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Find video protocols related to scientific articles indexed in Pubmed.
Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients.
J. Clin. Pathol.
PUBLISHED: 11-08-2014
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To evaluate the accuracy, consumable cost and time around testing (TAT) of a next-generation sequencing (NGS) assay, the Ion Torrent AmpliSeq Colon and Lung Cancer Panel, as an alternative to Sanger sequencing to genotype KRAS, NRAS and BRAF in colorectal cancer patients.
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Effects of combined administration of rapamycin, tolvaptan, and AEZ-131 on the progression of polycystic disease in PCK rats.
Am. J. Physiol. Renal Physiol.
PUBLISHED: 03-19-2014
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Both experimental and clinical studies have suggested that any potential treatment of polycystic kidney disease (PKD) should start early and last for a long time to be effective, with unavoidable side reactions and considerable costs. The aim of the present study was to test how low doses of rapamycin (RAPA; 0.15 mg/kg ip for 4 days/wk), tolvaptan (TOLV; 0.005% in diet), or AEZ-131 (AEZ; a novel ERK inhibitor, 30 mg/kg for 3 days/wk by gavage), alone and in association, affect the progression of polycystic renal disease in PCK rats. Rats were treated for 8 wk starting at 4-6 wk of age. The efficacy of low doses of such drugs in inhibiting their respective targets was confirmed by immunoblot experiments. Compared with rats in the control (CON) group, RAPA treatment caused a significant reduction in cyst volume density (CVD; -19% vs. the CON group) and was numerically similar to that in TOLV-treated rats (-18%, not significiant), whereas AEZ treatment was not effective. RAPA + TOLV treatment resulted in a significantly lower CVD (-49% vs. the CON group) and was associated with a striking decrease in cAMP response element-binding protein phosphorylation, and similar data were detected in RAPA + AEZ-treated rats (-42%), whereas TOLV + AEZ treatment had virtually no effect. RAPA administration significantly lessened body weight gain, whereas TOLV administration resulted a mild increase in diuresis and a significant increase in cAMP urinary excretion. Histological data of tubular proliferation were in full agreement with CVD data. In conclusion, this study demonstrates that the association of low doses of RAPA, TOLV, and AEZ slows the progression of PKD with limited side effects, suggesting the use of combined therapies also in clinical trials.
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EGFR analysis: Current evidence and future directions.
Diagn. Cytopathol.
PUBLISHED: 01-10-2014
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Until a few years ago, only lung cancer histological specimens were considered suitable for testing epidermal growth factor receptor (EGFR) mutations. Then, several retrospective studies were designed to test EGFR mutation on a sizeable number of parallel cytological and histological samples obtained from the same patients and, even more recently, several institutions reported their prospective clinical experiences on routine specimens. Basing on these studies the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology have recently considered cytological samples suitable for EGFR testing. Therefore, it seems timely to draw together the threads of this large body of information in order that cytopathologists can be knowledgeable partners in the multidisciplinary process of targeted cancer therapy and to help refine current testing guidelines. This review addresses (1) the more common proposed techniques including the use of direct cytologic smears cell blocks and liquid based cytology; (2) the issues related to current practice, which in Europe is external centralized testing that is usually done on samples containing very few cells; and (3) the future directions based on the implementation on lung cytology of next generation sequencing approaches. Diagn. Cytopathol. 2014;42:984-992. © 2014 Wiley Periodicals, Inc.
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Applications and limitations of oncogene mutation testing in clinical cytopathology.
Semin Diagn Pathol
PUBLISHED: 11-12-2013
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In an increased number of settings, cytology represents the only source of sampling and it often substitutes histology as an independent diagnostic modality. Thus, DNA molecular targets to stratify patients for targeted therapy are often evaluated on cytology. In addition, DNA mutational tests may refine indeterminate thyroid and pancreas cytology. This review discusses the applications and limitations of DNA mutational testing on cytology. With respect to histology, most cytological samples have the advantages of a purer population of tumor cells, with low stromal component, a better preserved DNA, and assessing at the same time of sample collection cellular adequacy for DNA testing. However, since in vitro diagnostic tests are licensed only for paraffin-tissue, all mutational assays on cytology are "home brew," requiring a rigorous validation process. This should take into account not only the performance characteristics of the molecular assay but also features inherent to any given cytological samples, such as its source, preparation type, fixation and staining modalities, and the most effective tumor cell enrichment methods. This calls for a change of cytotechnologists and cytopathologists mentality to collect and process the cytological samples not only for microscopy but also to assess clinically relevant molecular markers.
