Molecular markers in the diagnosis of thyroid nodules

An indeterminate thyroid nodule cytology result occurs about every sixth fine-needle aspiration. These indeterminate nodules harbor a 24% risk of malignancy (ROM); too high to ignore, but driving surgery where most nodules are benign. Molecular diagnostics have emerged to ideally avoid surgery when appropriate, and to trigger the correct therapeutic surgery when indicated, as opposed to an incomplete diagnostic surgery. No current molecular test offers both high sensitivity and high specificity. A molecular diagnostic test with high sensitivity (e.g. Afirma Gene Expression Classifier sensitivity 90%) offers a high Negative Predictive Value when the ROM is relatively low, such as < 30%. Only such tests can "rule-out" cancer. In this setting, a molecularly benign result suggests the same ROM as that of operated cytologically benign nodules (~6%). Thus, clinical observation can replace diagnostic surgery; increasing quality of life and decreasing medical costs. However, its low specificity cannot "rule-in" cancer as a suspicious result has a Positive Predictive Value (PPV) of ~40%, perhaps too low to routinely reflex to definitive cancer surgery. Conversely, high specificity tests (BRAF, RAS, PPAR/PAX-8, RET/PTC, PTEN) offer high PPV results, and only these tests can "rule-in" cancer. Here a positive molecular result warrants definitive therapeutic surgery. However, their low sensitivity cannot "rule-out" cancer and a negative molecular result cannot dissuade diagnostic surgery; limiting their cost-effectiveness. Whether or not there is a useful and cost-effective role to sequentially combine these approaches, or to modify existing approaches, is under investigation.

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Epstein-Barr Virus (EBV)-Encoded RNA: Automated In-Situ Hybridization (ISH) Compared with Manual ISH and Immunohistochemistry for Detection of EBV in Pediatric Lymphoproliferative Disorders

Pediatric and Developmental Pathology ◽

10.2350/07-07-0316.1 ◽

2009 ◽

Vol 12 (3) ◽

pp. 195-199 ◽

Cited By ~ 22

Author(s):

Naim K. Fanaian ◽

Cynthia Cohen ◽

Sandra Waldrop ◽

Jennifer Wang ◽

Bahig M. Shehata

Keyword(s):

In Situ Hybridization ◽

Predictive Value ◽

Epstein Barr Virus ◽

High Sensitivity ◽

High Specificity ◽

Lymphoproliferative Disorders ◽

Barr Virus ◽

Epstein Barr ◽

Low Sensitivity

Detection of Epstein-Barr virus (EBV) may be achieved by various methods, including EBV-encoded RNA (EBER) in-situ hybridization (ISH) and immunohistochemistry (IHC) for latent membrane protein (LMP-1). We compared novel automated ISH and IHC techniques in pediatric lymphoproliferative disorders with results obtained by manual ISH. Thirty-seven pediatric cases previously studied by manual EBER ISH (including 18 EBER-positive, 15 EBER-negative, and 4 EBER-equivocal cases) were used for the study. Automated EBER ISH and automated LMP-1 IHC were performed using the BondMax autostainer and prediluted EBER probe and EBV cell surface 1 to 4 at 1:50 dilution, respectively. Results of each of the automated techniques for EBV detection were compared with results by manual EBER ISH. Compared with manual EBER ISH as the gold standard, automated ISH had a sensitivity and specificity of 94% and 69%, respectively, accuracy of 83%, positive predictive value (PPV) of 79%, and negative predictive value (NPV) of 90%. Automated IHC had a sensitivity of 44%, specificity of 93%, accuracy of 67%, PPV of 88%, and NPV of 59%. Automated ISH and IHC correlated significantly ( P < 0.045). Automated ISH is useful for diagnosis of EBV-related pediatric neoplasms, being easy to perform and interpret and requiring only the technologist's time to set up and having a high sensitivity and NPV. The automated IHC protocol is of too low sensitivity for routine use, although results show high specificity and PPV.

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Factors Impacting the Performance Characteristics of Bile Duct Brushings: A Clinico-Cytopathologic Analysis of 253 Patients

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2017-0150-oa ◽

2018 ◽

Vol 142 (7) ◽

pp. 863-870 ◽

Cited By ~ 4

Author(s):

Ezgi Hacihasanoglu ◽

Bahar Memis ◽

Burcin Pehlivanoglu ◽

Vaidehi Avadhani ◽

Alexa A. Freedman, ◽

...

