CAM 20478

Molecular Markers in Fine Needle Aspirates of the Thyroid

Category:Laboratory   Last Reviewed:April 2019
Department(s):Medical Affairs   Next Review:April 2020
Original Date:February 2012    

Description:
Fine needle aspiration - tissue samples are obtained for cytologic examination using 23 to 27 gauge (commonly 25 gauge) needles with or without local anesthesia. (Ross, 2017).

Mutation analysis – Mutational analysis by sequencing or PCR which identifies individual molecular markers of malignancy including BRAF, RAS, RET/PTC, and PAX8/PPARgamma (Ross, 2017).

Gene expression classifier – measures mRNA to determine the activity level of a panel of 167 genes and uses an algorithm to predict malignancy based on gene expression (Ross, 2017). 

Background  
Fine-needle aspiration (FNA) is a traditional diagnostic approach to differentiate thyroid nodules that are malignant and need to be treated surgically from the majority of nodules that are benign and do not require surgery. It offers definitive diagnosis in the majority of cases, however, 10–25% of nodules yield an indeterminate cytologic diagnoses, in which cancer cannot be ruled out, leading to suboptimal management of these patients and frequently resulting in unnecessary surgical interventions (Nikiforov, Yip, & Nikiforova, 2013). The risk of malignancy with these cytologic classifications ranges from 5 to 32 percent (Ross, 2017).

Three approaches to detection of molecular markers from fine needle biopsy of thyroid nodules have been developed based on mutational and other molecular markers, which can be reliably detected in cells aspirated during the FNA procedure (Hodak & Rosenthal, 2013; Xing, Haugen, & Schlumberger, 2013).

A study of BRAF, RAS, RET/PTC, and PAX8/PPARgamma mutational analysis, reveals that detection of any mutation conferred a risk of histologic malignancy of 88 and 87 percent for samples showing FLUS/AUS and follicular neoplasm, respectively (Nikiforov et al., 2011). However, a 14 percent false negative rate limits the usefulness of this panel.

Expanding to using a next-generation sequencing assay, additional point mutations (including TERT, TP53, and others), as well as gene fusions that occur in thyroid cancer (Nikiforov et al., 2014) result in a negative predictive value for malignancy of 96 percent and a positive predictive value of 83 percent for cytology showing follicular neoplasm.

Using mRNA expression analysis and a gene expression classifier trained on FNA samples to detect benign thyroid nodules, the classifier had a negative predictive value for malignancy of 95 percent but the positive predictive value was only 38 percent, respectively(Alexander et al., 2012; Chudova et al., 2010; McIver et al., 2014).

A combined test using both miRNA gene expression combined with mutational analysis had a negative predictive value of 97 and 91 percent and a positive predictive value for malignancy of 68 and 82 percent, respectively (Labourier et al., 2015).

No one methodology has achieved clinical utility to reliably resolve all indeterminate cytology, and thus several professional organizations, including the American Association of Clinical Endocrinologists (AACE) (Gharib et al., 2016) and the American Thyroid Association (ATA) (Haugen et al., 2016), National Comprehensive Cancer Network (NCCN) (NCCN, 2016), have published guidelines for the evaluation of thyroid nodules, all of which endorse a similar multistep strategy suggesting molecular markers can be of use when cytology is indeterminate yet acknowledging its current limitations.

Regulatory Status 
Commercially available panels of molecular markers utilizing FNA specimens from the thyroid include miRInform™ (Asuragen) and Veracyte® (Afirma).

miRInform is a panel of 7 analytically validated molecular markers [mutations] (KRAS, BRAF, HRAS, NRAS, RET/PTC 1, RET/PTC3 and PAX8/PPARγ).

The Afirma "gene expression classifier" (GEC) is a proprietary diagnostic test offered by Veracyte, which claims to classify a thyroid nodule with indeterminate cytology as benign (with >95 percent negative predictive value) or as suspicious for malignancy (>50 percent risk of malignancy). The GEC measures the gene expression of 142 genes and applies a multi-dimensional algorithm to classify whether a nodule with an indeterminate cytologic diagnosis is benign or suspicious.

These commercially available, laboratory-developed tests are regulated under the Clinical Laboratory Improvement Amendments (CLIA). Premarket approval from the U.S. Food and Drug Administration (FDA) is not required when the assay is performed in a laboratory that is licensed by CLIA for high-complexity testing. 