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KRAS testing in metastatic colorectal carcinoma: challenges, controversies, breakthroughs and beyond.
J. Clin. Pathol.
PUBLISHED: 09-10-2013
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Metastatic colorectal cancer harbouring a mutation in codon 12 or 13 of the KRAS gene does not benefit from therapy with antibodies targeting the epidermal growth factor receptor (EGFR). The implementation of community KRAS testing is generating a rapid flow of new data that have implications for the pathologist and testing guidelines besides the physician. Therefore, it seems timely to draw together the threads of this large body of information in order that pathologists can be knowledgeable partners in the multidisciplinary process of targeted cancer therapy and to help refine current testing guidelines. This review addresses (1) the most relevant methodological and technical aspects of KRAS testing in terms of sample site (primary/metastatic), test specimens (resection/biopsy/cytology) and the diverse molecular methods available; (2) the issues related to daily practice, namely, the timing of the test, its turnaround time and the quality control procedures; and (3) the evidence related to the relationship between KRAS genetic intratumoural heterogeneity, clinical sensitivity of mutational detection tools and anti-EGFR treatment outcome. Hopefully, in the near future, elucidation of the potential of biomarker panels and of the mechanisms underlying primary and acquired resistance to anti-EGFR therapy will refine even further personalised treatment regimens for patients with metastatic colorectal cancer.
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Cytologically undetermined thyroids follicular lesions: surgical procedures and histological outcome in 472 cases.
Ann Ital Chir
PUBLISHED: 08-24-2013
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Fine needle cytology (FNC) of thyroid nodules is not always diagnostic. Most of FNCs undeterminated for malignancy belong to the cytological class of "follicular neoplasm/suspicious for follicular neoplasm" lesions (FN). In this group only 10-30% of cases are malignant and the most appropriate surgical management is still controversial. Here, this issue was addressed and the more reliable predictive criteria of malignancy were also evaluated.
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EGFR mutation detection by microfluidic technology: a validation study.
J. Clin. Pathol.
PUBLISHED: 06-21-2013
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Advanced non-small cell lung cancer samples are tested for epidermal growth factor receptor (EGFR) gene mutations. Their detection by direct sequencing is time-consuming. Conversely, the length analysis of fluorescently labelled PCR products is easier. To avoid labelled primers and the automated capillary electrophoresis apparatus, we validated a fast and sensitive chip-based microfluidic technology. The limit of detection of fragment length assay on microfluidic device was 5%, more sensitive than direct sequencing (12.5%). The novel methodology showed high accuracy in the analysis of samples whose mutational status was known. The accuracy in quantifying mutated alleles (mA) was evaluated by PCR products subcloning; the mA% provided by direct sequencing of subcloned PCR products showed a close correlation with the mA% provided by the microfluidic technology for both exon 19 (R(2)=0.9) and 21 (R(2)=0.9). Microfluidic-based on-chip electrophoresis makes EGFR testing more rapid, sensitive and cost-effective.
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Warthin tumor with signet-ring cell features as a pitfall in salivary gland cytopathology.
Acta Cytol.
PUBLISHED: 01-16-2013
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Warthin tumor (WT) is a common parotid lesion reliably diagnosed by fine-needle aspiration (FNA). Worrisome metaplastic changes may occur in WT. Their interpretation as mucoepidermoid carcinoma represents a diagnostic pitfall. Moreover, WT and mucoepidermoid carcinoma may coexist, making this distinction difficult. So it is worthwhile to report unusual WT features. We describe a WT with signet-ring cells (SRCs).
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EGFR mutations detected on cytology samples by a centralized laboratory reliably predict response to gefitinib in non-small cell lung carcinoma patients.
