Molecular Markers in Fine Needle Aspirates of the Thyroid

POLICY NUMBER

A.2.04.78

DESCRIPTION

To determine which patients need thyroid resection, many physicians will perform a cytologic examination of fine needle aspirate (FNA) samples from a thyroid lesion; however, this method has diagnostic limitations. As a result, assays using molecular markers have been developed to improve the accuracy of thyroid FNA biopsies.

Thyroid Nodules

Thyroid nodules are common, present in 5% to 7% of the U.S. adult population. However, most are benign, and most cases of thyroid cancer are curable surgically when detected early.

DiagnosisSampling thyroid cells by fine needle aspirate (FNA) is currently the most accurate procedure to distinguish benign thyroid lesions from malignant ones, reducing the rate of unnecessary thyroid surgery for patients with benign nodules and triaging patients with thyroid cancer to appropriate surgery.

About 60% to 70% of thyroid nodules are classified cytologically as benign, and 4% to 10% of nodules are cytologically deemed malignant. However, the remaining 20% to 30% have equivocal findings, usually due to overlapping cytologic features between benign and malignant nodules; these nodules usually require surgery for a final diagnosis. Thyroid FNA cytology is classified by Bethesda System criteria into the following groups: nondiagnostic; benign; follicular lesion of undetermined significance or atypia of undetermined significance; follicular neoplasm (or suspicious for follicular neoplasm); suspicious for malignancy; and malignant. Lesions with FNA cytology in the atypia of undetermined significance or follicular neoplasm of undetermined significance or follicular neoplasm categories are often considered indeterminate.

ManagementThere is some individualization of management for patients with FNA-indeterminate nodules, but many patients will require a surgical biopsy, typically thyroid lobectomy, with intraoperative pathology. Consultation would typically be the next step in the diagnosis. Approximately 80% of patients with indeterminate cytology undergo surgical resection; postoperative evaluation has revealed a malignancy rate ranging from 6% to 30%, making this a clinical process with very low specificity. Thus, if an analysis of FNA samples could reliably identify the risk of malignancy as low, there is potential for patients to avoid surgical biopsy.

Preoperative planning of optimal surgical management in patients with equivocal cytologic results is challenging because different thyroid malignancies require different surgical procedures (e.g. unilateral lobectomy versus total or subtotal thyroidectomy with or without lymph node dissection) depending on several factors, including histologic subtype and risk-stratification strategies (tumor size, patient age). If a diagnosis cannot be made intraoperatively, a lobectomy is typically performed, and if on postoperative histology, the lesion is malignant, a second surgical intervention may be necessary for completion of thyroidectomy.

Thyroid Cancer

Most thyroid cancers originate from thyroid follicular cells and include well-differentiated papillarythyroid carcinoma (PTC; 80% of all thyroid cancers) and follicular carcinoma (15%). Poorly differentiated and anaplastic thyroid carcinomas are uncommon and can arise de novo or from preexisting well-differentiated papillary or follicular carcinomas. Medullary thyroid carcinoma originates from parafollicular or C cells and accounts for about 3% of all thyroid cancers.

The diagnosis of malignancy in the case of PTC is primarily based on cytologic features. If a fine needle aspirate in a case of PTC is indeterminate, surgical biopsy with intraoperative pathology consultation is most often diagnostic, although its efficacy and therefore its use will vary across institutions, surgeons, and pathologists. In 2016, reclassification of encapsulated follicular-variant PTC as a noninvasive follicular tumor with papillary-like nuclei was proposed and largely adopted; this classification removes the word carcinoma from the diagnosis to acknowledge the indolent behavior of these tumors.

For follicular carcinoma, the presence of invasion of the tumor capsule or blood vessels is diagnostic, and cannot be determined by cytology because tissue sampling is necessary to observe these histologic characteristics. Intraoperative diagnosis of follicular carcinoma is challenging and often not feasible because extensive sampling of the tumor and capsule is usually necessary and performed on postoperative, permanent sections.

New approaches for improving the diagnostic accuracy of thyroid FNA include variant analysis for somatic genetic alterations, to more accurately classify which patients need to proceed to surgery (and may include the extent of surgery necessary) and a gene expression classifier to identify patients who do not need surgery and can be safely followed.

Genetic VariantsAssociated With Thyroid CancerA number of genetic variants have been discovered in thyroid cancer. The most common four gene variants are BRAF and RAS single nucleotide variants (SNVs), and RET/PTC and PAX8/PPARγ rearrangements.

