Use of the Afirma® Gene Expression Classifier for Preoperative Identification of Benign Thyroid Nodules with Indeterminate Fine Needle Aspiration Cytopathology
Use of the Afirma Gene Expression Classifier for Preoperative Identification of Benign Thyroid Nodules with Indeterminate Fine Needle Aspiration Cytopathology
0 , Gregory W. Randolph
1 February 11 , 2013 Diagnostic Syed Z. Ali
2 1 Professor of Pathology, Johns Hopkins University School of Medicine, 2 Memorial Sloan Kettering Cancer Institute and Associate Professor of Medicine (Endocrinology) Weill Cornell Medical College, 3 Chief Medical Officer, Veracyte, Inc., 4 Associate Professor of Surgery (Otology and Laryngology), Harvard Medical School, 5 Professor of Surgery (Surgical Oncology), Duke University School of Medicine
Ruling out malignancy in thyroid nodules historically depended on thyroid resection and histopathological evaluation until fine needle aspiration (FNA) biopsy was introduced into the United States in the 1970s. Thyroid FNA biopsy identified a majority of thyroid nodules as benign, obviating the need for surgery in over half of the patients. However, 15%-30% of thyroid FNAs have indeterminate cytology that still requires operation, even though most of these operated nodules prove to be benign post-operatively. In order to predict which cytologically indeterminate thyroid nodules are benign and to potentially avoid surgery on these nodules, a recently described commercially available Gene Expression Classifier (GEC) test (Afirma, Veracyte, Inc., South San Francisco, CA) has been developed that can be run on the FNA sample. This paper reviews the published literature and technology assessments/guidelines by independent parties and professional groups regarding the clinical utility as well as the analytic and clinical validity of the Afirma GEC.
No outside funding was provided for this review.
Thyroid nodules are common and typically benign. However, given that 5-10% of nodules are malignant, current
practice guidelines recommend evaluation with ultrasound followed by fine needle aspiration (FNA) biopsy for
most clinically significant thyroid nodules.1,2,3 Most diagnostic FNA biopsies are read as cytopathologically
benign or malignant, but 15%-30% remain indeterminate.2 Most patients with indeterminate lesions (defined in
the Bethesda System as Atypia of Undetermined Significance or Follicular Lesion of Undetermined Significance,
suspicious for Follicular or Hrthle Cell Neoplasm and suspicious for malignancy) are referred for a diagnostic
thyroid surgery.4 Approximately three-quarters of these nodules are ultimately found to be benign on final
In 2011, it is estimated that more than 450,000 thyroid FNAs were performed. In that same year, approximately
48,020 primary thyroid malignancies were diagnosed.7 In order to avoid diagnostic surgery on benign thyroid
nodules with indeterminate FNA cytopathology, pre-operative FNA-based genomics tests should predict a risk of
malignancy comparable to the risk of malignancy in a cytologically benign nodule that is resected
(approximately 5% or less). 8 At this level of risk, physicians can confidently recommend clinical and
sonographic monitoring in lieu of thyroid resection as they do for cytologically benign nodules under current
clinical management schemas.9 Recent reviews have evaluated known gene mutation marker panels
associated with thyroid malignancy and the Afirma GEC towards this end.10,11,12 A recent meta-review of a
panel of somatic mutation markers associated with malignancy such as BRAF, RAS, RET/PTC, and
PAX8/PPARgamma found sensitivity to be too low (63.7%) to achieve a high enough negative predictive value
(NPV) to recommend monitoring when these mutations are absent.13 The Afirma GEC employs a different
approach analyzing the mRNA expression of 167 genes with high enough sensitivity (92%) in indeterminate
cytology lesions to identify the signature of a benign thyroid nodule with 95% NPV: that is, similar to the risk of
malignancy in a resected thyroid nodule with a preoperatively benign FNA cytopathology diagnosis.14,15
When needle passes are made for cytologic analysis of sonographically suspicious thyroid nodules, two
dedicated passes also are made for Afirma GEC analysis and immediately stored in nucleic acid preservative
solution. If the FNA cytopathology is nondiagnostic, benign, or malignant, the sample collected for the Afirma
GEC is discarded. If the FNA cytopathology is indeterminate, the Afirma GEC sample undergoes RNA extraction
and nucleic acid amplification. Processed Afirma GEC samples are hybridized to a custom Afirma Thyroid
microarray and analyzed with a classification algorithm using linear support vector machine logic to produce
either a Benign or Suspicious test result. About 10% of FNA samples have inadequate RNA yield or quality
