Key words Bethesda system - BRAF mutation - fine-needle aspiration - papillary thyroid cancer
            - thyroid
Introduction 
            Nodular thyroid disease is one of the most frequently diagnosed pathologies. Some
               studies have shown that up to 70% of randomly selected individuals have nodular disease,
               which is more common in women and among older people [1 ]
               [2 ]
               [3 ]. A key challenge for clinicians is to decide which nodules require evaluation and
               intervention [4 ]. Although thyroid cancer (TC) only accounts for approximately 7-15% of all ultrasound
               (US) detected nodules, the incidence of TC, particularly papillary thyroid carcinoma
               (PTC), has increased dramatically in many countries over the past few decades [3 ]
               [5 ]. This can be explained by increased use of a high sensitivity diagnostic methods
               and medical radiation, iodine intake, carcinogens, elevated background radiation,
               environmental, ethnic and genetic factors or combinations of these factors [6 ].
            The fine needle aspiration (FNA) biopsy performed under US guidance remains the gold
               standard diagnostic test for the initial evaluation of a thyroid nodule. Reported
               sensitivity and specificity for US-guided FNA range from 65 to 98% and 72 to 100%,
               respectively [7 ]. FNA biopsy specimens are classified according to the Bethesda System for Reporting
               Thyroid Cytopathology into the 6 categories. Each of the categories has an implied
               cancer risk that links it to a rational clinical management guideline [8 ]. Due to the well-differentiated nature of most TCs and their morphologic overlap
               with benign nodules, indeterminate diagnostic categories, Atypia of Undetermined Significance/
               Follicular Lesion of Undetermined Significance (AUS/FLUS), Follicular Neoplasm/ Suspicious
               for a Follicular Neoplasm (FN/SFN), and Suspicious for Malignancy (SUSP), comprise
               10–26% of all cytology examinations [9 ]. According to Ali and Cibas estimated risk of malignancy varies from 5 to 15% for
               AUS/FLUS, 15 to 30% for FN/SFN, and 60 to 75% for SUSP category [8 ]. Due to malignancy risk cannot be excluded in indeterminate cases, surgery is typically
               recommended; however, up to two-thirds of these cases are found to be benign at the
               time of surgical resection [10 ]. This leads to unnecessary surgical procedures, complications, and morbidity, as
               well as increased health care expenses.
            As the preoperative PTC diagnostic criteria in indeterminate diagnostic categories
               remain unclear, the main goal of recent studies is to improve the accuracy of FNA
               biopsy assessment and to predict tumor behavior.
            The aim of this study was to estimate the diagnostic value of BRAF V600E mutation
               status combined with cytomorphological features for diagnosis of PTC in cytologically
               indeterminate thyroid nodules.
         Material and methods 
            A prospective study was performed between January 2012 and February 2016. All patients
               with a US-suspicious thyroid nodule underwent an US-guided FNA biopsy in Vilnius University
               Hospital Santaros Klinikos. Twenty-two cytomorphological features were analyzed. Patients
               were classified using Bethesda System for Reporting Thyroid Cytopathology [8 ]. Patients diagnosed with AUS/FLUS, FN/SFN, or SUSP were considered as the objects
               of this study and were involved in further investigation. Cytology specimens of these
               patients were analyzed for the BRAF V600E mutation. Patients who refused operation
               or were operated in other Clinics were excluded from further investigation. Operated
               patients diagnosed with TC on intraoperative biopsy, underwent total thyroidectomy
               with prophylactic unilateral or bilateral central lymph node dissection (of level
               VI) according to tumor localization. In addition, patients who preoperatively had
               suspicious lymph nodes on US, underwent modified radical lymph node dissection (of
               level II-V). The decision on the extension of the operation was not influenced by
               genetic investigation results. Surgically removed thyroid tissue was sent for routine
               histological examination and additional analysis of the BRAF V600E mutation for patients
               diagnosed with PTC in whom mutation was not detected in the initial FNA biopsy cytology
               specimen. All patients diagnosed with a PTC or benign nodular thyroid diseases were
               selected for further investigation. Detailed inclusion and exclusion criteria are
               presented in [Fig. 1 ].
            
