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Rev. lab. clín ; 12(3): e40-e46, jul.-sept. 2019. tab
Artigo em Espanhol | LILACS-Express | ID: ibc-ET1-4170


El análisis de ADN circulante a partir de sangre periférica ha demostrado ser de utilidad en campos clínicos tan diferentes como la oncología, los trasplantes y el cribado prenatal. Para su incorporación al laboratorio clínico es necesario asegurar protocolos preanalíticos adecuados, reproducibles y estandarizados. En este documento se pretenden dar unas recomendaciones preanalíticas para la obtención de ADN circulante a partir de sangre periférica. Incluyen el tipo de espécimen, el tipo de tubo de extracción, el modo de centrifugación de la muestra, la extracción del ADN circulante y cuantificación, así como su conservación

Cell-free DNA analysis in peripheral blood has been shown to be useful in oncology, organ transplantation, and prenatal screening. For its introduction into the clinical laboratory, it is necessary to ensure appropriate, reproducible and standardised pre-analytical protocols are in place. The aim of this document is to provide pre-analytical recommendations for obtaining of cell free DNA from peripheral blood. These recommendations include the type of sample and extraction tube, the method of centrifugation, the method for cell free DNA extraction, and measurement and storage conditions

Clin Chem Lab Med ; 2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31469650


Background Non-small cell lung cancer (NSCLC) patients benefit from targeted therapies both in first- and second-line treatment. Nevertheless, molecular profiling of lung cancer tumors after first disease progression is seldom performed. The analysis of circulating tumor DNA (ctDNA) enables not only non-invasive biomarker testing but also monitoring tumor response to treatment. Digital PCR (dPCR), although a robust approach, only enables the analysis of a limited number of mutations. Next-generation sequencing (NGS), on the other hand, enables the analysis of significantly greater numbers of mutations. Methods A total of 54 circulating free DNA (cfDNA) samples from 52 NSCLC patients and two healthy donors were analyzed by NGS using the Oncomine™ Lung cfDNA Assay kit and dPCR. Results Lin's concordance correlation coefficient and Pearson's correlation coefficient between mutant allele frequencies (MAFs) assessed by NGS and dPCR revealed a positive and linear relationship between the two data sets (ρc = 0.986; 95% confidence interval [CI] = 0.975-0.991; r = 0.987; p < 0.0001, respectively), indicating an excellent concordance between both measurements. Similarly, the agreement between NGS and dPCR for the detection of the resistance mutation p.T790M was almost perfect (K = 0.81; 95% CI = 0.62-0.99), with an excellent correlation in terms of MAFs (ρc = 0.991; 95% CI = 0.981-0.992 and Pearson's r = 0.998; p < 0.0001). Importantly, cfDNA sequencing was successful using as low as 10 ng cfDNA input. Conclusions MAFs assessed by NGS were highly correlated with MAFs assessed by dPCR, demonstrating that NGS is a robust technique for ctDNA quantification using clinical samples, thereby allowing for dynamic genomic surveillance in the era of precision medicine.

Rev. lab. clín ; 12(1): 38-52, ene.-mar. 2019. tab, graf
Artigo em Espanhol | IBECS | ID: ibc-176973


Este documento describe las causas de error más frecuentes en la medición de marcadores tumorales séricos proteicos en sus diferentes fases: preanalítica, analítica y postanalítica y recomendaciones para detectar y solventar problemas, así como la interpretación de los resultados de los marcadores tumorales en la práctica clínica

This document describes the most frequent causes of error in the measurement of 13 serum protein tumour markers in their different phases: preanalytical, analytical and 14 postanalytic and recommendations to detect and solve problems, as well as the 15 interpretation of the results of the Tumor Markers in clinical practice

Humanos , Biomarcadores Tumorais/análise , Técnicas de Laboratório Clínico/métodos , Neoplasias/diagnóstico , Padrões de Prática Médica , Perfil de Impacto da Doença , Reprodutibilidade dos Testes , Coleta de Amostras Sanguíneas/normas , Preservação de Amostras/métodos
Pathol Res Pract ; 215(2): 392-394, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30392916


Genetic screening for BRCA mutations should be offered to all women diagnosed with epithelial ovarian, fallopian tube, and/or peritoneal cancers given the implications for treatment options and cancer risk assessments. Yet, while germline breast cancer susceptibility gene 1 (BRCA1) and breast cancer susceptibility gene 2 (BRCA2) testing is commonly performed, BRCA1/2 somatic mutations testing is rather challenging since the poor quality of DNA extracted from formalin fixed paraffin embedded (FFPE) samples can significantly impair this process. Peritoneal lavage is routinely performed in surgeries of suspected ovarian malignancies. We have analyzed fresh tumor, peritoneal lavage and blood samples from ten patients and we have found an excellent agreement (88%) between fresh tumor and peritoneal lavage for BRCA mutation testing. Importantly, 112 of the 114 genomic alterations detected in fresh tumor samples were also found in peritoneal lavage fluids. Our data suggest that peritoneal washings can indeed streamline BRCA genes mutation testing procedures.

