The Integrated Diagnostic Approach to Thyroid Nodules

The Integrated Diagnostic Approach to Thyroid Nodules *

By Teresa Alasio, MD


The overwhelming majority of patients presenting with thyroid nodules usually receive a benign diagnosis when Ultrasound Guided Fine Needle Aspiration (USFNA) is performed. Arriving at the diagnosis requires a synergy of clinical, ultrasound, cytologic and, in some cases, molecular findings. We are fortunate to be practicing in an era where such a variety of diagnostic tools are available at our fingertips. Knowing when and where to use these tools goes a long way in the efficient utilization of available resources and ultimately providing the most complete and thorough diagnostic workup for patients with thyroid nodules.

Ultrasound Guided Fine Needle Aspiration (USFNA) is the first line diagnostic test in the diagnosis of thyroid nodules. Not all thyroid nodules need to be biopsied, however. The provisional 2014 American Thyroid Association Guidelines for Management of Thyroid Nodules and Differentiated Thyroid Cancer (ATA Guidelines) advocate incorporation of suspicious ultrasound features and not just overall size of a thyroid nodule when making the determination of whether or not to perform an USFNA. 1 Thyroid nodules, including those measuring less than 1cm, with suspicious ultrasound features, such as calcifications, heterogeneous echotexture or increased internal vascularity (Grade 3 or 4 Doppler flow), should undergo FNA for diagnosis and further testing. In comparison, thyroid nodules, even those measuring greater than 1cm, with reassuring ultrasound features, such as halo, comet tail artifact (indicating inspissated colloid) or Grade 1 Doppler flow, continued surveillance with ultrasound is recommended.

The Bethesda System for Reporting Thyroid Cytopathology (Ali, Cibas, eds. 2009) is strongly recommended as the terminology used by cytopathologist for reporting FNA cytology. 2 The Bethesda System has 6 diagnostic categories: I: Non-diagnostic; II: Benign; III: Atypia of Undetermined Significance (AUS); IV: Follicular Neoplasm or Suspicious for Follicular Neoplasm; V: Suspicious for Malignancy; VI: Malignant. Of these 6 categories, 15-30% of thyroid lesions fall into the ”indeterminate” categories, III and IV and it is for these cases that molecular testing has been shown to be helpful. Molecular testing is also applied to cases with cytology in Categories V and VI for purposes of risk stratification and treatment planning. Molecular testing is not recommended as a screening test for cytologically benign thyroid nodules (Category II).3,4 The same proposed Guidelines also advocate molecular testing for cytologically indeterminate nodules (Categories III and IV), and cite both the Gene Expression Classifier (GEC) and Next Generation Sequencing (NGS) as acceptable tests.1  These are the two major molecular tests that are currently available for thyroid nodules with indeterminate cytology.

The Gene Expression Classifier (GEC) test commercially known as Afirma (Veracyte, Inc.) measures the expression of 167 gene transcripts and is recommended for use in cytologically indeterminate thyroid nodules (Categories III and IV).3 Based on the results, nodules are classified as “benign” or “suspicious”, where the test has been designed to maximize the sensitivity and negative predictive value (NPV).  According to published results from a multicenter, prospective, blinded validation study, a “benign” GEC result in a nodule with indeterminate cytology is equivalent to a cytologically benign nodule.4 The significance of these results is that the high NPV allows for non-surgical management of patients with benign GEC results. It is also reported that a GEC result of “suspicious” carries a 40% risk of malignancy.4,5

Next Generation Sequencing (NGS), known as ThyroSeq, from the University of Pittsburgh, tests for a panel of mutations, including BRAF, RAS (NRAS, HRAS, KRAS), RET/PTC, PAX8/PPARg, along with a collection of other mutations which are mutually exclusive and have been shown to occur in thyroid neoplasms. Of the mutations tested for in the NGS assay, only BRAF (V600E) has been shown to be directly oncogenic in papillary thyroid cancer (PTC), and occurs in up to 40% of PTC cases.6,7 RAS mutations have been shown to exist in follicular neoplasm, both follicular adenomas and follicular carcinomas.8,9  In contrast with the GEC, molecular tests using Next Generation Sequencing carry a high Positive Predictive Value (PPV) and have clinical utility in Category V (Suspicious) and Category VI (Malignant) cases.  With an expanded panel of detectable mutations, the NPV of the ThyroSeq test (ThyroSeq V2) has been increased to over 90% as recent presentations have indicated.9   Larger multicenter studies with publication of findings will be needed to determine whether the negative predictive value of the ThyroSeq V2 test will hold up in routine practice. Papillary thyroid carcinomas (PTCs) with positive BRAF (V600E) mutation have been reported to be associated with poor prognostic factors, such as extrathyroidal invasion, lymph node metastases and recurrence.9, 10  Additional markers of aggressive tumor behavior have also been seen where BRAF or RAS mutations are co-existent with PIK3CA, AKT1 or TP53 in the same tumor in poorly differentiated and anaplastic tumors, and up to 4% of well differentiated PTCs which have more than one mutation are distinctively aggressive and typically present with distant metastases.10