                  Fig. 1  Flow diagram of study inclusion and exclusion criteria. *Cytology specimens of these
                  patients were analyzed for the BRAF V600E mutation. **  Histological specimens of
                  patients diagnosed with PTC in whom mutation was not detected in the initial FNA biopsy
                  cytology specimen were additionally analyzed for the BRAF V600E mutation. All non
                  PTC cases were BRAF V600E negative. 
            Fine needle aspiration biopsy cytological analysis 
            
            Every aspirate was transferred to a liquid-based preparation for routine cytological
               assessment. Smears stained with Papanicolaou stain and automatic BD PrepStain system
               were evaluated by one experienced cytologist. Bright-field microscope was used. Initially,
               whole preparation was examined with 10x magnifying lens. Presence of at least 6 groups
               of thyroid epithelial cells, with each group containing 7–10 cells satisfies the adequacy
               of the aspirate. Cytomorphological features including morphology of nuclei, anisokaryosis
               expression, chromatin morphology (homogenity, striation, and dispersion), presence
               of nucleoli, amount and intensity of cytoplasm, presence of degeneration features,
               Hürthle cells, lymphocyte, macrophage infiltration, normofollicular/macrofollicular,
               microfollicular structures, papillary structures, atypia, intranuclear cytoplasmic
               inclusions, psammoma bodies, amount and consistency of colloid, and presence of eosinophilic
               colloid bodies were analyzed with 40x or 100x magnifying lenses. Patients were classified
               using the Bethesda System for Reporting Thyroid Cytopathology [8 ].
            
            BRAF V600E mutation analysis 
            
            The method of genetic investigation of the BRAF V600E mutation was previously described
               by Beisa et al. [11 ]. Material from the liquid-based preparation (treated with RBC lysis solution) or
               histology specimen was transferred into 1.5-ml tubes. Genomic DNA was 
            
            Statistical analysis 
            
            All statistical analyses were performed with IBM SPSS STATISTICS, version 23.0. Continuous
               variables were checked for normal distribution by the Shapiro-Wilk test. Non-parametric
               data were expressed as medians and ranges, and analyzed by the Mann-Whitney U test.
               Categorical variables were reported as absolute values and percentages, and analyzed
               using Pearson Chi-Square test or Fisher’s Exact Test. A p-value less than 0.05 at
               95% confidence interval was considered statistically significant.
            
            To evaluate the diagnostic value of the preoperative data, including gender, age,
               cytomorphological features, Bethesda categories, and status of BRAF V600E mutation,
               for PTC diagnosis, a binary logistic regression model was used.
            
            Mathematically, logistic regression was expressed by the equation:
            
            Consequently, the probability of the event occurring P(Y=1) (diagnosis of PTC is true)
               was defined as follows:
            
            And the probability of the event not occurring P(Y=0) (diagnosis of PTC is false)
               was defined as follows:
            
            P(Y=0)=1 - P(Y=1)
            
            In this model ln P(Y =1) / P(Y =0) is the logit function of probability ratio P(Y =1) / P(Y =0).
               C is the intercept parameter, and b1 , b2 , b3 , …, bn  are the slope parameters of regression equation. Accordingly, C, b1 , b2 , b3 , …, bn  are the regression equation coefficients, which were obtained using data of study
               sample and which represent the values of how the criterion variables change when the
               predictor variables change. X1 , X2 , X3 , …, Xn  are the independent explanatory criterions predictor variables, which can gain value
               of 0 (if the feature is absent) or 1 (if the feature is present). The symbol “e” represents
               natural logarithm base (e ≈ 2,7182818284…).
            
            For assessment of the logistic regression model pertinence for the data of study sample,
               were used: the Hosmer–Lemeshow goodness-of-fit test (to assess the model compatibility
               with data of study sample), the classification table (to evaluate the predictive accuracy
               of the model), the Nagelkerke R2  (R square) pseudo-determinations coefficient (to assess the efficiency of the model),
               and Wald χ2 statistics (to assess the significance of corresponding coefficients in
               this model).
            
            The cutoff of 0.5 was selected and patients were divided into two groups of PTC risk:
               low risk group (when PTC risk<0.5) and high risk group (when PTC risk≥0.5).
            