Papillary carcinomas carry SNVs of the BRAF and RASgenes, as well as RET/PTC and TRK rearrangements, all of which can activate the mitogen-activated protein kinase pathway. These mutually exclusive variants are found in more than 70% of papillary carcinomas. BRAF SNVs are highly specific for PTC. Follicular carcinomas harbor either RAS SNVs or PAX8/PPARγ rearrangements. These variants have been identified in 70% to 75% of follicular carcinomas. Genetic alterations involving the PI3K/AKT signaling pathway also occur in thyroid tumors, although they are rare in well-differentiated thyroid cancers and have a higher prevalence in less differentiated thyroid carcinomas. Additional variants known to occur in poorly differentiated and anaplastic carcinomas involve the TP53 and CTNNB1 genes. Medullary carcinomas, which can be familial or sporadic, frequently possess SNVs located in the RET gene.

Studies have evaluated the association between various genes and cancer phenotype in individuals with diagnosed thyroid cancer.

Telomerase reverse transcriptase (TERT) promoter variants occur with varying frequency in different thyroid cancer subtypes. Overall, TERT C228T or C250T variants have been reported in approximately 15% of thyroid cancers, with higher rates in the undifferentiated and anaplastic subtypes compared with the well-differentiated subtypes. TERT variants are associated with several demographic and histopathologic features such as older age and advanced TNM stage. TERT promoter variants have been reported to be independent predictors of disease recurrence and cancer-related mortality in well-differentiated thyroid cancer. Also, the co-occurrence of BRAF or RAS variants with TERT or TP53 variants may identify a subset of thyroid cancers with unfavorable outcomes.

Molecular Diagnostic Testing

Variant Detection and Rearrangement TestingSNVs in specific genes, including BRAF, RAS, and RET, and evaluation for rearrangements associated with thyroid cancers can be accomplished with Sanger sequencing or pyrosequencing or with real-time polymerase chain reaction (PCR) of single or multiple genes or by next-generation sequencing (NGS) panels. Panel tests for genes associated with thyroid cancer, with varying compositions, are also available. For example, Quest Diagnostics offers a Thyroid Cancer Mutation Panel, which includes BRAF and RAS variant analysis and testing for RET/PTC and PAX8/PPARγ rearrangements.

The ThyroSeq v3 Next-Generation Sequencing panel (Sonic Healthcare) is an NGS panel of 112 genes. The test is indicated when FNA cytology suggests atypia of uncertain significance or follicular lesion of undetermined significance, follicular neoplasm or suspicious for follicular neoplasm, or suspicious for malignancy. In particular, it has been evaluated in patients with follicular neoplasm and/or suspicious for follicular neoplasm on FNA as a test to increase both sensitivity and specificity for cancer diagnosis. ThyGenX is an NGS panel that sequences 8 genes and identifies specific gene variants and translocations associated with thyroid cancer. ThyGenX is intended to be used in conjunction with the ThyraMIR microRNA expression test when the initial ThyGenX test is negative.

Gene Expression ProfilingGenetic alterations associated with thyroid cancer can be assessed using gene expression profiling, which refers to the analysis of messenger RNA (mRNA) expression levels of many genes simultaneously. Several gene expression profiling tests are available and stratify tissue from thyroid nodules biologically.

The Afirma Gene Expression Classifier (Afirma GEC; Veracyte) analyzed the expression of 142 different genes to determine patterns associated with benign findings on surgical biopsy. It was designed to evaluate thyroid nodules that have an “indeterminate” classification on FNA as a method to select patients ("rule out") who are at low-risk for cancer. In 2017, Veracyte migrated the Afirma GEC microarray analysis to a next-generation RNA sequencing platform and now markets the Afirma Gene Sequencing Classifier (Afirma GSC) which evaluates 10,196 genes with 1,115 core genes.

Other gene expression profiles have been reported in investigational settings, but have not been widely validated or used commercially; they are not addressed in this policy.

ThyraMIR is a microRNA expression-based classifier intended for use in thyroid nodules with indeterminate cytology on FNA following a negative result from the ThyGenX Thyroid Oncogene Panel.

Algorithmic TestingAlgorithmic testing involves the use of two or more tests in a prespecified sequence, with a subsequent test automatically obtained depending on results of an earlier test.