Policy: 

  1. Mutation analysis (Eg. BRAF V600E, RET/PTC, RAS, PAX8/PPAR) or the use of gene expression classifier (Eg. Afirma GEC) in fine-needle aspirates of the thyroid that are cytologically characterized as follicular cell neoplasm (FN) / suspicious for follicular neoplasm (SFN), atypia of undetermined significance (AUS) or follicular lesion of undetermined significance (FLUS) is considered MEDICALLY NECESSARY in adult patients  (>18 years of age) patients being evaluated for thyroid carcinoma to assist in patient management decisions.
  2. Mutation analysis (Eg. BRAF V600E, RET/PTC, RAS, PAX8/PPAR) or the use of gene expression classifier (Eg.Afirma GEC) in fine-needle aspirates of the thyroid that are cytologically characterized as Hurthle cell, papillary or anaplastic neoplasm is considered NOT MEDICALLY NECESSARY in adult patients (>18 years of age) patients being evaluated for thyroid carcinoma.
  3. Mutation analysis (Eg. BRAF V600E, RET/PTC, RAS, PAX8/PPAR) or the use of gene expression classifier (Eg.Afirma GEC) in fine-needle aspirates of the thyroid that are cytologically characterized as follicular or Hurthle cell neoplasm (FN) / suspicious for follicular neoplasm (SFN), atypia of undetermined significance (AUS) or follicular lesion of undetermined significance (FLUS), papillary or anaplastic neoplasms is considered INVESTIGATIONAL in pediatric (≤18 years of age) patients being evaluated for thyroid carcinoma.
  4. The microRNA profiling tests (Eg.RosettaGX Reveal) in fine-needle aspirates of the thyroid that are cytologically characterized as follicular or Hurthle cell neoplasm (FN) / suspicious for follicular neoplasm (SFN), atypia of undetermined significance (AUS) or follicular lesion of undetermined significance (FLUS), papillary or anaplastic neoplasms is considered INVESTIGATIONAL in adult (>18 years of age) and pediatric (≤18 years of age) patients being evaluated for thyroid carcinoma.
  5. Mutation analysis (Eg. BRAF V600E, RET/PTC, RAS, PAX8/PPAR) or the use of gene expression classifier (Eg.Afirma GEC) or  the microRNA profiling tests (Eg.RosettaGX Reveal) is considered INVESTIGATIONAL in adult (>18 years of age) and pediatric (≤18 years of age) patients in all other situations.

Rationale  
Practice Guidelines and Position Statements
National Comprehensive Cancer Network
NCCN guidelines for thyroid carcinoma (NCCN, 2016) state: "Molecular diagnostic testing to detect individual mutations (e.g., BRAF, RET/PTC, RAS, PAX8/PPAR [peroxisome proliferator-activated receptors] gamma) or pattern recognition approaches using molecular classifiers may be useful in the evaluation of FNA samples that are indeterminate to assist in management decisions. The choice of the precise molecular test depends on the cytology and the clinical question being asked." Indeterminate groups include: "1) follicular or Hurthle cell neoplasms; and 2) AUS/FLUS." The NCCN Panel further recommended (category 2B) "molecular diagnostic testing for evaluating FNA results that are suspicious for: 1) follicular or Hurthle cell neoplasms; or 2) AUS/FLUS."

The NCCN guidelines also state that "the molecular testing (both the Gene Expression Classifier and the individual mutation analysis) was available in the majority of NCCN Member Institutions (>75%). About 70% of the panelists would recommend using a gene expression classifier in the evaluation of follicular lesions. The gene expression classifier measures the expression of at least 140 genes. BRAF mutation analysis was recommended by 50% of the panelists in the evaluation of thyroid nodules (not restricted to the follicular lesions). Furthermore, about 60% of the panelists would recommend BRAF testing in the evaluation of follicular lesions" (NCCN, 2016)

American Thyroid Association (ATA)
The 2015 ATA guidelines on the management of adult patients with thyroid nodules and differentiated thyroid cancer make the following recommendations on the use of molecular markers (Haugen et al., 2016):

  • If molecular testing is being considered, patients should be counseled regarding the potential benefits and limitations of testing and about the possible uncertainties in the therapeutic and long-term clinical implications of results. (Strong recommendation; low-quality evidence)
  • If intended for clinical use, molecular testing should be performed in Clinical Laboratory Improvement Amendments/College of American Pathologists (CLIA/CAP)-certified molecular laboratories, or the international equivalent, because reported quality assurance practices may be superior compared to other settings. (Strong recommendation; low-quality evidence)
  • For nodules with AUS/FLUS cytology, after consideration of worrisome clinical and sonographic features, investigations such as repeat FNA or molecular testing may be used to supplement malignancy risk assessment in lieu of proceeding directly with a strategy of either surveillance or diagnostic surgery. Informed patient preference and feasibility should be considered in clinical decision-making. (Weak recommendation; moderate-quality evidence)
  • Diagnostic surgical excision is the long-established standard of care for the management of FN/SFN cytology nodules. However, after consideration of clinical and sonographic features, molecular testing may be used to supplement malignancy risk assessment data in lieu of proceeding directly with surgery. Informed patient preference and feasibility should be considered in clinical decision-making. (Weak recommendation; moderate-quality evidence)

The guidelines also state that "there is currently no single optimal molecular test that can definitively rule in or rule out malignancy in all cases of indeterminate cytology, and long-term outcome data proving clinical utility are needed" (Haugen et al., 2016).