            To assess the diagnostic characteristics of a model, cases were sorted by the risk
               of PTC diagnosis and results of the final histological examination into true positives
               (when risk of PTC diagnosis was high and after final histological examination PTC
               was confirmed), true negatives (when risk of PTC diagnosis was low and after final
               histological examination benign nodular thyroid disease was confirmed), false positives
               (when risk of PTC diagnosis was high and after final histological examination benign
               nodular thyroid disease was confirmed), and false negatives (when risk of PTC diagnosis
               was low and after final histological examination PTC was confirmed).
            
            The diagnostic characteristics of the model were expressed with sensitivity, specificity,
               positive predictive value, negative predictive value, and accuracy with their 95%
               confidence intervals.
            Results 
            General characteristics of patients 
            
            A total of 1883 patients underwent an US-guided FNA biopsy. Three hundred forty patients
               were classified as AUS/FLUS, FN/SFN, and SUSP. Two hundred thirty-five of these patients
               underwent thyroid surgery in our Clinics due to suspected malignancy. Sixteen patients
               were excluded from this study: 10 diagnosed with follicular TC, 3 with medullary TC,
               2 with anaplastic TC, and 1 with lymphoma.
            
            A total of 219 patients were involved in this study for further investigation. Out
               of them, 188 (85.8%) were female and 31 (14.2%) - male. The mean age of the patients
               was 54.3±13.4 years. After a cytological investigation, 42 (19.2%) out of the 219
               FNA biopsies were classified as AUS/FLUS, 126 (57.5%) as FN/SFN, and 51 (23.3%) as
               SUSP. Histological investigation of the surgically removed thyroid tissue revealed
               77 PTC cases: 14 (33.3%) patients from AUS/FLUS category, 22 (17.5%) from FN/SFN,
               and 41 (80.4%) from SUSP. Out of all PTC patients, 55 (71.4%) had classical type of
               PTC, 19 (24.7%) had follicular type, and 3 (3.9%) had oncocytic type.
            
            Based on the results of the histological examination, the patients were divided into
               two comparative groups: 77 (35.2%) - the PTC group, and 142 (64.8%) - the group of
               benign nodular thyroid disease. Out of 77 patients of PTC group, 71 (92.2%) were female
               and 6 (7.8%) – male, and the mean age of this group was 53.6±12.4 years. Out of 142
               patients diagnosed with benign nodular thyroid disease, 117 (82.4%) were female and
               25 (17.6%) – male, and the mean age of this group was 54.6±14 years. Female gender
               was significantly related to PTC diagnosis (p=0.047). There was no statistically significant
               difference between these two groups when comparing the mean age (p=0.405).
            
            BRAF V600E mutation in the FNA cytological specimen was found for 37 (48.1%) patients
               from PTC group and for 0 patients from benign nodular thyroid disease group. After
               the additional genetic investigation of the postoperative histological specimens in
               cytologically BRAF V600E-negative PTC cases, 15 additional BRAF V600E positive cases
               were identified. A total of 52 (67.5%) PTC cases were positive for the BRAF V600E
               mutation and 25 (32.5%) were negative. All patients from the benign group were BRAF
               V600E negative. The molecular analysis results of the cytology and histology specimens
               revealed that in PTC group were statistically significantly more patients with BRAF
               V600E mutation comparing with benign nodular thyroid disease group (p=0.000).
            
            Cytomorphological features were compared between PTC and benign nodular thyroid disease
               groups. The presence of high anisokaryosis (18.2% vs. 8.5%, p=0.034), streaked chromatin
               (68.8% vs. 37.3%, p=0.000), dark cytoplasm (44.2% vs. 19%, p=0.000), lymphocyte infiltration
               (63.6% vs. 49.3%, p=0.042), papillary structures (50.6% vs. 8.5%, p=0.000), atypia
               (96.1% vs. 76.1%, p=0.000), intranuclear cytoplasmic inclusions (55.8% vs. 10.6%,
               p=0.000), psammoma bodies (10.4% vs. 1.4%, p=0.004), densely colloid (45.5% vs. 12%,
               p=0.000), and eosinophilic colloid bodies (29.9% vs. 13.4%, p=0.003) were shown to
               be significantly related to PTC. Lesions with homogenous chromatin (62.3% vs. 91.5%,
               p=0.000), light cytoplasm (55.8% vs. 81%, p=0.000), prominent amount of colloid (6.5%
               vs. 16.2%, p=0.040), and liquid colloid (33.8% vs. 73.2%) were shown to be significantly
               related to benign nodular thyroid disease. Nuclei morphology, presence of coarsely
               and finely dispersed chromatin, nucleoli, degeneration, Hürthle cells, macrophage
               infiltration, mormofollicular/macrofolicular, and amount of cytoplasm demonstrated
               statistically insignificant differences between groups. Detailed data are presented
               in [Table 1 ].
            
