College of American Pathologists



Molecular Diagnostics of Thyroid Tumors

Posted November 4, 2012

Feriyl Bhaijee, MB, ChB
CAP Cancer Committee

The molecular genetics of thyroid carcinoma can be translated into clinical practice as an ancillary tool for diagnosis and prognostication.1 The two most common types of thyroid carcinoma, papillary and follicular carcinoma, harbor four nonoverlapping genetic alterations—BRAF and RAS point mutations and RET/PTC and PAX8/PPARγ rearrangements in more than 70% of cases.

BRAF V600E mutation is the most common known genetic event in papillary thyroid carcinoma, and it represents a specific marker for papillary carcinoma and related tumor types.1 It also correlates with aggressive characteristics, such as extrathyroidal extension, advanced stage at presentation, lymph node or distant metastases, and increased tumor recurrence and tumor-related mortality; thus, it is a useful prognostic indicator.2-5 RET/PTC rearrangements are also found in papillary thyroid carcinomas, especially in young patients and patients with radiation exposure.6-9 RET/PTC-positive tumors usually present with classic papillary histology and have a high rate of lymph node metastases.10

RAS (NRAS, HRAS, KRAS) point mutations are found in the follicular variant of papillary carcinomas, follicular carcinomas, and follicular adenomas.1 Papillary carcinomas with RAS mutations are usually encapsulated with a low rate of lymph node metastases.10 The presence of RAS mutations in cold adenomatous nodules and goiter nodules suggests that these lesions are likely true neoplasms, and they should be categorized as follicular adenomas.1

PAX8/PPARγ rearrangement occurs in the convention type of follicular carcinomas and oncocytic carcinomas. PAX8/PPARγ-positive tumors are usually small, with frequent vascular invasion, and tend to occur in younger patients.11,12 Occasionally, follicular variant papillary carcinomas and follicular adenomas may also harbor the PAX8/PPARγ rearrangement.11,13

While FNA cytology is usually diagnostic for thyroid lesions, 10% to 40% of FNA samples may be “indeterminate for malignancy.”14-17 Recent evidence suggests that molecular analysis of these FNA samples may improve the accuracy of cytologic diagnosis and guide patient management. For example, the presence of a BRAF mutation in an FNA sample indicates more than 99% probability of thyroid cancer, and it serves as a marker of aggressive behavior.1 Preoperatively detected BRAF-positive nodules should be extensively excised,18 with more aggressive treatment and follow-up.19 Detection of a RAS mutation in FNA samples correlates with malignancy in 74% to 88% of cases,20,21 and it is a useful marker for pre operative diagnosis of follicular variant of papillary carcinoma and follicular carcinoma, both of which are difficult to diagnose by cytology alone.

The American Thyroid Association’s recent Revised Management Guidelines for Patients with Thyroid Nodules and Differentiated Thyroid Cancer recommends the use of molecular markers, such as BRAF, RAS, RET/PTC, and PAX8/PPARγ, for indeterminate FNA cytology to guide patient management.22 Molecular analysis of excised thyroid lesions has limited diagnostic value for papillary carcinomas, but the PAX8/PPARγ rearrangement is characteristically seen in follicular carcinoma, and its presence in a follicular lesion should prompt a thorough examination for histologic features of malignancy.1

The most appropriate molecular analytic technique is determined by the mutation type suspected and sample type available for analysis.1 Freshly-collected FNA samples or snap-frozen tumor samples generally offer the highest quality DNA and RNA for molecular testing, but formalin-fixed or cytologic ethanol-fixed samples can also be used. Point mutations, such as BRAF and RAS, can be reliably detected by a variety of techniques including Sanger sequencing, pyrosequencing, and real-time PCR.23 The detection of chromosomal rearrangements, such as RET/PTC or PAX8/PPARγ, can be achieved by RT-PCR or by fluorescence in situ hybridization analysis.

In summary, four mutation types can be identified in papillary and follicular thyroid carcinomas: BRAF, RAS, RET/PTC, and PAX8/PPARγ. These mutations impact tumor diagnosis and prognostication, which may direct clinical management. Therefore, pathologists should perform molecular analysis of thyroid nodules when clinically indicated.