and are reported by the Afirma GEC as No Result. 16
The incidence of thyroid cancer in the U.S. has risen dramatically. In 2009, there were 37,200 new cases of
thyroid cancer, while in 2013, it is anticipated there will be 60,220 new cases.17,18 At the same time, there has
been an increase in the utilization of thyroid FNA and subsequent thyroid surgery.19 The prevalence of thyroid
nodules increases with age and is more common in females. Approximately 50% of women 50 years have at
least one thyroid nodule based on published ultrasound and autopsy series.20 Two thirds of thyroid nodules
have benign FNA cytopathology and monitoring is implemented, whereas those with indeterminate or malignant
cytology are generally referred for surgery. Because thyroid nodules with indeterminate FNA cytopathology
have a 25% risk of malignancy when resected, 75% of these operations will likely be on nodules determined to
be benign post-operatively.5,6 Thyroid surgery is associated with potential complications, including temporary
and permanent hypocalcemia, recurrent laryngeal nerve injury (with voice change, dysphagia, and potentially
airway compromise if bilateral), and bleeding, with an incidence as high as 2-10%.21,22,23 While there is strong
evidence that high volume thyroid surgeons on average have fewer complications than low volume
counterparts, 50% of thyroid operations in the U.S. are still performed by surgeons who perform 5
thyroidectomies/year.24 Hypothyroidism is an expected sequelae of thyroid surgery, with patients requiring
lifelong thyroid hormone supplementation or replacement therapy.
Published Reviews, Recommendations and Guidelines
Systematic evidence reviews. Palmetto Government Benefits Administrators (Palmetto GBA), the CMS
Medicare Administrative Contractor with oversight for the Afirma GEC, has published itsassessment of the test
as an update to its local coverage article on molecular diagnostics. This review determined that the test meets
criteria for analytical and clinical validity, and clinical utility as a reasonable and necessary Medicare benefit,
effective January 1, 2012.25
Recommendations by independent groups. As part of the CLIA Laboratory licensure process, the analytical
and clinical validation data for the Afirma GEC were independently assessed by reviewers from the California
Department of Public Health and the New York State Department of Health.26,27 Both of these reviews resulted
in a favorable licensure outcome.
Guidelines by professional groups. The National Comprehensive Cancer Network (NCCN) thyroid carcinoma
guidelines were updated in December, 2012 to state Molecular diagnostics may be useful to allow
reclassification of follicular lesions (follicular neoplasm or follicular lesion of undetermined significance) as more
likely to be benign or more likely to be malignantIf molecular testing predicts a risk of malignancy comparable
to the risk of malignancy seen with a benign FNA cytology (approximately 5% or less), consider observation.
The NCCN guidelines for abnormal gene/gene expression profile testing are associated with Level of Evidence
2A (lower level evidence, uniform NCCN consensus that the intervention is appropriate).8,28
Analytical Validity: test accuracy, reliability in measuring differences in expression of relevant
genes (analytic sensitivity and specificity), and robustness.
Building on an earlier study by Chudova et al. 14, a large collaborative study by Walsh et al. reviewed over 30
sub-studies on the Afirma GEC, finding high analytic sensitivity and specificity after dilution of thyroid neoplasm
FNA samples with adjacent normal tissue or benign neoplasms (such as nodular hyperplasia and lymphocytic
thyroiditis), as well as dilution with blood and genomic DNA, respectively.14,29
High reproducibility was found in studies of interlaboratory concordance (R 2 0.98), as well as intra-assay,
interassay, and intra-nodule concordance (R2 0.99, 0.98, and 0.95, respectively).29
The assay was robust to a wide range of temperature, storage and stressed shipping conditions and was
reproducible across different operators, runs, and reagent lots with routine use of control reagents/samples for
in-process Quality Control monitoring.29
Clinical Validity: test accuracy in correctly determining which indeterminate cytology FNA biopsies
are benign compared to expert surgical histopathology.
Two prospective multicenter studies evaluated the negative predictive value (NPV) for the Afirma GEC, which
is the key diagnostic performance metric used to make a decision to monitor patients in lieu of referral for
diagnostic thyroid surgery.14,15 Both studies utilized diagnosis of the surgical pathology specimen by a central
panel of blinded academic endocrine histopathologists as the reference standard for clinical validation.