            
               
                  
                     
                     
                        Table 1  Cytomorphological features statistical comparison in two comparative groups, n=219.
                      
                  
                     
                     
                        
                        
                           Papillary thyroid cancer, n=77
                         
                        
                        
                           Benign nodular thyroid disease, n=142
                         
                        
                        
                           Value of p Asymp. Sig.(2-sided)
                              
                         
                         
                      
                  
                     
                     
                        
                        
                           Nuclei (n)
                         
                         
                     
                     
                        
                        
                            Monomorphic
                         
                        
                        
                           1 (1.3%)
                         
                        
                        
                           1 (0.7%)
                         
                        
                        
                           1 *** 
                         
                         
                     
                     
                        
                        
                            Polymorphic
                         
                        
                        
                           76 (98.7%)
                         
                        
                        
                           141 (99.3%)
                         
                        
                         
                     
                     
                        
                        
                           Anisokaryosis (n)
                         
                         
                     
                     
                        
                        
                            None
                         
                        
                        
                           0 (0%)
                         
                        
                        
                           2 (1.4%)
                         
                        
                        
                           0.542 ***
                         
                         
                     
                     
                        
                        
                            Low
                         
                        
                        
                           10 (13%)
                         
                        
                        
                           35 (24.6%)
                         
                        
                        
                           
                              0.041  *
                         
                         
                     
                     
                        
                        
                            Moderate
                         
                        
                        
                           53 (68.8%)
                         
                        
                        
                           93 (65.5%)
                         
                        
                        
                           0.617 *
                         
                         
                     
                     
                        
                        
                            High
                         
                        
                        
                           14 (18.2%)
                         
                        
                        
                           12 (8.5%)
                         
                        
                        
                           
                              0.034  *
                         
                         
                     
                     
                        
                        
                           Homogenous chromatin (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           29 (37.7%)
                         
                        
                        
                           12 (8.5%)
                         
                        
                        
                           
                              0.000  *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           48 (62.3%)
                         
                        
                        
                           130 (91.5%)
                         
                        
                         
                     
                     
                        
                        
                           Streaked chromatin (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           24 (31.2%)
                         
                        
                        
                           89 (62.7%)
                         
                        
                        
                           
                              0.000  *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           53 (68.8%)
                         
                        
                        
                           53 (37.3%)
                         
                        
                         
                     
                     
                        
                        
                           Coarsely dispersed chromatin (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           51 (66.2%)
                         
                        
                        
                           100 (70.4%)
                         
                        
                        
                           0.522 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           26 (33.8%)
                         
                        
                        
                           42 (29.6%)
                         
                        
                         
                     
                     
                        
                        
                           Finely dispersed chromatin (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           37 (48.1%)
                         
                        
                        
                           86 (60.6%)
                         
                        
                        
                           0.075 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           40 (51.9%)
                         
                        
                        
                           56 (39.4%)
                         
                        
                         
                     
                     
                        
                        
                           Nucleoli (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           8 (10.4%)
                         
                        
                        
                           28 (19.7%)
                         
                        
                        
                           0.075 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           69 (89.6%)
                         
                        
                        
                           114 (80.3%)
                         
                        
                         
                     
                     
                        
                        
                           Amount of cytoplasm (n)
                         
                         
                     
                     
                        
                        
                            Sufficient
                         
                        
                        
                           47 (61%)
                         
                        
                        
                           83 (58.5%)
                         
                        
                        
                           0.710 *
                         
                         
                     
                     
                        
                        
                            Abundant
                         
                        
                        
                           30 (39%)
                         
                        
                        
                           59 (41.5%)
                         
                        
                         
                     
                     
                        
                        