Keyword(s):

Bile Duct ◽

Predictive Value ◽

High Specificity ◽

Daily Practice ◽

Performance Characteristics ◽

Lower Sensitivity ◽

Current State ◽

Risk Of Malignancy ◽

Low Sensitivity ◽

Sensitivity Specificity

Context.— Literature on factors impacting bile duct brushings (BDBs) performance characteristics remain limited. Objective.— To capture the current state of daily practice with BDB sign-out. Design.— Two hundred fifty-three of 444 BDBs signed out by more than 7 cytopathologists, with histopathologic and/or clinical follow-up of at least 18 months, were examined. Results.— One hundred thirty-five of 253 BDBs (53%) had histologically confirmed malignancies, 22 (9%) had cancer-related deaths, and 96 (38%) were benign. Cytologic diagnoses in the 444 BDBs were nondiagnostic (11 [2.5%]), negative (284 [64%]), atypical (62 [13.9%]), suspicious (34 [7.7%]), and malignant (53 [11.9%]). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of malignancy detection were 35%, 100%, 100%, 58%, and 66%, respectively. When atypical, suspicious, and malignant (ASM) categories were combined, sensitivity increased (58%), specificity and PPV dropped (97%), and accuracy increased (73%). Carcinoma type (bile-duct versus pancreatic-ductal) had no effect on accuracy (P = .60) or diagnostic class (P = .84), nor did time of performance (first 7.5 versus latter 7.5 years, P = .13). Interestingly, ThinPrep + cell block (n = 41) had higher sensitivity (61%) and lower specificity (80%) than ThinPrep only (versus 51% and 100%, respectively). Sensitivity and specificity were higher (47% and 100%) in nonstented than stented specimens (59% and 97%). Relative risk of malignancy for “suspicious” (2.30) and “atypical” (2.28) categories was lower but not very different from that of “malignant” category (2.41). Conclusions.— Bile duct brushings had fairly low sensitivity but high specificity and PPV with no false positives. Sensitivity almost doubled and specificity dipped minimally when ASM categories were combined, highlighting the need for better classification criteria for atypical/suspicious cases. Higher specificity, PPV, NPV, and accuracy but lower sensitivity in stented BDBs suggest that they be called malignant only when evidence is overwhelmingly convincing.

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Correlation of fine needle aspiration cytology and histopathology of neck swellings

International Journal of Otorhinolaryngology and Head and Neck Surgery ◽

10.18203/issn.2454-5929.ijohns20180986 ◽

2018 ◽

Vol 4 (3) ◽

pp. 648

Author(s):

C. S. Asha ◽

B. R. Suchit Roy

Keyword(s):

Salivary Gland ◽

Lymph Node ◽

Predictive Value ◽

Age Groups ◽

Invasive Procedure ◽

High Specificity ◽

Cost Effective ◽

Needle Aspiration ◽

Predictive Values ◽

Specificity And Sensitivity

Background: Neck swellings are a common clinical finding affecting all age groups. FNAC is a minimally invasive procedure helpful in the diagnosis of various neck swellings. The purpose of this study is to determine the accuracy of FNAC in the diagnosis of neck swellings by comparing it with the histopathology which is taken as the gold standard.Methods: A prospective study which included 90 patients who attended ENT and surgery departments of Government Medical College, Trivandrum with neck swellings from July 2006-2007. FNAC of the swelling was done and the FNAC results were compared with the histopathology results. The specificity, sensitivity, positive and negative predictive values and accuracy of FNAC were calculated. Results: Of the 90 patients, thyroid swelling formed the major group followed by lymph node, salivary gland and miscellaneous swellings. Thyroid swellings had a female predominance while the other three groups namely lymph node, salivary gland and miscellaneous groups showed a male preponderance. When the neck swellings namely thyroid, salivary gland, lymph node and miscellaneous group were taken into consideration as a whole, the sensitivity of FNAC for detecting malignancy was 64.3%. The specificity, positive predictive value, negative predictive value and accuracy were 97.4%, 81.8%, 93.7% and 92% respectively.Conclusions: FNAC can be rated as a safe, simple, reliable, cost effective and rapid diagnostic tool with high specificity and sensitivity for the initial evaluation of neck swellings.