The diagnosis of thyroid nodules requires an integrated approach which includes clinical history, ultrasound features, FNA cytology and, in relevant instances, molecular testing results.  The decision whether to proceed or refrain from surgical intervention must take into consideration as much diagnostic information that there is available for each individual patient.  The provisional 2014 Guidelines by the American Thyroid Association have valuable utility because the diagnostic criteria and recommendations for testing are based on a consensus of endocrinologists, surgeons, radiologists and pathologists, reflecting the integrated diagnostic approach to patient with thyroid nodules.



  1. American Thyroid Association, 2014 American Thyroid Association Guidelines on the Thyroid Nodules and Differentiated Thyroid Cancer – Highlights, Consensus and Controversies.
  2. Ali SZ, Cibas ES (2009). The Bethesda System for Reporting Thyroid Cytology: Definitions, Criteria and Explanatory Notes. Springer.
  3. Alexander EK, Kennedy GC, Baloch ZW, Cibas ES, Chudova D, Diggans J, Friedman L, Kloos RT, LiVolsi VA, Mandel SJ, Raab SS, Rosai J, Steward DL, Walsh PS, Wilde JI, Zeigler MA, Lanman RB, Haugen BR (2012). Preoperative diagnosis of benign thyroid nodules with indeterminate cytology. New England Journal of Medicine, 2012: 367: 705-715.
  4. Alexander EK, Schorr M, Klopper J, Kim C, Sipos J, Nabhan F, Parker C, Steward, Mandel SJ, Haugen B. (2013). Multicenter clinical experience with the Afirma Gene Expression Classifier. J Clin Endocrinology and Metabolism, Oct 2013 doi: 10.1210/jc.2013-2482.
  5. Duick DS, Klopper JP, Diggans JC, Friedman L, Kennedy GC, Lanman RB, McIver B. (2012). The impact of benign Gene Expression Classifier test results on the endocrinologist – patient decision to operate on patients with thyroid nodules with indeterminate fine needle aspiration cytology. Thyroid 22(10): 996-1001.
  6. Nikiforova MN, Wald AI, Roy S, Durso MB and Nikiforov YE. (2013). Targeted next-generational sequencing panel (Thyroseq) for detection of mutations in thyroid cancer. J Clin Endocrinology and Metabolism, Nov 2013; 98(11): E1852-E1860.
  7. Nikiforov YE, Ohori NP, Hodak SP, Carty SE, LeBeau SO, Ferris RL, Yip L, Seethala RR, Tublin ME, Stang MT, Coyne C, Johnson JT, Stewart AF, Nikiforova MN (2011). Impact of mutational testing on the diagnosis and management of patients with cytologically indeterminate thyroid nodules: A prospective analysis of 1056 FNA samples. J Clin Endocrinology Metabolism, November 2011, 96(11): 3390-3397.
  8. Nikiforov YE, Carty SE, Chiosea SI, Coyne C, Duvvuri U, Ferris RL, Gooding WE, Hodak SP, LeBeau SO, Ohori NP, Seethala, Tublin ME, Yip LY, Nikiforova MN, (2014). Highly accurate diagnosis of cancer in thyroid nodules with follicular neoplasm/suspicious for a follicular neoplasm cytology by ThyroSeq v2 next-generation sequencing assay. Cancer: 120(23): 3627-3634.
  9. Melck AL, Yip L, Carty SE. 2010. The utility of BRAF testing in the management of papillary thyroid cancer. The Oncologist 2010; 15: 1285-1293.
  10. Hsiao SJ and Nikiforov YE (2014). Molecular approaches to thyroid cancer diagnosis. Endocrine Related Cancer (2014) 21, T301-T313.

*This article originally appeared in “White Plains Hospital Cancer and Blood News”, Volume 2(1), January 12, 2015.