                           Cytoplasm intensity (n)
                         
                         
                     
                     
                        
                        
                            Light
                         
                        
                        
                           43 (55.8%)
                         
                        
                        
                           115 (81%)
                         
                        
                        
                           
                              0.000 *
                         
                         
                     
                     
                        
                        
                            Dark
                         
                        
                        
                           34 (44.2%)
                         
                        
                        
                           27 (19%)
                         
                        
                         
                     
                     
                        
                        
                           Degeneration (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           37 (48.1%)
                         
                        
                        
                           80 (56.3%)
                         
                        
                        
                           0.241 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           40 (51.9%)
                         
                        
                        
                           62 (43.7%)
                         
                        
                         
                     
                     
                        
                        
                           Hürthle cells (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           57 (74%)
                         
                        
                        
                           91 (64.1%)
                         
                        
                        
                           0.133*
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           20 (26%)
                         
                        
                        
                           51 (35.9%)
                         
                        
                         
                     
                     
                        
                        
                           Lymphocyte infiltration (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           28 (36.4%)
                         
                        
                        
                           72 (50.7%)
                         
                        
                        
                           
                              0.042 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           49 (63.6%)
                         
                        
                        
                           70 (49.3%)
                         
                        
                         
                     
                     
                        
                        
                           Macrophage infiltration (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           28 (36.4%)
                         
                        
                        
                           65 (45.8%)
                         
                        
                        
                           0.179 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           49 (63.6%)
                         
                        
                        
                           77 (54.2%)
                         
                        
                         
                     
                     
                        
                        
                           Normofollicular/Macrofollicular structures (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           51 (66.2%)
                         
                        
                        
                           79 (55.6%)
                         
                        
                        
                           0.127 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           26 (33.8%)
                         
                        
                        
                           63 (44.4%)
                         
                        
                         
                     
                     
                        
                        
                           Microfollicular structures (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           28 (36.4%)
                         
                        
                        
                           36 (25.4%)
                         
                        
                        
                           0.087 *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           49 (63.6%)
                         
                        
                        
                           106 (74.6%)
                         
                        
                         
                     
                     
                        
                        
                           Papillary structures (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           38 (49.4 %)
                         
                        
                        
                           130 (91.5%)
                         
                        
                        
                           
                              0.000  *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           39 (50.6%)
                         
                        
                        
                           12 (8.5%)
                         
                        
                         
                     
                     
                        
                        
                           Atypia (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           3 (3.9%)
                         
                        
                        
                           34 (23.9%)
                         
                        
                        
                           
                              0.000  ***
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           74 (96.1%)
                         
                        
                        
                           108 (76.1%)
                         
                        
                         
                     
                     
                        
                        
                           Intranuclear cytoplasmic inclusions (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           34 (44.2%)
                         
                        
                        
                           127 (89.4%)
                         
                        
                        
                           
                              0.000  *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           43 (55.8%)
                         
                        
                        
                           15 (10.6%)
                         
                        
                         
                     
                     
                        
                        
                           Psammoma bodies (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           69 (89.6%)
                         
                        
                        
                           140 (98.6%)
                         
                        
                        
                           
                              0.004  ***
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           8 (10.4%)
                         
                        
                        
                           2 (1.4%)
                         
                        
                         
                     
                     
                        
                        
                           Amount of colloid (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           16 (20.8%)
                         
                        
                        
                           21 (14.8%)
                         
                        
                        
                           0.259 *
                         
                         
                     
                     
                        
                        
                            Occasional
                         
                        
                        
                           51 (66.2%)
                         
                        
                        
                           79 (55.6%)
                         
                        
                        
                           0.127 *
                         
                         
                     
                     
                        
                        
                            Frequent
                         
                        
                        
                           5 (6.5%)
                         
                        
                        
                           19 (13.4%)
                         
                        
                        
                           0.119 *
                         
                         
                     
                     
                        
                        
                            Prominent
                         
                        
                        
                           5 (6.5%)
                         
                        
                        
                           23 (16.2%)
                         
                        
                        
                           
                              0.040  *
                         
                         
                     
                     
                        
                        
                           Colloid consistency (n)
                         
                         
                     
                     
                        
                        
                            No colloid
                         
                        
                        