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Evaluation of the clinical usefulness of a chemiluminometric method for measuring creatine kinase MB

Clinical Chemistry ◽

10.1093/clinchem/36.10.1809 ◽

1990 ◽

Vol 36 (10) ◽

pp. 1809-1811 ◽

Cited By ~ 4

Author(s):

J R Pearson ◽

F Carrea

Keyword(s):

Creatine Kinase ◽

Predictive Value ◽

Characteristic Curve ◽

High Sensitivity ◽

High Specificity ◽

Receiver Operator Characteristic Curve ◽

Diagnostic Efficiency ◽

Predictive Values ◽

Creatine Kinase Mb ◽

Rule Out

Abstract The use of creatine kinase isoenzymes (CK-MB) in the diagnosis of acute myocardial infarction (AMI) is well established. We evaluated the use of a new chemiluminometric method (CK-Ciba) for measuring CK-MB by calculating its sensitivity, specificity, positive and negative predictive values, and diagnostic efficiency for diagnosing AMI. We tested 633 samples from 229 patients within 4 h of receipt. The patients were divided into four groups: (1) patients who had an AMI, (2) patients who had AMI ruled out, (3) patients who had CK-MB measured for reasons other than to rule out AMI, and (4) patients who had only one sample drawn. Only patients in Groups 1 and 2 were used in the study. AMI was diagnosed by a cardiologist. The prevalence of AMI in our population was 0.18. A receiver-operator characteristic curve was used to establish optimal values for identifying AMI with the CK-Ciba results: CK-MB greater than or equal to 10 micrograms/L and a CK-MB index of greater than or equal to 3.0 (micrograms of CK-MB per U of CK x 100). Using these values, we calculated a sensitivity of 1.00, specificity of 0.97, positive predictive value of 0.87, negative predictive value of 1.00, and a diagnostic efficiency of 0.97. We conclude that the CK-Ciba method has high sensitivity, high specificity, and good predictive values for CK-MB and is appropriate to use to rule out AMI.

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Evaluation of RNA Extraction-Free Method for Detection of SARS-CoV-2 in Salivary Samples for Mass Screening for COVID-19

BioMed Research International ◽

10.1155/2021/5568350 ◽

2021 ◽

Vol 2021 ◽

pp. 1-6

Author(s):

Sally A. Mahmoud ◽

Subhashini Ganesan ◽

Esra Ibrahim ◽

Bhagyashree Thakre ◽

Juliet G. Teddy ◽

...

Keyword(s):

Predictive Value ◽

Rna Extraction ◽

Screening Method ◽

High Sensitivity ◽

High Specificity ◽

Cost Effective ◽

Kappa Coefficient ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Good Agreement

In this COVID-19 pandemic, there is a dire need for cost-effective and less time-consuming alternatives for SARS-CoV-2 testing. The RNA extraction-free method for detecting SARS-CoV-2 in saliva is a promising option. This study found that it has high sensitivity (85.34%), specificity (95.04%), and was comparable to the gold standard nasopharyngeal swab (NPS) sample tests. The method showed good agreement between salivary and NPS samples, with a kappa coefficient of 0.797. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fisher Applied Biosystems showed high sensitivity, positive predictive value (PPV), and negative predictive value (NPV) but also showed a higher percentage of invalid reports. On the other hand, the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples, and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction-free method for salivary sample serves as an effective alternative screening method for COVID-19.

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Predictive Evaluation on Cytological Sample of Metastatic Melanoma: The Role of BRAF Immunocytochemistry in the Molecular Era

Diagnostics ◽

10.3390/diagnostics11061110 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1110

Author(s):

Andrea Ronchi ◽

Marco Montella ◽

Federica Zito Marino ◽

Michele Caraglia ◽

Anna Grimaldi ◽

...