Cancer Cytopathol
PUBLISHED: 01-11-2013
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Epidermal growth factor receptor (EGFR) mutations are reliably detected by referral laboratories, even if most lung cancer cytology specimens sent to such laboratories contain very few cells. However, EGFR mutations may be distributed heterogeneously within tumors, thereby raising concerns that mutations detected on cytology are not representative of the entire tumor and, thus, are less reliable in predicting response to tyrosine kinase inhibitor (TKI) treatment than mutations detected on histology. To address this issue, the authors reviewed their clinical practice archives and compared the outcome of TKI treatment among patients who were selected by cytology versus patients who were selected by histology.
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Next-Generation Sequencing of Lung Cancer EGFR Exons 18-21 Allows Effective Molecular Diagnosis of Small Routine Samples (Cytology and Biopsy).
PLoS ONE
PUBLISHED: 01-01-2013
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Selection of lung cancer patients for therapy with tyrosine kinase inhibitors directed at EGFR requires the identification of specific EGFR mutations. In most patients with advanced, inoperable lung carcinoma limited tumor samples often represent the only material available for both histologic typing and molecular analysis. We defined a next generation sequencing protocol targeted to EGFR exons 18-21 suitable for the routine diagnosis of such clinical samples. The protocol was validated in an unselected series of 80 small biopsies (n=14) and cytology (n=66) specimens representative of the material ordinarily submitted for diagnostic evaluation to three referral medical centers in Italy. Specimens were systematically evaluated for tumor cell number and proportion relative to non-neoplastic cells. They were analyzed in batches of 100-150 amplicons per run, reaching an analytical sensitivity of 1% and obtaining an adequate number of reads, to cover all exons on all samples analyzed. Next generation sequencing was compared with Sanger sequencing. The latter identified 15 EGFR mutations in 14/80 cases (17.5%) but did not detected mutations when the proportion of neoplastic cells was below 40%. Next generation sequencing identified 31 EGFR mutations in 24/80 cases (30.0%). Mutations were detected with a proportion of neoplastic cells as low as 5%. All mutations identified by the Sanger method were confirmed. In 6 cases next generation sequencing identified exon 19 deletions or the L858R mutation not seen after Sanger sequencing, allowing the patient to be treated with tyrosine kinase inhibitors. In one additional case the R831H mutation associated with treatment resistance was identified in an EGFR wild type tumor after Sanger sequencing. Next generation sequencing is robust, cost-effective and greatly improves the detection of EGFR mutations. Its use should be promoted for the clinical diagnosis of mutations in specimens with unfavorable tumor cell content.
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PAX8 is expressed in anaplastic thyroid carcinoma diagnosed by fine-needle aspiration: a study of three cases with histological correlates.
Eur. J. Endocrinol.
PUBLISHED: 01-01-2013
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It is difficult to diagnose anaplastic thyroid carcinoma (ATC) in a fine-needle aspiration (FNA) sample because, given the loss of morphological and immunophenotypical follicular thyroid features, its cytology resembles that of other undifferentiated neoplasms. Recent studies have shown that immunostaining for paired box gene 8 (PAX8), a transcription factor expressed in normal thyroid, is effective for diagnosing ATCs on histology. The aim of this study was to evaluate whether PAX8 could be used to identify ATCs on cytology also.
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EGFR and KRAS mutations detection on lung cancer liquid-based cytology: a pilot study.
J. Clin. Pathol.
PUBLISHED: 09-22-2011
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In advanced non-small-cell lung carcinomas epidermal growth factor receptor (EGFR) and KRAS testing is often performed on cytology. Liquid-based cytology (LBC), which eliminates the need for slide preparation by clinicians, may be very useful. In 42 LBC DNA was extracted twice. One sample was obtained directly from CytoLyt solution, whereas the other DNA sample was derived after smear preparation and laser capture microdissection (LCM) of Papanicolaou-stained cells. EGFR and KRAS mutational analyses were performed by direct sequencing. On CytoLyt-derived DNA four EGFR (9%) and five KRAS (12%) gene mutations were found. When direct sequencing was performed after LCM, the rate of cases that displayed either EGFR or KRAS mutations increased from 21% to 40%. Although time-consuming, LCM makes direct sequencing highly sensitive even on LBC preparations containing only a few cells.
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Multicentric encapsulated papillary oncocytic neoplasm of the thyroid: A case diagnosed by a combined cytological, histological, immunohistochemical, and molecular approach.
Diagn. Cytopathol.