AACE/ACE/AME
Guidelines from the American Association of Clinical Endocrinologists, American College of Endocrinology (ACE) and Associazione Medici Endocrinologi (AME) recommend the following (Gharib et al., 2016):

  • "Molecular testing should be considered to complement not replace cytologic evaluation, where the results are expected to influence clinical management."
  • "As a general rule, not recommended in nodules with established benign or malignant cytologic characteristics."
  • "Consider the detection of BRAF and RET/PTC and, possibly, PAX8/PPARG and RAS mutations if such detection is available."
  • "Because of the insufficient evidence and the limited follow-up, they do not recommend either in favor of or against the use of gene expression classifiers (GECs) for cytologically indeterminate nodules."
  • "Currently, with the exception of mutations such as BRAFV600E that have a PPV approaching 100% for papillary thyroid carcinoma (PTC), evidence is insufficient to recommend in favor of or against the use of mutation testing as a guide to determine the extent of surgery"

References

  1. Alexander, E. K., Kennedy, G. C., Baloch, Z. W., Cibas, E. S., Chudova, D., Diggans, J., . . . Haugen, B. R. (2012). Preoperative diagnosis of benign thyroid nodules with indeterminate cytology. N Engl J Med, 367(8), 705-715. doi:10.1056/NEJMoa1203208
  2. Chudova, D., Wilde, J. I., Wang, E. T., Wang, H., Rabbee, N., Egidio, C. M., . . . Kennedy, G. C. (2010). Molecular classification of thyroid nodules using high-dimensionality genomic data. J Clin Endocrinol Metab, 95(12), 5296-5304. doi:10.1210/jc.2010-1087
  3. Gharib, H., Papini, E., Garber, J. R., Duick, D. S., Harrell, R. M., Hegedüs, L., . . . Vitti, P. (2016). AMERICAN ASSOCIATION OF CLINICAL ENDOCRINOLOGISTS, AMERICAN COLLEGE OF ENDOCRINOLOGY, AND ASSOCIAZIONE MEDICI ENDOCRINOLOGI MEDICAL GUIDELINES FOR CLINICAL PRACTICE FOR THE DIAGNOSIS AND MANAGEMENT OF THYROID NODULES – 2016 UPDATE. http://dx.doi.org/10.4158/EP161208.GL. doi:i1530-891X-22-s1-1
  4. Haugen, B. R., Alexander, E. K., Bible, K. C., Doherty, G. M., Mandel, S. J., Nikiforov, Y. E., . . . Wartofsky, L. (2016). 2015 American Thyroid Association Management Guidelines for Adult Patients with Thyroid Nodules and Differentiated Thyroid Cancer: The American Thyroid Association Guidelines Task Force on Thyroid Nodules and Differentiated Thyroid Cancer. Thyroid, 26(1), 1-133. doi:10.1089/thy.2015.0020
  5. Hodak, S. P., & Rosenthal, D. S. (2013). Information for clinicians: commercially available molecular diagnosis testing in the evaluation of thyroid nodule fine-needle aspiration specimens. Thyroid, 23(2), 131-134. doi:10.1089/thy.2012.0320
  6. Labourier, E., Shifrin, A., Busseniers, A. E., Lupo, M. A., Manganelli, M. L., Andruss, B., . . . Beaudenon-Huibregtse, S. (2015). Molecular Testing for miRNA, mRNA, and DNA on Fine-Needle Aspiration Improves the Preoperative Diagnosis of Thyroid Nodules With Indeterminate Cytology. J Clin Endocrinol Metab, 100(7), 2743-2750. doi:10.1210/jc.2015-1158
  7. McIver, B., Castro, M. R., Morris, J. C., Bernet, V., Smallridge, R., Henry, M., . . . Reddi, H. (2014). An independent study of a gene expression classifier (Afirma) in the evaluation of cytologically indeterminate thyroid nodules. J Clin Endocrinol Metab, 99(11), 4069-4077. doi:10.1210/jc.2013-3584
  8. NCCN, N. C. C. N. (2016). NCCN Clinical Practice Guidelines in Oncology: Thyroid Carcinoma Version 1.2016. Retrieved from https://www.nccn.org/professionals/physician_gls/f_guidelines.asp#detection
  9. Nikiforov, Y. E., Carty, S. E., Chiosea, S. I., Coyne, C., Duvvuri, U., Ferris, R. L., . . . Nikiforova, M. N. (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. doi:10.1002/cncr.29038
  10. Nikiforov, Y. E., Ohori, N. P., Hodak, S. P., Carty, S. E., LeBeau, S. O., Ferris, R. L., . . . Nikiforova, M. N. (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 Endocrinol Metab, 96(11), 3390-3397. doi:10.1210/jc.2011-1469
  11. Nikiforov, Y. E., Yip, L., & Nikiforova, M. N. (2013). New strategies in diagnosing cancer in thyroid nodules: impact of molecular markers. Clin Cancer Res, 19(9), 2283-2288. doi:10.1158/1078-0432.ccr-12-1253
  12. Ross, D. (2017). Diagnostic approach to and treatment of thyroid nodules - UpToDate. In D. Cooper (Ed.), UpToDate. Waltham. MA.
  13. Xing, M., Haugen, B. R., & Schlumberger, M. (2013). Progress in molecular-based management of differentiated thyroid cancer. Lancet, 381(9871), 1058-1069. doi:10.1016/s0140-6736(13)60109-9