Approximately one quarter of study sites were academic and three quarters were community-based (total sites
In both studies, NPV was >94% for cytologically indeterminate thyroid FNAs with atypia/follicular lesions of
undetermined significance and follicular/Hrthle cell neoplasm diagnoses, but lower when the cytology was
suspicious for malignancy. Overall, the NPV for the Afirma GEC was similar to the NPV for a resected thyroid
nodule with benign cytopathology.5,30
In the second, larger study 15, although the NPV was 95% for all indeterminate cytology nodules (at the 24%
risk of malignancy expected in clinical practice), the NPV was 85% for FNAs with a cytopathology diagnosis
suspicious for malignancy. Sensitivity was 92% for indeterminate nodules overall. Clinical specificity for
indeterminate nodules rose from 0% for cytopathology alone to 52% with the Afirma GEC, meaning that half of
the benign nodules with indeterminate cytopathology could be identified with this pre-operative test.
Clinical Utility: net benefit of test in improving health outcomes by allowing recommendation for
monitoring instead of a diagnostic surgery on benign thyroid nodules.
Duick et al. was a retrospective analysis based on chart review of 368 patients (395 indeterminate thyroid
nodules) cared for by 51 physicians at 21 practice locations in 11 states. When compared to historical controls,
the relative rate of operation on cytologically indeterminate nodules fell 90%, from 74% historically to 7.6% with
Afirma GEC benign results (p < 0.001).16 The comparisons between historical controls and operative rates
based on the binomial test achieved more than 99% power in detecting a less than 25% change.31 With Afirma
GEC benign results, in 92.4% of the cases, physicians recommended watchful waiting in lieu of a diagnostic
thyroid resection. The residual rate of surgery was similar to the historic 9% resection rate on cytologically
benign thyroid nodules and may relate to other clinical parameters and issues of patient and physician
preference, including issues related to nodule size.5
These results were consistent with a previously conducted web- and mail-based opinion survey of 84
physician practices, with a mean of 89% of physicians reporting that they recommended watchful waiting for
patients with cytologically indeterminate FNAs but benign Afirma GEC results.32
Limitations. In the clinical validity studies, thyroid FNAs with indeterminate cytology diagnoses that were
cytologically suspicious for malignancy did not have sufficiently low NPV to generally recommend monitoring.10
Secondly, the Duick et al clinical utility study used historical rather than contemporary controls.16 Although
historical controls were used, these were appropriately validated based on a meta-review of 11 recent thyroid
pathology studies where thyroid nodule evaluation was similar to current community practice.5
The clinical validity studies reviewed would fall into the Level 1 category in the Evaluation of Genomic
Applications in Practice and Prevention (EGAPP) hierarchy of data sources and study designs, based on two
prospective, multicenter, double blinded cohort studies.33 A validated clinical decision rule was based on
classification concordance of Afirma GEC benign results with blinded expert surgical pathology benign
diagnosis. 11 Sensitivity in most indeterminate FNAs was high enough (92%) to achieve a NPV of 94-95%, which
is comparable to a thyroid nodule that is benign on cytopathology but undergoes surgical resection (93-94%).5,
30 However, the Afirma GEC NPV for FNAs where the cytopathology was suspicious for malignancy was only
85%. While this lowers the residual risk of malignancy from 62% to 15%, surgical consultation still should be
planned in these patients. The test utilized interlaboratory comparisons in a large collaborative study, an EGAPP
criterion for Level 1 hierarchy of analytic validity study design.34 Improvement in the net health outcome is
based on avoidance of surgery in patients with indeterminate thyroid FNA cytology that would have been found
to be benign on surgical pathology. Clinical utility of the Afirma GEC was evaluated in clinical practice, outside
of the investigational setting, in an opinion survey and a controlled study consistent with EGAPP Level 3 criteria
for clinical utility study design. The Afirma GEC potentially can improve the net health outcome by providing an
alternative to diagnostic thyroid surgery, and therein the risk of downstream complications of surgery, in
patients with benign thyroid nodules but indeterminate FNA cytopathology. In summary, the studies reviewed
here regarding clinical and analytic validity, and clinical utility support recommendation for offering patients the
alternative of using the Afirma GEC to monitor patients in lieu of thyroid resection when applied in the specific
case of thyroid FNAs where there is indeterminate cytopathology: atypia/follicular lesion of undetermined
significance, and follicular/Hrthle cell neoplasm.
Dr. Lanman is an employee of Veracyte, Inc. The other co-authors have no conflict of interest.
The co-authors wish to thank the Office of Public Health Genomics for inviting us to submit this brief technical
review paper, and for the helpful comments of the editor and independent reviewers.
1. Gharib H, Papini E, Paschke R, Duick DS, Valcavi R, Hegeds L, Vitti P. American Association of Clinical Endocrinologists, Associazione Medici Endocrinologi, and European Thyroid Association medical guidelines for clinical practice for the diagnosis and management of thyroid nodules: executive summary of recommendations. J Endocrinol Invest. 2010;33(5 Suppl):51-6. PubMed PMID:20543551.