                           16 (20.8%)
                         
                        
                        
                           21 (14.8%)
                         
                        
                        
                           0.259 *
                         
                         
                     
                     
                        
                        
                            Liquid
                         
                        
                        
                           26 (33.8%)
                         
                        
                        
                           104 (73.2%)
                         
                        
                        
                           
                              0.000  *
                         
                         
                     
                     
                        
                        
                            Densely
                         
                        
                        
                           35 (45.5%)
                         
                        
                        
                           17 (12%)
                         
                        
                        
                           
                              0.000  *
                         
                         
                     
                     
                        
                        
                           Eosinophilic colloid bodies (n)
                         
                         
                     
                     
                        
                        
                            Absent
                         
                        
                        
                           54 (70.1%)
                         
                        
                        
                           123 (86.6%)
                         
                        
                        
                           
                              0.003  *
                         
                         
                     
                     
                        
                        
                            Present
                         
                        
                        
                           23 (29.9%)
                         
                        
                        
                           19 (13.4%)
                         
                        
                         
                      
               
               
               *  Pearson's chi-squared test (χ2 ); **  Mann-Whitney-Wilcoxon test; ***  Fisher's exact test
               
               Values in bold represent statistically significant correlations.
                
            
            
            
            Diagnostic value of BRAF V600E mutation status combined with cytomorphological features
               for PTC diagnosis 
            
            According to our logistic regression model, we determined that out of all preoperative
               data (gender, age, cytomorphological features, Bethesda categories) and status of
               BRAF V600E mutation significant features for PTC diagnosis were: liquid colloid consistency
               (this feature is defined by the variable X1  in the logistic equation and its coefficient is -1.46, which shows an indirect dependency
               of PTC diagnosis), papillary structures (this feature is defined by the variable X2  in the logistic equation and its coefficient is 2.16, which shows a direct dependency
               of PTC diagnosis), eosinophilic colloid bodies (this feature is defined by the variable
               X3  in the logistic equation and its coefficient is 1.57, which shows a direct dependency
               of PTC diagnosis), and BRAF V600E mutation (this feature is defined by the variable
               X4  in the logistic equation and its coefficient is 22.79, which shows a direct dependency
               of PTC diagnosis). Other features, as shown by our logistic regression based model,
               do not have a significant effect on histological examination results (adding an additional
               variable does not improve the model). The logistic regression model was expressed
               by logit function of probability ratio z:
            
            Z=(- 1.82) + (- 1.46) × (liquid colloid consistency) + 2.16 × (papillary structures)
               + 1.57 × (eosinophilic colloid bodies) + 22.79 × (BRAF V600E mutation).
            
            The Hosmer–Lemeshow test produced a p-value of 0.998. Nagelkerke's R2  is equal to 0.76. According to Wald's criterion, all regressors are statistically
               significant, except for BRAF V600E mutation, which has been exempted due to the high
               significance for the final results of the logistic regression model.
            
            Out of 219 patients, the regression analysis classified 156 (71.2%) as having a low
               risk of PTC, and 63 (28.8%) patients as - high risk of PTC diagnosis. In low risk
               group, there were 15 (9.6%) histologically confirmed PTC cases and 141 (90.4%) - benign
               nodular thyroid disease cases. In high risk group, there were 62 (98.4%) and 1 (1.6%)
               cases, respectively.
            
            According the PTC risk groups classified by our logistic regression model and results
               of the final histological examination 62 cases were considered as true positive, 141
               as true negative, 1 as false positive, and 15 as false negative. PTC risk groups classified
               by our logistic regression model have sensitivity of 80.5% (95% CI: 69.9 to 88.7),
               specificity of 99.3% (95% CI: 96.1 to 100), positive predictive value of 98.4% (95%
               CI: 89.8 to 99.8), negative predictive value of 90.4% (95% CI: 85.7 to 93.7), and
               accuracy of 92.7% (95% CI: 88.4 to 95.8) for PTC diagnosis.
            
