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Background: Although squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) can be easily diagnosed clinically, proper diagnosis is sometimes difficult when based on clinical information alone. Objective: To know what causes clinical misdiagnosis between SCC and BCC, and evaluate whether dermoscopy can improve diagnostic accuracy. Methods: Clinical and dermoscopic photographs of inversely diagnosed cases (histologically confirmed BCC with a clinical impression of SCC or vice versa) were randomly presented to six dermatologists and the reasons for each correct or incorrect diagnosis were analyzed. Results: Among 154 cases (SCCs or BCCs), 13 cases were inversely diagnosed; 9 SCCs were clinically misdiagnosed as BCC and 4 BCCs were clinically misdiagnosed as SCC. Clinically, scales, pigmentation and rolled border were meaningful factors to discern two carcinomas. Scales without both pigmentation and rolled border was favored for SCC, but BCC favored vice versa. Ulceration, telangiectasia and translucency contributed as confusing factors for proper diagnosis. Dermoscopy improved overall diagnostic accuracy to odds ratio 2.86. Conclusion: SCC has a higher tendency to be clinically misdiagnosed as BCC than vice versa. Pigmentation and rolled border are factors causing misdiagnosis of SCC as BCC and BCC may be misdiagnosed as SCC in the presence of scaling. Dermoscopy seems to improve the clinical diagnostic accuracy but has limitations for some ambiguous lesions.