RESUMEN
BACKGROUND: Commercial targeted genomic profiling with next generation sequencing using formalin-fixed paraffin embedded (FFPE) tissue has recently entered into clinical use for diagnosis and for the guiding of therapy. However, there is limited independent data regarding the accuracy or robustness of commercial genomic profiling in gliomas. METHODS: As part of patient care, FFPE samples of gliomas from 71 patients were submitted for targeted genomic profiling to one commonly used commercial vendor, Foundation Medicine. Genomic alterations were determined for the following grades or groups of gliomas; Grade I/II, Grade III, primary glioblastomas (GBMs), recurrent primary GBMs, and secondary GBMs. In addition, FFPE samples from the same patients were independently assessed with conventional methods such as immunohistochemistry (IHC), Quantitative real-time PCR (qRT-PCR), or Fluorescence in situ hybridization (FISH) for three genetic alterations: IDH1 mutations, EGFR amplification, and EGFRvIII expression. RESULTS: A total of 100 altered genes were detected by the aforementioned targeted genomic profiling assay. The number of different genomic alterations was significantly different between the five groups of gliomas and consistent with the literature. CDKN2A/B, TP53, and TERT were the most common genomic alterations seen in primary GBMs, whereas IDH1, TP53, and PIK3CA were the most common in secondary GBMs. Targeted genomic profiling demonstrated 92.3%-100% concordance with conventional methods. The targeted genomic profiling report provided an average of 5.5 drugs, and listed an average of 8.4 clinical trials for the 71 glioma patients studied but only a third of the trials were appropriate for glioma patients. CONCLUSIONS: In this limited comparison study, this commercial next generation sequencing based-targeted genomic profiling showed a high concordance rate with conventional methods for the 3 genetic alterations and identified mutations expected for the type of glioma. While it may not be feasible to exhaustively independently validate a commercial genomic profiling assay, examination of a few markers provides some reassurance of its robustness. While potential targeted drugs are recommended based on genetic alterations, to date most targeted therapies have failed in glioblasomas so the usefulness of such recommendations will increase with development of novel and efficacious drugs.
Asunto(s)
Formaldehído/química , Perfilación de la Expresión Génica , Genómica , Glioma/diagnóstico , Parafina/química , Adolescente , Adulto , Anciano , Neoplasias Encefálicas/diagnóstico , Neoplasias Encefálicas/genética , Fosfatidilinositol 3-Quinasa Clase I , Receptores ErbB/genética , Receptores ErbB/metabolismo , Femenino , Glioma/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Inmunohistoquímica , Hibridación Fluorescente in Situ , Isocitrato Deshidrogenasa/genética , Isocitrato Deshidrogenasa/metabolismo , Masculino , Persona de Mediana Edad , Mutación , Fosfatidilinositol 3-Quinasas/genética , Fosfatidilinositol 3-Quinasas/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/metabolismo , Adulto JovenRESUMEN
Cerebrospinal fluid (CSF) is a physiologically essential fluid produced by the brain that is involved in protecting the brain and in the exchange of nutrients and waste products. CSF has long been utilized to confirm clinical suspicion of various infectious and inflammatory disorders, such as meningitis and multiple sclerosis. However, there has been increasing interest in collecting CSF in order to study the clinical significance of additional biomarkers. This chapter outlines the procedures necessary to collect, process, store, and utilize CSF obtained for the purposes of biobanking from both living and deceased patients.
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Bancos de Muestras Biológicas , Biomarcadores/líquido cefalorraquídeo , Líquido Cefalorraquídeo/química , Manejo de Especímenes/métodos , Encéfalo/patología , Humanos , Meningitis/líquido cefalorraquídeo , Meningitis/patología , Esclerosis Múltiple/líquido cefalorraquídeo , Esclerosis Múltiple/patologíaRESUMEN
An autopsy is a specialized surgical procedure consisting of external and internal examination of a deceased individual for the purposes of documenting abnormalities and determining or confirming medical diagnoses that may have contributed to their death. One of the benefits of an autopsy is the opportunity to collect and store biospecimens for the purposes of biobanking. This chapter outlines the procedures necessary to procure, store, and utilize biospecimens obtained during an autopsy. With the emergence of molecular diagnostics, this chapter also discusses factors that influence the integrity of autopsy biospecimens prior to procurement. These include the postmortem interval, as well as premortem factors such as the patient's agonal state, biospecimen temperature, and pH.
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Autopsia/tendencias , Bancos de Muestras Biológicas/tendencias , Patología Molecular/tendencias , Manejo de Especímenes/tendencias , Humanos , Control de Calidad , Manejo de Especímenes/métodos , TemperaturaRESUMEN
The packaging and shipment of biospecimens is a multistep process for which a distinct set of regulations needs to be followed, depending on whether a biospecimen is shipped domestically or internationally and whether the shipment contains hazardous materials. Shipments may be delayed if these regulations are not followed. Once learned, the process is straightforward. Major principles include double or triple packaging, adequate absorbent material, appropriate coolant, accurate labeling, and complete documentation. Training in packaging and shipping is often offered at major biomedical institutions and is a requirement to avoid shipping biohazards.