2. Cooper DS , Doherty GM , Haugen BR , Kloos RT , Lee SL , Mandel SJ , Mazzaferri EL , McIver B , Pacini F , Schlumberger M , Sherman SI , Steward DL , Tuttle RM . Revised American Thyroid Association management guidelines for patients with thyroid nodules and differentiated thyroid cancer . Thyroid . 2009 Nov; 19 ( 11 ): 1167 - 214 . PubMed PMID : 19860577 .
3. Tuttle RM , Ball DW , Byrd D , Dilawari RA , Doherty GM , Duh QY , Ehya H , Farrar WB , Haddad RI , Kandeel F , Kloos RT , Kopp P , Lamonica DM , Loree TR , Lydiatt WM , McCaffrey JC , Olson JA Jr, Parks L , Ridge JA , Shah JP , Sherman SI , Sturgeon C , Waguespack SG , Wang TN , Wirth LJ . Thyroid carcinoma . J Natl Compr Canc Netw . 2010 Nov; 8 ( 11 ): 1228 - 74 . PubMed PMID : 21081783 .
4. Cibas ES , Ali SZ . The Bethesda System for Reporting Thyroid Cytopathology. Thyroid. 2009 Nov; 19 ( 11 ): 1159 - 65 . PubMed PMID : 19888858 .
5. Wang CC , Friedman L , Kennedy GC , Wang H , Kebebew E , Steward DL , Zeiger MA , Westra WH , Wang Y , Khanafshar E , Fellegara G , Rosai J , Livolsi V , Lanman RB . A large multicenter correlation study of thyroid nodule cytopathology and histopathology . Thyroid . 2011 Mar; 21 ( 3 ): 243 - 51 . PubMed PMID : 21190442 .
6. Bryson PC , Shores CG , Hart C , Thorne L , Patel MR , Richey L , Farag A , Zanation AM . Immunohistochemical distinction of follicular thyroid adenomas and follicular carcinomas . Arch Otolaryngol Head Neck Surg . 2008 Jun; 134 ( 6 ): 581 - 6 . PubMed PMID : 18559722 .
7. Siegel R , Ward E , Brawley O , Jemal A. Cancer statistics , 2011 : the impact of eliminating socioeconomic and racial disparities on premature cancer deaths . CA Cancer J Clin . 2011 Jul-Aug; 61 ( 4 ): 212 - 36 . PubMed PMID : 21685461 .
8. NCCN Clinical Practice Guidelines Thyroid Carcinoma Version 1 . 2013 . December 21 , 2012 .
9. Li H , Robinson KA , Anton B , Saldanha IJ , Ladenson PW . Cost-effectiveness of a novel molecular test for cytologically indeterminate thyroid nodules . J Clin Endocrinol Metab . 2011 Nov; 96 ( 11 ): E1719 - 26 . PubMed PMID : 21865367 .
10. Jameson JL . Minimizing unnecessary surgery for thyroid nodules . N Engl J Med. 2012 Aug 23 ; 367 ( 8 ): 765 - 7 .
PubMed PMID : 22731671 .
11. Kim MI , Alexander EK . Diagnostic use of molecular markers in the evaluation of thyroid nodules . Endocr Pract . 2012 Sep-Oct; 18 ( 5 ): 796 - 802 . PubMed PMID : 22982803 .
12. Melillo RM , Santoro M. Molecular biomarkers in thyroid FNA samples . J Clin Endocrinol Metab . 2012 Dec; 97 ( 12 ): 4370 - 3 . PubMed PMID : 23223485 .
13. Ferraz C , Eszlinger M , Paschke R. Current state and future perspective of molecular diagnosis of fine-needle aspiration biopsy of thyroid nodules . J Clin Endocrinol Metab . 2011 Jul; 96 ( 7 ): 2016 - 26 . PubMed PMID : 21593119 .
14. Chudova D , Wilde JI , Wang ET , Wang H , Rabbee N , Egidio CM , Reynolds J , Tom E , Pagan M , Rigl CT , Friedman L , Wang CC , Lanman RB , Zeiger M , Kebebew E , Rosai J , Fellegara G , LiVolsi VA , Kennedy GC . Molecular classification of thyroid nodules using high-dimensionality genomic data . J Clin Endocrinol Metab . 2010 Dec; 95 ( 12 ): 5296 - 304 . PubMed PMID : 20826580 .
15. 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 , Zeiger MA , Lanman RB , Haugen BR . Preoperative diagnosis of benign thyroid nodules with indeterminate cytology . N Engl J Med. 2012 Aug 23 ; 367 ( 8 ): 705 - 15 .
