RESUMEN
Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA's results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es.
RESUMEN
Determinar las características clínicas, patológicas y evolución de pacientes con cáncer de mama hereditario y esporádico evaluados en un centro oncológico nacional. Material y métodos: Se realizó un estudio retrospectivo observacional en el Instituto Nacional de Enfermedades Neoplásicas (2009-2010) que evaluó las características clínicas, patológicas y sobrevida de 95 pacientes con cáncer de mama esporádico, y 59 casos con patrón hereditario diagnosticados en base a la historia familiar por el servicio de Genética. Resultados: La media de edad fue significativamente menor en los casos hereditarios que los esporádicos (53,5 vs. 44,8 años; p<0.001). Las pacientes con cáncer esporádico fueron diagnosticadas en estadios clínicos más avanzados debido a diferencias significativas en el tamaño tumoral. El fenotipo triple negativo fue más frecuente en los casos con patrón hereditario que los esporádicos (44.1 vs. 28.9%; p=0.036). La indicación de quimioterapia neoadyuvante fue significativamente mayor en el grupo esporádico. Las tasas de sobrevida libre de enfermedad y sobrevida global no alcanzaron significancia estadística. Conclusiones: Los casos de cáncer de mama hereditario presentan con mayor frecuencia fenotipo triple negativo y son diagnosticados a menor edad en promedio que los esporádicos. Las tasas de sobrevida global y sobrevida libre de enfermedad fueron similares entre ambos grupos.
Describe the clinicopathological characteristics and outcome in patients with hereditary and sporadic breast cancer selected from a national cancer center. Material and methods: We conducted a retrospective observational study at the Instituto Nacional de Enfermedades Neoplásicas (2009-2010), including 95 sporadic and 59 hereditary breast cancer patients. They were diagnosed on basis of their family history by the Department of Genetics. Results: The median age at diagnosis of hereditary cases were significant lower than sporadic (53,5 vs. 44,8 years; p=<0.001). Sporadic cancer patients were diagnosed at more advanced stage mainly because of an increased tumor size. Triple-negative cases were statistically more common in the hereditary than sporadic group (44.1 vs. 28.9%; p=0.036). Indication for neoadjuvant chemotherapy was more frecuent in sporadic cases. Overall survival and disease-free survival did not reach statistical significance. Conclusions: Hereditay breast cancer tumors preferentially show a triple negative phenotype and patients are diagnosed at younger age than sporadic cases. Overall survival and disease-free survival were both similar between the two groups.