            Convenient for clinical use online PTC diagnosis probability calculator for cytologically
               indeterminate thyroid nodules is available at www.ptc-calc.we2host.lt.
            Discussion and conclusions 
         Discussion and conclusions 
            Thyroid US with FNA remains the gold standard for evaluation of thyroid nodules [4 ]. TC accounts only for approximately 7–15% of all thyroid nodules detected by US
               [3 ]. PTC comprises the majority (85–90%) of all thyroid malignancies [12 ]. In our study, PTC consisted 87.7% of all TC cases. In general, PTC has a good prognosis
               with 25-year rates of cause-specific mortality about 5% after appropriate treatment
               [13 ]. However, 20 to 30% of patients develop local recurrence or distant metastasis and
               1% die from PTC [14 ]. Due to increasing prevalence of thyroid nodules and the lack of specific diagnostic
               tests for TC, accurate clinical diagnosis prior to surgery became an important challenge
               to physicians [1 ]
               [15 ].
            Thyroid US is a widespread technique that is used as a first-line diagnostic procedure
               for detecting and characterizing nodular thyroid disease [16 ]. It is indisputable that US-guided FNA is a safe, cost-effective, and reliable diagnostic
               method in the differential diagnosis of variable thyroid nodules. The Bethesda System
               for Reporting Thyroid Cytopathology classifies FNA biopsy specimens into 6 categories,
               each with certain degree of probability for malignancy, guiding the standard-of-care
               for patients with thyroid nodules [17 ]. However, some cytologic results such as indeterminate create confusion for clinicians
               in thyroid nodule management [18 ]. Indeterminate diagnostic categories comprise 10–26% of all cytology examinations
               [9 ]. About 50% patients undergo thyroid surgery due to cytologically indeterminate nodules;
               however, one-third of these cases are found to be malignant at the time of histological
               examination [19 ]. In our study, about 76.3 % patients underwent surgery due to indeterminate cytologically
               and 39.6% of them were finally diagnosed with TC. According to Ali and Cibas estimated
               risk of malignancy varies from 5 to 15% for AUS/FLUS, 15 to 30% for FN/SFN, and 60
               to 75% for SUSP category [8 ]. According to our data, the malignancy rate of the AUS/FLUS category was 36.4%,
               FN/SFN – 21.2%, SUSP – 83.1%. These results correspond to the data of recent studies
               [20 ]. This discrepancy might have resulted from continuous improvement in FNA technique,
               since the data for the Bethesda system were collected several years ago. Differences
               may also relate to random variation or institutional differences in pathologic interpretation
               [11 ]. Because the incidence of malignancy within indeterminate lesions ranges varies
               widely, there are no clear guidelines for the management of these lesions [21 ].
            Recently, molecular testing of FNA biopsy specimens for genetic alterations frequently
               associated with TC has emerged as another valuable diagnostic tool [22 ]. Several prospective studies reported that by molecular testing of thyroid nodules
               for BRAF, RAS, RET/PTC, and PAX8/PPARγ mutations in cytological material, the difference
               of any mutation was a strong indicator of cancer because about 97% of mutation-positive
               nodules had a malignant diagnosis at histology [16 ].
            Among the various oncogenic events identified in PTC, BRAF V600E is the most common
               mutation, it ranges from 30 to 80% (depending on the geographical region) [6 ]
               [22 ]. Because the BRAF V600E mutation has a high specificity (99%) and high positive
               predictive value, it can be used to improve the diagnostic accuracy of US-guided FNA
               and to overcome the limitations of US-FNA [3 ]
               [18 ]. On the other hand, reported low sensitivity of BRAF V600E mutation in indeterminate
               thyroid nodules dramatically limits the applicability of this molecular marker. Moreover,
               Naif et al. meta-analysis showed that BRAF V600E mutation analysis of FNA cytology
               has only 30% sensitivity for PTC in those cases that were reported as indeterminate
               [23 ]. In our analysis, we established a relatively high rate (67.5%) of BRAF-positive
               PTCs in patients with cytologically indeterminate nodules. This can be partially explained
               by the fact that in our study BRAF V600E mutation status was established from both,
               FNA biopsy and histology specimens. Moreover, high rate of BRAF V600E positive cases
               may be related to the distribution of histological types of PTC. According to literature,
               BRAF V600E mutation is detected for about 60% of the classical PTC type cases, and
               only up to 12% for patients diagnosed with follicular type of PTC [24 ]. In our study, 71.4% patients had classical type of PTC, 24.7% had follicular type,
