Background
Methods
FNA samples
Ethics
Diagnosis
HD | CD | BRAF | ||
PTC (70) | n | WT | V600E | |
PTC | 41 | 15 | 26 | |
IFP | 10 | 10 | 0 | |
SPTC | 19 | 9 | 10 | |
BN (48) | IFP | 28 | 28 | 0 |
BN | 20 | 20 | 0 |
DNA and RNA extraction
miRNA extraction from FNA samples and miRNA expression assay by reverse-transcriptase PCR
PCR protocol
Gene expression real-time PCR assay
BRAF V600E detection
Statistical analyses
Results
BRAF status characterization
Quantitative markers of gene expression
Building molecular computational models: classification of malignant and benign samples
HD | CD | BRAF | ||
PTC (38) | n | WT | V600E | |
PTC | 22 | 10 | 12 | |
IFP | 5 | 5 | 0 | |
SPTC | 11 | 4 | 7 | |
BN (13) | IFP | 7 | 7 | 0 |
BN | 6 | 13 | 0 |
Actual mal_ben
|
Group size
|
Predicted
| |
---|---|---|---|
Benign | Malignant | ||
Benign | 13 | 12 | 1 |
(92.31 %) | (7.69 %) | ||
Malignant | 38 | 2 | 36 |
(5.26 %) | (94.74 %) |
Actual mal_ben
|
Group size
|
Predicted
| |
---|---|---|---|
Benign | Malignant | ||
Benign | 13 | 9 | 4 |
(69.23 %) | (30.77 %) | ||
Malignant | 38 | 0 | 38 |
(0.00 %) | (100.00 %) |
Unknown samples | Benign probability | Malignant probability | Predicted diagnosis | Cytological diagnosis | Pathological diagnosis | BRAF status |
---|---|---|---|---|---|---|
A | 0.0700 | 0.9300 | Malignant | SPTC | Malignant | V600E |
B | 0.0530 | 0.9470 | Malignant | SPTC | Malignant | V600E |
C | 0.1075 | 0.8925 | Malignant | SPTC | Malignant | V600E |
D | 0.0177 | 0.9823 | Malignant | SPTC | Malignant | V600E |
E | 0.1964 | 0.8036 | Malignant | SPTC | Malignant | V600E |
F | 0.1380 | 0.8620 | Malignant | SPTC | Malignant | V600E |
G | 0.0935 | 0.9065 | Malignant | SPTC | Malignant | WT |
H | 0.1369 | 0.8631 | Malignant | SPTC | Malignant | WT |
I | 0.1458 | 0.8542 | Malignant | SPTC | Malignant | V600E |
L | 0.2110 | 0.7890 | Malignant | SPTC | Malignant | WT |
M | 0.0415 | 0.9585 | Malignant | SPTC | Malignant | WT |
Unknown samples | Benign probability | Malignant Probability | Predicted diagnosis | Cytological diagnosis | Pathological diagnosis | BRAF status |
---|---|---|---|---|---|---|
A | 0.0302 | 1.0000 | Malignant | SPTC | Malignant | V600E |
B | 0.0011 | 1.0000 | Malignant | SPTC | Malignant | V600E |
C | 0.0004 | 0.9996 | Malignant | SPTC | Malignant | V600E |
D | 0.0000 | 1.0000 | Malignant | SPTC | Malignant | V600E |
E | 0.3242 | 0.6758 | Malignant | SPTC | Malignant | V600E |
F | 0.0223 | 0.9777 | Malignant | SPTC | Malignant | V600E |
G | 0.0009 | 0.9991 | Malignant | SPTC | Malignant | WT |
H | 0.1759 | 0.8241 | Malignant | SPTC | Malignant | WT |
I | 0.0847 | 0.9153 | Malignant | SPTC | Malignant | V600E |
L | 0.2007 | 0.7993 | Malignant | SPTC | Malignant | WT |
M | 0.0000 | 1.0000 | Malignant | SPTC | Malignant | WT |
Principal component analysis
ROC curve analysis
Sensitivity | Specificity | AUC | SE | 95 % CI | p-value | |
---|---|---|---|---|---|---|
TC1 | 38.5 | 92.9 | 0.634 | 0.0816 | 0.487 to 0.764 | 0.0953 |
c-KIT* | 95.7 | 88.2 | 0.973 | 0.0261 | 0.883 to 0.998 | <0.0001 |
miR146b* | 87.8 | 100.00 | 0.931 | 0.0364 | 0.824 to 0.983 | <0.0001 |
miR-222 | 48.8 | 68.7 | 0.551 | 0.0955 | 0.405 to 0.690 | 0.9171 |