Algorithmic Testing Using Afirma GEC With Afirma MTC and Afirma BRAFIn addition to Afirma GSC, Veracyte also markets two “malignancy classifiers” that use mRNA expression-based classification to evaluate for BRAF variants (Afirma BRAF) or variants associated with medullary thyroid carcinoma (Afirma MTC). The table below describes the testing algorithms for Afirma MTC and Afirma BRAF.

Afirma MTC and Afirma BRAF Testing Algorithms

Afirma GSC: Afirma Gene Sequencing Classifier; Afirma MTC: Afirma medullary thyroid carcinoma In a description of the Afirma BRAF test, the following have been proposed as benefits of the mRNA-based expression test for BRAF variants: (1) PCR-based methods may have low sensitivity, requiring that a large proportion of the nodule have a relevant variant; (2) testing for only one variant may not detect patients with low-frequency variants that result in the same pattern of pathway activation; and (3) PCR-based approaches with high analytic sensitivity may require a large of amount of DNA that is difficult to isolate from small FNA samples.

The testing strategy for both Afirma MTC and Afirma BRAF is to predict malignancy from an FNA sample with increased pretest probability for malignancy. A positive result with Afirma MTC or Afirma BRAF would inform preoperative planning such as planning for a hemi- vs a total thyroidectomy or performance of a central neck dissection.

Algorithmic Testing Using ThyGenX and ThyraMIRThe ThyGenX Thyroid Oncogene Panel (Interpace Diagnostics; testing is done at Asuragen Clinical Laboratory) is an NGS panel designed to assess patients with indeterminate thyroid FNA results. It includes sequencing of 8 genes associated with papillary thyroid carcinoma and follicular carcinomas. ThyGenX has replaced the predicate miRInform Thyroid test that assesses for 17 validated gene alterations.

ThyraMIR (Interpace Diagnostics) is a microRNA expression-based classifier intended for use in thyroid nodules with indeterminate cytology on FNA following a negative result from the ThyGenX Thyroid Oncogene Panel.

The testing strategy for combined ThyGenX and ThyraMIR testing is first to predict malignancy. A positive result on ThyGenX would “rule in” patients for surgical resection. The specific testing results from a ThyGenX positive test would be used to inform preoperative planning when positive. For a ThyGenX negative result, the reflex testing involves the ThyraMIR microRNA expression test to “rule out” for a surgical biopsy procedure given the high negative predictive value of the second test. Patients with a negative result from the ThyraMIR test would be followed with active surveillance and avoid a surgical biopsy.

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory-developed tests must meet the general regulatory standards of the Clinical Laboratory Improvement Amendments. Thyroid variant testing and gene expression classifiers are available under the auspices of the Clinical Laboratory Improvement Amendments. Laboratories that offer laboratory-developed tests must be licensed by the Clinical Laboratory Improvement Amendments for high-complexity testing. To date, the U.S. Food and Drug Administration has chosen not to require any regulatory review of this test.

In 2013, the THxID™-BRAF kit (bioMérieux), an in vitro diagnostic device, was approved by the Food and Drug Administration through the premarket approval process to assess specific BRAF variants in melanoma tissue via real-time PCR. However, there are currently no diagnostic tests for thyroid cancer mutation analysis with approval from the Food and Drug Administration.

The table below provides a summary of commercially available molecular diagnostic tests for indeterminate thyroid pathology.

Summary of Molecular Tests for Indeterminate Thyroid Cytopathology FNA Specimens

FNA: fine needle aspirate; GEC: Gene Expression Classifier; GSC: Gene Sequencing Classifier; mRNA: messenger RNA; MTC: medullary thyroid carcinoma; PCR: polymerase chain reaction.ªThe miRInform® test is the predicate test to ThyGenX™ and is not commercially available.

POLICY

For individuals who have thyroid nodules without strong clinical or radiologic findings suggestive of malignancy in whom surgical decision making would be affected by test results, the use of either of the following types of molecular marker testing or gene variant analysis in fine needle aspirates of thyroid nodules with indeterminate cytologic findings (ie, Bethesda diagnostic category III [atypia/follicular lesion of undetermined significance] or Bethesda diagnostic category IV [follicular neoplasm/suspicion for a follicular neoplasm]) may be considered medically necessary:

• Afirma® Genomic Sequencing Classifier; or

• ThyroSeq®.