Proteína BRCA1/genética , Proteína BRCA2/genética , Cistadenocarcinoma Seroso/genética , Análise Mutacional de DNA/métodos , Neoplasias Ovarianas/genética , Lavagem Peritoneal/métodos , Proteína BRCA1/análise , Proteína BRCA2/análise , Biomarcadores Tumorais/análise , Feminino , Humanos
Oncotarget ; 9(1): 488-494, 2018 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-29416630


Background: Circulating tumor DNA (ctDNA) levels correlate well with tumor bulk. In this paper we aim to estimate the prognostic value of the dynamic quantification of ctDNA levels. Materials and Methods: A total of 251 serial plasma samples from 41 non-small-cell lung cancer patients who carried an activating EGFR mutation were analysed by digital PCR. For survival analysis, ctDNA levels were computed as a time-dependent covariate. Results: Dynamic ctDNA measurements had prognostic significance (hazard ratio for overall survival and progression free survival according to p.T790M mutant allele frequency; 2.676 and 2.71 respectively; P < 0.05). In the same way, patients with p.T790M-negative or unchanging or decreasing plasma levels of sensitizing EGFR mutation were 12 and 4.8 times more likely to maintain response or stable disease, respectively, than patients in which the opposite occurred (P < 0.05).On average, the p.T790M mutation was detected in plasma 51 days before the assessment of progression disease by CT-scan. Finally, ctDNA outperformed CTCs for assessing tumor progression (P = 0.021). Conclusions: The appearance or increase in a unit of the p.T790M allele frequency almost triples the risk of death and progression. This information can be used to design clinical trials aiming to estimate whether T790M positive patients should start second line treatment based on molecular data rather than imaging data.

Oncotarget ; 8(36): 60291-60298, 2017 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-28947971


BACKGROUND: Liquid biopsy has evolved from being a promising line to becoming a validated approach for biomarker testing. However, its utility for individualization of therapy has been scarcely reported. In this study, we show how monitoring levels of EGFR mutation in plasma can be useful for the individualization of treatment. RESULTS: Longitudinal EGFR mutation levels in plasma always correlated with tumor response ascertained by RECIST criteria. Moreover, decreasing EGFR mutation levels were detected in all patients benefiting from locoregional radiotherapy, whereas the opposite occurred when a patient progressed soon after radiotherapy treatment. Similarly, increasing EGFR mutation levels anticipated disease progression after TKI dose reduction, discontinuation of treatment, or reduced bioavailability due to drug interactions. In addition, EGFR mutation levels were useful to monitor treatment outcome of new therapies and constituted a decisive factor when the clinical situation of the patient did not correlate with responses ascertained by radiologist. Finally, our results indicate that cancer associated body fluids (pleural, pericardial or cerebrospinal fluid) are certainly a suitable source for biomarker testing that can extend EGFR mutation detection to biofluids other than blood. MATERIALS AND METHODS: A total of 180 serial plasma samples from 18 non-small-cell lung cancer patients who carried an activating EGFR mutation were investigated by digital PCR. CONCLUSIONS: Monitoring levels of EGFR mutation in plasma allows resolving doubts that frequently arise in daily clinical practice and constitutes a major step towards achieving personalized medicine.

Transl Lung Cancer Res ; 5(6): 665-672, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28149760


BACKGROUND: The implementation of liquid biopsy for biomarker testing and response to treatment monitoring in cancer patients would presumable increase laboratory throughput, requiring the development of automated methods for circulating free DNA (cfDNA) isolation. METHODS: The present study compares the MagNA Pure Compact (MPC) Nucleic Acid Isolation Kit I and Maxwell® RSC (MR) ccfDNA Plasma Kit and the later with QIAamp Circulating Nucleid Acid (QCNA) Kit using 57 plasma samples from cancer patients. cfDNA concentration was measured using the Qubit fluorometer. DNA fragments lengt were assessed using the Agilent 2100 Bioanalyzer. Circulating tumor DNA (ctDNA) was quantified by digital PCR (dPCR). RESULTS: Firstly, we observed that MPC method significantly extracted less cfDNA than MR (P<0.0001). However, there were no significant differences in extraction yields of QCNA and MR kits. cfDNA isolation yield was also associated with tumor stage but not with tumor location. Secondly, an oligonucleosomal DNA ladder pattern was observed in 88% of the samples and significant differences in the recovery of mono-, di- and tri-nucleosomes DNA fragments were observed between MPC and MR methodologies. Finally, tumor mutation quantification on cfDNA was performed on 38 paired samples using digital PCR. Mutant allele fractions (MAFs) between paired samples were not significantly different. CONCLUSIONS: Methods for isolation of cfDNA can affect DNA yield and molecular weight fractions recovery. These observations should be taken into account for cfDNA analysis in routine clinical practice.