Keyword(s):

Metastatic Melanoma ◽

Molecular Analysis ◽

Predictive Value ◽

Diagnostic Performance ◽

Cost Effective ◽

Needle Aspiration ◽

Braf V600e ◽

Mutational Status ◽

Needle Aspiration Cytology ◽

Sensitivity Specificity

Background: Cutaneous malignant melanoma is an aggressive neoplasm. In advanced cases, the therapeutic choice depends on the mutational status of BRAF. Fine needle aspiration cytology (FNA) is often applied to the management of patients affected by melanoma, mainly for the diagnosis of metastases. The evaluation of BRAF mutational status by sequencing technique on cytological samples may be inconvenient, as it is a time and biomaterial-consuming technique. Recently, BRAF immunocytochemistry (ICC) was applied for the evaluation of BRAF V600E mutational status. Although it may be useful mainly in cytological samples, data about BRAF ICC on cytological samples are missing. Methods: We performed BRAF ICC on a series of 50 FNA samples of metastatic melanoma. BRAF molecular analysis was performed on the same cytological samples or on the corresponding histological samples. Molecular analysis was considered the gold standard. Results: BRAF ICC results were adequate in 49 out of 50 (98%) cases, positive in 15 out of 50 (30%) cases and negative in 34 out of 50 (68%) of cases. Overall, BRAF ICC sensitivity, specificity, positive predictive value and negative predictive value results were 88.2%, 100%, 100% and 94.1%, respectively. The diagnostic performance of BRAF ICC results was perfect when molecular evaluation was performed on the same cytological samples. Hyperpigmentation represents the main limitation of the technique. Conclusions: BRAF ICC is a rapid, cost-effective method for detecting BRAF V600E mutation in melanoma metastases, applicable with high diagnostic performance to cytological samples. It could represent the first step to evaluate BRAF mutational status in cytological samples, mainly in poorly cellular cases.

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Classification of Male Breast Lesions According to the IAC Yokohama System for Reporting Breast Cytopathology

Acta Cytologica ◽

10.1159/000512041 ◽

2020 ◽

pp. 1-8

Author(s):

Melissa Oosthuizen ◽

Rubina Razack ◽

Jenny Edge ◽

Pawel Tomasz Schubert

Keyword(s):

Predictive Value ◽

Best Practice ◽

Internal Audit ◽

Needle Aspiration ◽

Male Breast ◽

Histopathological Diagnosis ◽

Breast Lesions ◽

Risk Of Malignancy ◽

Sensitivity Specificity

Objective: This study aims to determine the diagnostic utility of the International Academy of Cytology (IAC) Yokohama System for reporting breast cytopathology in lesions of the male breast. Study Design: Fine-needle aspiration biopsy (FNAB) reports between 2015 and 2019 were retrospectively recategorized according to the 5-tiered IAC Yokohama Reporting System. Our database yielded a total of 1,532 FNAB reports from breast lesions, obtained from 1,350 male patients. The risk of malignancy (ROM) and diagnostic performance of FNAB were determined using follow-up histopathological diagnosis and/or clinical follow-up, where available, for each category. Results: The category distribution were as follows: inadequate, 40%; benign, 57%; atypical, 0.6%; suspicious for malignancy, 0.7%; and malignant, 1.6%. The ROM in each category was nondiagnostic, 11%; benign, 3%; atypical, 28%; suspicious for malignancy, 56%; and malignant, 100%. The sensitivity, specificity, positive predictive value, and negative predictive value were recorded as 63, 100, 100, and 84.6% respectively, when only malignant cases were considered as positive tests. Conclusion: This study validates the IAC Yokohama System for reporting male breast cytopathology. In accordance with the aim of the Yokohama System to establish best practice guidelines for reporting breast cytopathology, this comprehensive scheme facilitates comparisons between local and international institutions. The ROM acts as an internal audit for quality assurance within one’s own laboratory and provides guidance for clinical management. It highlights inefficiencies such as high inadequacy rates for category 1 and also features strengths with impressive specificity for categories 4 and 5.

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The Association of “GOOP” on Gross Examination of Fine Needle Aspiration Samples and On-Site Adequacy

Respiration ◽

10.1159/000517923 ◽

2021 ◽

pp. 1-4

Author(s):

Nikhil Meena ◽

Thaddeus Bartter ◽

Roshen Mathew ◽

Abhishek Kumar ◽

Winnie Elma Roy ◽

...