PUBLISHED: 06-03-2011
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Fine-needle aspiration (FNA) diagnosis of oncocytic lesions is challenging. In fact, oncocytic changes occur in inflammatory, hyperplastic, and neoplastic settings, including both benign and malignant tumors. The rare oncocytic variant of papillary thyroid carcinoma (PTC), shows papillae composed by cells with large oncocytic granular cytoplasm featuring clear PTC nuclear features. A morphological similar, but biologically distinct lesion, is the encapsulated papillary oncocytic neoplasia. Here, we first report on FNA, its cytological features together with histological, immunohistochemical, and molecular correlates.
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Cytology-based gene mutation tests to predict response to anti-epidermal growth factor receptor therapy: a review.
Diagn. Cytopathol.
PUBLISHED: 06-21-2010
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Recent therapeutic progresses in nonsmall cell lung cancer (NSCLC) and in colorectal cancer (CRC) are based on agents that specifically target the epidermal growth factor receptor (EGFR). To identify the patients most likely to benefit from such therapies, EGFR or KRAS gene mutation tests are mandatory, respectively, in NSCLC and in CRC. In patients with locally advanced or metastatic disease, exploiting cytological samples for these tests avoids not curative surgery. Here, we review the studies that have applied gene mutation assays on cytological samples of NSCLC and CRC to select patients for anti-EGFR therapy. We argue that the standard of quality of gene mutation tests on cytological samples is closely dependent on the extent of the cytopathologists involvement.
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UbcH10 overexpression in human lung carcinomas and its correlation with EGFR and p53 mutational status.
Eur. J. Cancer
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UbcH10 codes for the cancer related E2 Ubiquitin Conjugating Enzyme, an enzymatic molecule with a key role in the ubiquitin-proteasome pathway. Current studies have suggested a critical role of UbcH10 in a variety of malignancies, including human thyroid, breast, ovarian and colorectal carcinomas. The aim of this study has been to extend the analysis of UbcH10 expression to lung cancer. This neoplasia represents one of the leading cause of cancer mortality worldwide, and new tools for an accurate diagnosis/prognosis are needed.
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Cytological and molecular features of papillary thyroid carcinoma with prominent hobnail features: a case report.
Acta Cytol.
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Papillary thyroid carcinoma (PTC) with prominent hobnail features is a recently recognized PTC variant. Its histological hallmark is represented by elongated cells showing a high nuclear/cytoplasmic ratio and a hobnail appearance. Few histological studies have been performed showing aggressive clinical and pathological features. Thus, a better patient management might benefit from its early diagnosis on fine needle aspiration (FNA) samples. To date, the FNA cytology of PTC with prominent hobnail features has not been described.
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Foamy gland pancreatic ductal adenocarcinoma diagnosed on EUS-FNA: a histochemical, immunohistochemical, and molecular report.
Diagn. Cytopathol.
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The foamy gland pattern (FGP) may impart to pancreatic ductal adenocarcinoma (PDA) a deceptively benign appearance. Thus, its diagnosis on FNA is challenging. A case of PDA with FGP, that was suspected on Diff Quik smears, diagnosed on cell-block preparation and confirmed by ancillary stains and molecular techniques, is here reported. The diagnostic interpretation of foamy atypical cells on direct smears may benefit from cell block preparation and from ancillary techniques.
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EGFR mutations detection on liquid-based cytology: is microscopy still necessary?
J. Clin. Pathol.
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Currently, there is a trend towards an increasing use of liquid-based cytology (LBC) to diagnose non-small cell lung cancer. In this study, to detect epidermal growth factor receptor mutations, different molecular techniques were applied to LBC samples with and without laser capture microdissection (LCM). In 58 LBCs, DNA was extracted twice. One sample was obtained directly from CytoLyt solution, whereas the other DNA sample was derived after slide preparation and LCM of Papanicolaou-stained cells. The rate of mutant cases obtained by direct sequencing was discordant between CytoLyt-derived (10.3%) and LCM-derived (17.2%) DNA. However, the same mutant rate (17.2%) was achieved on the matched samples by high-resolution melting analysis, fragment and TaqMan assays. Thus, LCM and direct sequencing may be replaced by more sensitive non-sequencing methods directly performed on CytoLyt-derived DNA, an easier and faster approach to improve epidermal growth factor receptor testing standardisation on LBCs.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.