               and 3.9% had oncocytic type. BRAF V600E mutation was found for 78.2%, 42.1%, and 33.3%
               patients, respectively. Even we have found relatively high BRAF V600E mutation rate,
               it is still too low for reliable differentiation between PTC and benign nodular thyroid
               disease when the mutation is absent.
            Several studies investigated cytomorphological features in FNA of indeterminate thyroid
               nodules, and found an association between malignancy and cytologic atypia, which is
               frequently described in FNA reports. The malignancy risk of cytologic atypia in indeterminate
               thyroid nodules varies among different studies between 28% and 71% [17 ]
               [21 ]
               [25 ]
               [26 ]. Kato with colleagues hypothesized that individual descriptors (cytomorphological
               features) of atypia could further differentiate malignant tumors from benign lesions,
               and therefore compared the risk of malignancy in FNA reports describing atypia to
               FNAs with no atypia. They established the exact risk of specific atypical cytomorphological
               features, and suggested that the presence of four or more cytomorphological features
               in the cytology report, or the presence of nuclear inclusions and grooves together
               increased the risk of malignancy to 80% [26 ]. In our study, we found that the presence of high anisokaryosis, streaked chromatin,
               dark cytoplasm, lymphocyte infiltration, papillary structures, atypia, intranuclear
               cytoplasmic inclusions, psammoma bodies, densely colloid, and eosinophilic colloid
               bodies were significantly related to PTC. Lesions with homogenous chromatin, light
               cytoplasm, prominent amount of colloid, and liquid colloid were shown to be significantly
               related to benign nodular thyroid disease. However, cytomorphology of FNA biopsy alone
               cannot sufficiently differentiate indeterminate thyroid nodules.
            To the best of our knowledge, this is the first study to evaluate the use of BRAF
               V600E mutation status combined with cytomorphological features for diagnosing PTC
               in indeterminate thyroid nodules. Analysis of BRAF V600E mutation status combined
               with cytomorphological features by the logistic regression model determined that out
               of all cytomorphological features significant for PTC diagnosis were only: liquid
               colloid consistency (indirect dependency of PTC diagnosis), papillary structures (direct
               dependency of PTC diagnosis), and eosinophilic colloid bodies (direct dependency of
               PTC diagnosis). The estimated sensitivity of our diagnostic model was - 80.5%, specificity
               - 99.3%, positive predictive value - 98.4%, negative predictive value - 90.4%, and
               accuracy - 92.7%.
            However, this study has several limitations, which have to be taken into account when
               interpreting the results. First of all, this is a cohort and monocentral study. Secondly,
               the study solves only a part of the diagnostic problems, since only most common TC
               diagnosis (PTC) is considered. For diagnosis of medullary TC measurement of serum
               calcitonin level is a sensitive and specific test. This test should be performed for
               all patients, who are suspected for TC. Currently, there are no reliable criteria
               for diagnosis of follicular TC, but by active surveillance of low risk group patients,
               the decision on surgical treatment can be made by assessing the dynamic of clinical
               signs, for example, tumor growth tendencies, changes in the Bethesda cytological category.
               The fact that part of the BRAF V600E mutation was established from histology specimens
               can be considered as a limitation of this study, but it also reflects the benefits
               of patient surveillance and repeated FNA biopsies.
            To sum up, our model has diagnostic specification which can help clinicians to make
               decision for the best therapeutic approach. For the patients without presence of extrathiroidal
               extension on US examination, normal calcitonin blood level and cytologically indeterminate
               thyroid nodules who are assigned to a low risk group by our PTC diagnosis probability
               calculator (available at www.ptc-calc.we2host.lt) the active surveillance can be offered.
               For these patients, an US examination with a FNA biopsy and BRAF V600E mutation analysis
               should be repeated. Surgical treatment should be recommended for all patients assigned
               to a high risk group.
            In conclusion, evaluation of BRAF V600E mutation status combined with cytomorphological
               features for diagnosis of PTC in cytologically indeterminate thyroid nodules can significantly
               improve diagnostic accuracy and reduce the number of diagnostic operations. Our PTC
               diagnosis probability calculator for cytologically indeterminate thyroid nodules is
               available at www.ptc-calc.we2host.lt.