The use of any of the following types of molecular marker testing or gene variant analysis in fine needle aspirates of thyroid nodules with indeterminate findings (Bethesda diagnostic category III [atypia/follicular lesion of undetermined significance] or Bethesda diagnostic category IV [follicular neoplasm/suspicion for a follicular neoplasm]) or suspicious findings (Bethesda diagnostic category V [suspicious for malignancy]) to rule in malignancy to guide surgical planning for initial resection rather than a 2-stage surgical biopsy followed by definitive surgery may be considered medically necessary:

• ThyroSeq;

• ThyraMIR® microRNA/ThyGenX®;

• Afirma BRAF after Afirma Genomic Sequencing Classifier; or

• Afirma MTC after Afirma Genomic Sequencing Classifier.

Gene expression classifiers, genetic variant analysis, and molecular marker testing in fine needle aspirates of the thyroid not meeting criteria outlined above, including but not limited to use of single-gene TERT testing, are considered investigational.

POLICY EXCEPTIONS

None

POLICY GUIDELINES

The coverage guidelines outlined in the Medical Policy Manual should not be used in lieu of the Member's specific benefit plan language.

In individuals who do not undergo surgical biopsy or thyroidectomy on the basis of gene expression classifier or molecular marker results, regular active surveillance is indicated.

Use of molecular marker testing based on fine needle aspirate of a thyroid nodule to rule in malignancy prior to surgical biopsy may guide surgical planning, particularly factors such as choice of surgical facility provider to ensure that the capability is available to conduct a frozen section pathologic reading during surgical biopsy so that surgical approach may be adjusted accordingly in a single surgery.

Genetic Counseling

Experts recommend formal genetic counseling for individuals who are at risk for inherited disorders and who wish to undergo genetic testing. Interpreting the results of genetic tests and understanding risk factors can be difficult for some individuals; genetic counseling helps individuals understand the impact of genetic testing, including the possible effects the test results could have on the individual or their family members. It should be noted that genetic counseling may alter the utilization of genetic testing substantially and may reduce inappropriate testing. Genetic counseling should be performed by an individual with experience and expertise in genetic medicine and genetic testing methods.

Medically Necessary is defined as those services, treatments, procedures, equipment, drugs, devices, items or supplies furnished by a covered Provider that are required to identify or treat a Member's illness, injury or Mental Health Disorders, and which Company determines are covered under this Benefit Plan based on the criteria as follows in A through D:

A. consistent with the symptoms or diagnosis and treatment of the Member's condition, illness, or injury; and

B. appropriate with regard to standards of good medical practice; and

C. not solely for the convenience of the Member, his or her Provider; and

D. the most appropriate supply or level of care which can safely be provided to Member. When applied to the care of an Inpatient, it further means that services for the Member's medical symptoms or conditions require that the services cannot be safely provided to the Member as an Outpatient.

For the definition of medical necessity, “standards of good medical practice” means standards that are based on credible scientific evidence published in peer-reviewed medical literature generally recognized by the relevant medical community, and physician specialty society recommendations, and the views of medical practitioners practicing in relevant clinical areas and any other relevant factors. BCBSMS makes no payment for services, treatments, procedures, equipment, drugs, devices, items or supplies which are not documented to be Medically Necessary. The fact that a Physician or other Provider has prescribed, ordered, recommended, or approved a service or supply does not in itself, make it Medically Necessary.

Investigative is defined as the use of any treatment procedure, facility, equipment, drug, device, or supply not yet recognized as a generally accepted standard of good medical practice for the treatment of the condition being treated and; therefore, is not considered medically necessary. For the definition of Investigative, “generally accepted standards of medical practice” means standards that are based on credible scientific evidence published in peer-reviewed medical literature generally recognized by the relevant medical community, and physician specialty society recommendations, and the views of medical practitioners practicing in relevant clinical areas and any other relevant factors. In order for equipment, devices, drugs or supplies [i.e, technologies], to be considered not investigative, the technology must have final approval from the appropriate governmental bodies, and scientific evidence must permit conclusions concerning the effect of the technology on health outcomes, and the technology must improve the net health outcome, and the technology must be as beneficial as any established alternative and the improvement must be attainable outside the testing/investigational setting. 

POLICY HISTORY

03/22/2012: Approved by Medical Policy Advisory Committee.

01/14/2013: Added CPT codes 81404, 81405, and 81479 to the Code Reference section.