 Coding Section 

Codes Number Description
CPT  0018U  Oncology (thyroid), microRNA profiling by RT-PCR of 10 microRNA sequences, utilizing fine needle aspirate, algorithm reported as a positive or negative result for moderate to high risk of malignancy
Proprietary Test: ThyraMIR® 
  0026U  Oncology (thyroid), DNA and mRNA of 112 genes, next-generation sequencing, fine needle aspirate of thyroid nodule, algorithmic analysis reported as a categorical result ("Positive, high probability of malignancy" or "Negative, low probability of malignancy")
Proprietary Test: ThyroSeq® 
  81445  Targeted genomic sequence analysis panel, solid organ neoplasm, DNA analysis, and RNA analysis when performed, 5-50 genes (eg, ALK, BRAF, CDKN2A, EGFR, ERBB2, KIT, KRAS, NRAS, MET, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements, if performed 
  81479   Unlisted molecular pathology procedure 
  81599 Unlisted multianalyte assay with algorithmic analysis

Procedure and diagnosis codes on Medical Policy documents are included only as a general reference tool for each policy. They may not be all-inclusive.

This medical policy was developed through consideration of peer-reviewed medical literature generally recognized by the relevant medical community, U.S. FDA approval status, nationally accepted standards of medical practice and accepted standards of medical practice in this community, Blue Cross and Blue Shield Association technology assessment program (TEC) and other non-affiliated technology evaluation centers, reference to federal regulations, other plan medical policies and accredited national guidelines. 

"Current Procedural Terminology© American Medical Association.  All Rights Reserved"  

History From 2014 Forward     

04/04/2019 

Annual review, no change to policy intent. Updating coding. 

08/04/2018 

Corrected formatting. No other changes. 

05/01/2018 

Interim review, rewriting entire policy to address medical necessity for BRAF, V600E, RET/PTC, RAS, PAX8/PPAR. Clarification of medically necessary, not medically necessary and investigational uses for this testing. 

02/05/2018 

Interim review adding medical necessity criteria for ThyroSeqv2, ThyraMIR microRNA/ThyGenX, Afirma BRAF after Afirma Gene Expression Classifier or Afirma MTC after Afirma Gene Expression Classifier. Also updating background, description, guidelines, rationale and references. 

04/25/2017 

Updated category to Laboratory. No other changes 

04/17/2017 

Annual review, no change to policy intent. 

01/03/2017 

Annual review, no change to policy intent. 

01/21/2016 

Updated review date

01/13/2016 

Interim review, major revision to policy including medical necessity criteria. This testing was previously considered investigational. Also updated rationale and references. 

01/05/2016 

Added CPT Code 81479 to Coding Section. No other changes made to policy.

12/1/2015

Updating CPT codes for 2016. No change to policiy intent. 

02/19/2015

Annual review, no change to policy intent. Updated rationale and references. Added guidelines and coding. 

02/17/2014

Annual review, updated title, description, regulatory status, rationale, summary and references. Added policy language that states: "The use of a gene expression classifier in fine-needle aspirates of the thyroid that are cytologically considered to be indeterminate, atypical or suspicious for malignancy is considered to be investigational." 

 


Go Back