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Shifted termination assay (STA) fragment analysis to detect BRAF V600 mutations in papillary thyroid carcinomas

So Young Kang15, Soomin Ahn1, Sun-Mi Lee2, Ji Yun Jeong3, Ji-Youn Sung4, Young Lyun Oh1* and Kyoung-Mee Kim1*

Author affiliations

1 Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Ilwon-dong, Gangnam-gu, Seoul 135-710, Korea

2 Department of Pathology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA

3 Department of Pathology, Kyungpook National University Hospital, Kyungpook National University School of Medicine, Daegu, Korea

4 Department of Pathology, KyungHee University Medical Center, KyungHee University School of Medicine, Seoul, Korea

5 Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746, Korea

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Citation and License

Diagnostic Pathology 2013, 8:121  doi:10.1186/1746-1596-8-121

Published: 24 July 2013



BRAF mutation is an important diagnostic and prognostic marker in patients with papillary thyroid carcinoma (PTC). To be applicable in clinical laboratories with limited equipment, diverse testing methods are required to detect BRAF mutation.


A shifted termination assay (STA) fragment analysis was used to detect common V600 BRAF mutations in 159 PTCs with DNAs extracted from formalin-fixed paraffin-embedded tumor tissue. The results of STA fragment analysis were compared to those of direct sequencing. Serial dilutions of BRAF mutant cell line (SNU-790) were used to calculate limit of detection (LOD).


BRAF mutations were detected in 119 (74.8%) PTCs by STA fragment analysis. In direct sequencing, BRAF mutations were observed in 118 (74.2%) cases. The results of STA fragment analysis had high correlation with those of direct sequencing (p < 0.00001, κ = 0.98). The LOD of STA fragment analysis and direct sequencing was 6% and 12.5%, respectively. In PTCs with pT3/T4 stages, BRAF mutation was observed in 83.8% of cases. In pT1/T2 carcinomas, BRAF mutation was detected in 65.9% and this difference was statistically significant (p = 0.007). Moreover, BRAF mutation was more frequent in PTCs with extrathyroidal invasion than tumors without extrathyroidal invasion (84.7% versus 62.2%, p = 0.001). To prepare and run the reactions, direct sequencing required 450 minutes while STA fragment analysis needed 290 minutes.


STA fragment analysis is a simple and sensitive method to detect BRAF V600 mutations in formalin-fixed paraffin-embedded clinical samples.

Virtual Slides

The virtual slide(s) for this article can be found here: webcite

BRAF; Mutation; Termination assay; Sequencing; Thyroid; Papillary carcinoma