09/03/2013: Policy title changed from "Mutation Analysis in Fine Needle Aspirates of the Thyroid" to "Molecular Markers in Fine Needle Aspirates of the Thyroid." The policy statement was changed from mutation analysis in fine-needle aspirates of the thyroid that are cytologically considered to be indeterminate, atypical or suspicious for malignancy is considered to be investigational. It was updated to two separate policy statements as follows:  1) Mutation analysis in fine-needle aspirates of the thyroid is considered to be investigational. 2) 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.

07/11/2014: Policy reviewed; no changes to policy statement. Removed deleted CPT codes from the Code Reference section: 83891, 83896, 83898, 83902, 83907, 83909, 83912, and 83913.

12/31/2014: Code Reference section updated to revise the description of the following CPT codes: 81404 and 81405.

07/31/2015: Code Reference section updated for ICD-10.

09/11/2015: Policy description updated to add information regarding mutation testing and gene expression profiling. No change in policy statements. Investigative definition updated in the Policy Guidelines section.

12/31/2015: Code Reference section updated to add new 2016 CPT code 81545.

06/06/2016: Policy number A.2.04.78 added.

06/27/2017: Code Reference section updated to revise code descriptions for CPT codes 81404 and 81405, effective 07/01/2017.

09/29/2017: Code Reference section updated to add new CPT code 0018U. Effective 10/01/2017.

12/22/2017: Code Reference section updated to revise descriptions for CPT codes 81404 and 81405 effective 01/01/2018.

01/25/2018: Code Reference section updated to add new 2018 CPT code 0026U.

04/09/2018: Policy description updated regarding thyroid nodules and gene expression profiling. Added statement that the use of either Afirma GEC or ThyroSeq v2 in fine needle aspirates of thyroid nodules with indeterminate cytologic findings may be considered medically necessary in patients meeting certain criteria. Added medically necessary statement for molecular marker testing and gene variant analysis in fine needle aspirates of thyroid nodules. Revised investigational statement to state that gene expression classifiers, genetic variant analysis, and molecular marker testing in fine needle aspirates of the thyroid not meeting criteria, including Rosetta GX Reveal, are considered investigational. Policy Guidelines updated regarding genetics nomenclature and genetic counseling. Code Reference section updated to change investigational codes table to medically necessary codes table. Added ICD-10 diagnosis codes C73 and D44.0.

07/18/2018: Policy description updated regarding molecular tests. Policy statement updated to include single-gene TERT testing as investigational. Policy Guidelines updated regarding genetic counseling.

09/22/2020: Policy description updated regarding molecular tests. First medically necessary policy statement re-worded. Policy statement criteria updated to change "Afirma Gene Expression Classifier" to "Afirma Genomic Sequencing Classifier" and "ThyroSeq v2" to "ThyroSeq." Policy Guidelines updated to remove genetics nomenclature information. Code Reference section updated to add new CPT codes 0204U and 0208U, effective 10/01/2020.

12/16/2020: Code Reference section updated to add new CPT code 81546, effective 01/01/2021.

03/25/2021: Code Reference section updated to add new CPT code 0245U, effective 04/01/2021.

12/08/2021: Policy description updated. Policy statements unchanged. Policy Guidelines updated to define medically necessary. Code Reference section updated to add new CPT code 0287U, effective 01/01/2022.

09/09/2022: Policy description updated. Policy statement and Policy Guidelines updated to change "patients" to "individuals." Code Reference section updated to remove deleted CPT code 81545.

09/21/2023: Policy description updated. Policy statements unchanged. Code Reference section updated to remove deleted CPT code 0208U.

06/27/2024: Code Reference section updated to make note of deleted CPT code 0204U. Effective 06/30/2024.

09/12/2024: Policy reviewed; no changes.

09/22/2025: Policy description updated regarding tests. Investigational statement revised to remove the use of the RosettaGX Reveal test as this test has been discontinued. Code Reference section updated to remove deleted CPT code 0204U.

SOURCE(S)

Blue Cross Blue Shield Association policy # 2.04.78

CODE REFERENCE

This may not be a comprehensive list of procedure codes applicable to this policy.

The code(s) listed below are ONLY medically necessary if the procedure is performed according to the "Policy" section of this document.

Medically Necessary Codes

CPT copyright American Medical Association. All rights reserved. CPT is a registered trademark of the American Medical Association.