PubMed PMID : 22731672 .
16. Duick DS , Klopper JP , Diggans JC , Friedman L , Kennedy GC , Lanman RB , McIver B. 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 cytopathology . Thyroid . 2012 Oct; 22 ( 10 ): 996 - 1001 .
PubMed PMID : 22873825 .
17. Jemal A , Siegel R , Ward E , Hao Y , Xu J , Thun MJ . Cancer statistics, 2009 . CA Cancer J Clin . 2009 JulAug; 59 ( 4 ): 225 - 49 . PubMed PMID : 19474385 .
18. Siegel R , Naishadham D , Jemal A. Cancer statistics , 2013 . CA Cancer J Clin . 2013 Jan; 63 ( 1 ): 11 - 30 . PubMed PMID : 23335087 .
19. Davies L , Welch HG . Increasing incidence of thyroid cancer in the United States , 1973 - 2002 . JAMA. 2006 May 10 ; 295 ( 18 ): 2164 - 7 . PubMed PMID : 16684987 .
20. Mazzaferri EL . Management of a solitary thyroid nodule . N Engl J Med. 1993 Feb 25 ; 328 ( 8 ): 553 - 9 . PubMed PMID : 8426623 .
21. Randolph GW (ed). Surgery of the Thyroid and Parathyroid Glands. 2nd edition Philadelphia, PA: Elsevier Saunders , 2012 .
22. Sosa JA , Bowman HM , Tielsch JM , Powe NR , Gordon TA , Udelsman R. The importance of surgeon experience for clinical and economic outcomes from thyroidectomy . Ann Surg . 1998 Sep; 228 ( 3 ): 320 - 30 . PubMed PMID : 9742915 .
23. Bergenfelz A , Jansson S , Kristoffersson A , Mrtensson H , Reihnr E , Wallin G , Lausen I. Complications to thyroid surgery: results as reported in a database from a multicenter audit comprising 3,660 patients . Langenbecks Arch Surg . 2008 Sep; 393 ( 5 ): 667 - 73 . PubMed PMID : 18633639 .
24. Saunders BD , Wainess RM , Dimick JB , Doherty GM , Upchurch GR , Gauger PG . Who performs endocrine operations in the United States? Surgery . 2003 Dec; 134 ( 6 ): 924 - 31 ; discussion 931. PubMed PMID : 14668724 .
25. Palmetto GBA . Local Coverage Article for MolDx: AFIRMA Assay by Veracyte Update (Article ID Number 26 . Statley D . CLIA Examiner I Report. September 29 , 2010 .
27. Klees RF . Assay Validation Review. July 27 , 2012 .
28. NCCN Biomarkers Compendium . Accessed December 21 , 2012 .
29. Walsh PS , Wilde JI , Tom EY , Reynolds JD , Chen DC , Chudova DI , Pagan M , Pankratz DG , Wong M , Veitch J , Friedman L , Monroe R , Steward DL , Lupo MA , Lanman RB , Kennedy GC . Analytical performance verification of a molecular diagnostic for cytology-indeterminate thyroid nodules . J Clin Endocrinol Metab . 2012 Dec; 97 ( 12 ): E2297 - 306 . PubMed PMID : 23087323 .
30. Lewis CM , Chang KP , Pitman M , Faquin WC , Randolph GW . Thyroid fine-needle aspiration biopsy: variability in reporting . Thyroid . 2009 Jul; 19 ( 7 ): 717 - 23 . PubMed PMID : 19485775 .
31. Agresti A , Coull BA . Approximate Is Better than Exact for Interval Estimation of Binomial Proportions . Amer Statistician 1998 May; 52 ( 2 ): 119 - 126 .
32. Monroe R , Zalles C , Traweek T , OReilly K , Romanowsky J , Brunt K , Kennedy GC , Lanman RB 2011 Clinical practice impact of a novel mRNAbased gene expression classifier in thyroid nodules with indeterminate fine needle aspiration cytopathology . Thyroid 21:A-101 (Poster 244; abstract).
33. Teutsch SM , Bradley LA , Palomaki GE , Haddow JE , Piper M , Calonge N , Dotson WD , Douglas MP , Berg AO . The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Initiative: methods of the EGAPP Working Group . Genet Med . 2009 Jan; 11 ( 1 ): 3 - 14 . PubMed PMID : 18813139 .
34. National Office of Public Health Genomics , CDC. ACCE model system for collecting, analyzing and disseminating information on genetic tests . Accessed November 4 , 2012 .