methods would be the ideal ones. Objective: To validate the screening tests established actually, comparing it with the biopsy considered as the "gold standard". Materials and Methods: A cross-sectional study was performed, with prospective data collection in a cohort of VIH+ patients, who have male homosexual anal relations, belonging to Gregorio Marañón and Infanta Leonor Hospitals in a period of 2 years. Results: A total of 179 patients were selected with 286 visits to the screening Outpatient Clinic in which 3 parallel screening tests were performed (anal cytology, HPV genotyping and high resolution anoscopy (AAR) with a biopsy directed on a suspicious or random area). The sensitivity and specificity for the detection of high-grade dysplasia and cancer and their degree of agreement with the biopsy was as follows: cytology 3.23%/94.43% (k: 0.03), high HPV genotyping. risk 90.32%/27.45% (k: 0.05), AAR 32.26%/87.45 (k: 0, 17), the diagnostic accuracy of the three tests being very low. Conclusion: Cytology shows a very low diagnostic accuracy compared to the genotype that represents the highest one. In light of our results, clinical protocols as they are currently being developed should be abandoned.