Keyword(s):

Positive Predictive Value ◽

Fine Needle Aspiration ◽

Predictive Value ◽

Needle Aspiration ◽

Fine Needle ◽

Study Interval ◽

White Material ◽

Gross Examination ◽

Malignant Diagnosis ◽

Rule Out

Background: Rapid on-site cytologic evaluation (ROSE) is not always available for fine needle aspiration (FNA) specimens. We have examined the relationships between the presence of “GOOP” (defined as gooey white material) on FNA aspirates, on-site adequacy (OSA), and diagnosis. Methods: Consecutive FNA samples obtained over the study interval were included. Samples were assessed macroscopically for the presence or absence of GOOP (GOOP+ or GOOP−). GOOP+ samples were further characterized as shiny (G+S) or cheesy (G+C). Gross descriptors were correlated with OSA and final diagnoses. Results: Of the 204 sites biopsied, 102 were malignant, 94 benign, and 8 nondiagnostic. The presence of GOOP was highly predictive for adequacy (positive predictive value 98%). While these correlations for GOOP positivity were significant, the absence of GOOP did not rule out adequacy or malignancy. The presence of GOOP was also significantly correlated with a malignant diagnosis. Conclusions: We have prospectively demonstrated that the presence of GOOP correlates strongly with adequacy. This may be of value for those for whom ROSE is not available and, when available, may help prioritize specimens for on-site review.

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Punção Aspirativa de Nódulos da Tiroide: Vale a Pena Repetir?

Acta Médica Portuguesa ◽

10.20344/amp.8215 ◽

2017 ◽

Vol 30 (6) ◽

pp. 472

Author(s):

Vera Fernandes ◽

Tânia Pereira ◽

Catarina Eloy

Keyword(s):

Fine Needle Aspiration ◽

Thyroid Nodules ◽

Significant Proportion ◽

Cost Effective ◽

Needle Aspiration ◽

Fine Needle ◽

High Concordance ◽

Benign Nodules ◽

Cytology Result ◽

Undetermined Significance

Introduction: The fine-needle aspiration has a significant role in assessing the malignancy risk of thyroid nodules. There is uncertainty regarding the value of repeat fine-needle aspiration in benign nodules. This study aims to evaluate the concordance of results in consecutive fine-needle aspiration and to study the relevance of repetition in benign results.Material and Methods: Retrospective study of the 4800 thyroid nodules fine-needle aspiration held in Instituto de Patologia e Imunologia Molecular da Universidade do Porto between January 1, 2014 and May 2, 2016. Of the initial sample, we selected the repeated fine-needle aspiration on the same nodule.Results: The first fine-needle aspiration result of the 309 nodules underwent revaluation was non-diagnostic in 103 (33.3%), benign in 120 (38.8%) and atypia/follicular lesion of undetermined significance in 86 (27.8%). The agreement between the first and second fine-needle aspiration was significantly higher in cases with an initial benign result (benign: 85.8%, non-diagnostic: 27.2% and atypia/ follicular lesion of undetermined significance: 17.4%, p < 0.005). The fine-needle aspiration repeating motifs in initially benign nodules (n = 78) were repetition suggestion in 58, nodule growth in 17 and suspicious ultrasonographic features in 3.Discussion: The fine-needle aspiration repetition in nodules with initial non-diagnostic and atypia/follicular lesion of undetermined significance result changed the initial diagnosis in a significant proportion of patients, modifying their therapeutic approach. The high concordance of results in initially benign nodules makes fine-needle aspiration repetition not cost-effective in most cases.Conclusion: The fine-needle aspiration should be repeated when the initial cytology result is non-diagnostic or atypia/follicular lesion of undetermined significance.

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Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

The Open Microbiology Journal ◽

10.2174/1874285801610010176 ◽

2016 ◽

Vol 10 (1) ◽

pp. 176-182 ◽

Cited By ~ 8

Author(s):

Reza Ranjbar ◽

Payam Behzadi ◽

Caterina Mammina

Keyword(s):

Dna Microarray ◽

Francisella Tularensis ◽

High Specificity ◽

Cost Effective ◽

High Rate ◽

Molecular Diagnostic ◽

Microarray Technology ◽

Microarray Probe ◽

Specificity And Sensitivity ◽

Oligo Microarray

Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

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