  1. Nikiforov YE. Molecular analysis of thyroid tumors. Mod Pathol. 2011;24:S34–43.
  2. Nikiforova MN, Kimura ET, Ghandi M, et al. BRAF mutations in thyroid tumors are restricted to papillary carcinomas and anaplastic or poorly differentiated carcinomas arising from papillary carcinomas. J Clin Endocrinol Metab. 2003;88(11):5399–5404.
  3. Xing M, Westra WH, Tufano RP, et al. BRAF mutation predicts a poorer clinical prognosis for papillary thyroid cancer. J Clin Endocrinol Metab. 2005;90(12):6373–6379.
  4. Xing M. BRAF mutation in papillary thyroid cancer: pathogenic role, molecular bases, and clinical implications. Endocr Rev. 2007;28(7):742–762.
  5. Elisei R, et al. BRAF V600E mutation and outcome of patients with papillary thyroid carcinoma: a 15-year median follow-up study. J Clin Endocrinol Metab. 2008;93(10):3943–3949.
  6. Nikiforov YE, Rowland JM, Bove KE, Monforte-Munoz H, Fagin JA. Distinct pattern of ret oncogene rearrangements in morphological variants of radiation-induced and sporadic thyroid papillary carcinomas in children. Cancer Res. 1997;57(9):1690–1694.
  7. Soares P, Fonseca E, Wynford-Thomas D,Sobrinho-Simõ.es M. Sporadic ret-rearranged papillary carcinoma of the thyroid: a subset of slow growing, less aggressive thyroid neoplasms? J Pathol. 1998;185(1):71–78.
  8. Rabes HM, Demidchik EP, Sidorow JD, et al. Pattern of radiation-induced RET and NTRK1 rearrangements in 191 post-chernobyl papillary thyroid carcinomas: biological, phenotypic, and clinical implications. Clin Cancer Res. 2000;6(3):1093–1103.
  9. Fenton CL, Lukes Y, Nicholson D, et al. The ret/PTC mutations are common in sporadic papillary thyroid carcinoma of children and young adults. J Clin Endocrinol Metab. 2000;85(3):1170–1175.
  10. Adeniran AJ, Zhu Z, Ghandi M, et al. Correlation between genetic alterations and microscopic features, clinical manifestations, and prognostics characteristics of thyroid papillary carcinomas. Am J Surg Pathol. 2006;30(2):216–222./
  11. Nikiforova MN, Lynch RA, Biddinger PW, et al. RAS point mutations and PAX8/PPAR gamma rearrangement in thyroid tumors: evidence for distinct molecular pathways in thyroid follicular carcinoma. J Clin Endocrinol Metab. 2003;88(5):2318–2326.
  12. French CA, Alexander EK, Cibas ES, et al. Genetic and biological subgroups of low-stage follicular thyroid cancer. Am J Pathol. 2003;162(4):1053–1060.
  13. Castro P, Rebocho AP, Soares RJ, et al. PAX8-PPARγ rearrangement is frequently detected in the follicular variant of papillary thyroid carcinoma. J Clin Endocrinol Metab. 2006;91(1):213–220.
  14. Greaves TS, Olvera M, Florentine BD, et al. Follicular lesions of thyroid: a 5-year fine-needle aspiration experience. Cancer. 2000;90(6):335–341.
  15. Sclabas GM, Staerkel GA, Shapiro SE, et al. Fine-needle aspiration of the thyroid and correlation with histopathology in a contemporary series of 240 patients. Am J Surg. 2003;186(6):702–709.
  16. Gharib H. Changing trends in thyroid practice: understanding nodular thyroid disease. Endocr Pract. 2004;10(1):31–39.
  17. Cooper DS, Doherty GM, Haugen BR, et al. Management guidelines for patients with thyroid nodules and differentiated thyroid cancer. Thyroid. 2006;16(2):109–142.
  18. Yip L, Nikiforova MN, Carty SE, et al. Optimizing surgical treatment of papillary thyroid carcinoma associated with BRAF mutation. Surgery. 2009;146(6):1215–1223.
  19. Xing M. Prognostic utility of BRAF mutation in papillary thyroid cancer. Mol Cell Endocrinol. 2010;321(1):86–93.
  20. Nikiforov YE, Steward DL, Robinson-Smith TM, et al. Molecular testing for mutations in improving the fine-needle aspiration diagnosis of thyroid nodules. J Clin Endocrinol Metab. 2009;94(6):2092–2098.
  21. Cantara S, Capezzone M, Marchisotta S, et al. Impact of proto-oncogene mutation detection in cytological specimens from thyroid nodules improves the diagnostic accuracy of cytology. J Clin Endocrinol Metab. 2010;95(3):1365–1369
  22. American Thyroid Association (ATA) Guidelines Taskforce on Thyroid Nodules and Differentiated Thyroid Cancer, Cooper DS, Doherty GM, et al. Revised American Thyroid Association management guidelines for patients with thyroid nodules and differentiated thyroid cancer. Thyroid. 2009;19(11):1167–1214.
  23. Nikiforova MN. Principles of molecular diagnostics in thyroid samples. In: Nikiforov YE, Biddinger PW, Thompson LDR, eds. Diagnostic pathology and molecular genetics of the thyroid. Baltimore, MD: Lippincott Williams & Wilkins;2009:160–213.

Download this article in Microsoft Word format.
Download this article in PDF format.

NewsPath® Editor: Kyle L. Eskue, MD
This newsletter is produced in cooperation with the College of American Pathologists Public Affairs Committee and the NewsPath Editorial Board and may be reproduced in whole or in part as a service to the medical community. Copyright © 2012 by the College of American Pathologists.
Please e-mail any comments to


Related Links