Development and Analytical Validation of an Expanded Mutation Detection Panel for Next-Generation Sequencing of Thyroid Nodule Aspirates

Ablordeppey, Kenny Kwabena; Timmaraju, Venkata Arun; Song‐Yang, Joanna Wanmin; Yaqoob, Sharon; Narick, Christina; Mireskandari, Alidad; Finkelstein, Sydney; Kumar, Gyanendra

doi:10.1016/j.jmoldx.2019.11.003

Cited by 25 publications

(34 citation statements)

References 26 publications

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“…We previously showed that this limited panel can identify almost 50% of malignant lesions commonly found in the pediatric population, suggesting a potential clinical role for mutational analysis in the surgical management of pediatric patients 6 . ThyGeNEXT is a broader NGS panel that interrogates an array of gene mutations in ALK, BRAF , GNAS , HRAS , KRAS , NRAS , PIK3CA , PTEN , RET , or TERT and 38 fusion transcripts involving well‐known oncogenes such as ALK , BRAF , NTRK , or RET 7 . This expanded panel can identify additional weak and strong oncogenic drivers in adult thyroid nodule biopsies 8 .…”

Section: Introductionmentioning

confidence: 99%

miRNA expression can classify pediatric thyroid lesions and increases the diagnostic yield of mutation testing

Franco

Labourier²,

Ablordeppey³

et al. 2020

Pediatric Blood & Cancer

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Background: Genetic alterations in multiple cell signaling pathways are involved in the molecular pathogenesis of thyroid cancer. Oncogene mutation testing and gene-expression profiling are routinely used for the preoperative risk management of adult thyroid nodules. In this study, we evaluated the potential value of miRNA biomarkers for the classification of pediatric thyroid lesions.Procedure: Double-blind case-control study with 113 resected pediatric lesions: 66 malignant and 47 benign. Quantitative and qualitative molecular data generated with a 10-miRNA expression panel (ThyraMIR) and a next-generation sequencing oncogene panel (ThyGeNEXT) were compared with clinicopathological parameters.Results: miRNAs were differentially expressed in benign versus malignant tumors with distinct expression patterns in different histopathology categories. The 10-miRNA classifier identified 39 (59%) malignant lesions with 100% specificity. A positive classifier score was associated with lymph node metastasis, extrathyroidal extension and intrathyroidal spread. Genetic alterations associated with increased risk for malignancy were detected in 35 (53%) malignant cases, 20 positive for point mutations in BRAF, HRAS, KRAS, NRAS, PIK3CA, or TERT and 15 positive for gene rearrangements involving ALK, NTRK3, PPARG, or RET. The 10-miRNA classifier correctly identified 11 mutation-negative malignant cases. The performance of the combined molecular test was 70% sensitivity and 96% specificity with an area under the curve of 0.924. Conclusions:These data suggest that the regulatory miRNA pathways underlying thyroid tumorigenesis are similar in adults and children. miRNA expression can identify malignant lesions with Abbreviations: CHOP, The Children's Hospital of Philadelphia; CI, confidence intervals; CLT, chronic lymphocytic thyroiditis; cPTC, classic papillary thyroid cancer; DH, diffuse hyperplasia; dsvPTC, diffuse sclerosing variant papillary thyroid cancer; DTC, differentiated thyroid cancer; FA, follicular adenoma; FNA, fine-needle aspiration; FTC, follicular thyroid cancer; fvPTC, follicular variant papillary thyroid cancer; mixPTC, mixed papillary thyroid cancer; MNG, multinodular goiter; NIFTP, noninvasive follicular thyroid neoplasm with papillary-like nuclear features; oPTC, oncocytic papillary thyroid cancer; OR, odds ratio; pFA, follicular adenoma with papillary changes.

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Section: Introductionmentioning

confidence: 99%

miRNA expression can classify pediatric thyroid lesions and increases the diagnostic yield of mutation testing

Franco

Labourier²,

Ablordeppey³

et al. 2020

Pediatric Blood & Cancer

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“…ThyGeNEXT ® , are oncogenic driver mutation panels. 4,5 Strong driver mutations that are highly predictive of malignancy, such as BRAF V600E mutations, RET fusions, and TERT promoter mutations, have proven useful in surgical decision making. [6][7][8][9][10][11][12][13] However, the most common mutations in indeterminate nodules are RAS, which are weak driver mutations with a lower PPV.…”

Section: Some Commercially Available Molecular Tests Such As Thyrosementioning

confidence: 99%

“…19 In the current version of MPT, designated MPTX, an analytically validated expanded, next generation sequencing test (ThyGeNEXT) is used in combination with the microRNA risk classifier test (ThyraMIR). 4,21,22 The expanded mutation panel includes NTRK and ALK fusions that have targeted therapies, as well as TERT and RET protooncogene mutations that are markers of aggressive disease. 6,[23][24][25][26][27][28] In MPTX testing, samples with no detectable mutational change and those that have weak driver mutations are further risk stratified using the microRNA classifier, which incorporates two thresholds for malignancy risk.…”

Section: Some Commercially Available Molecular Tests Such As Thyrosementioning

confidence: 99%

“…The objective is to distinguish patients who are more likely to benefit from conservative management (ie, continued surveillance) from those who are more likely to benefit from surgical intervention. Some commercially available molecular tests, such as ThyroSeq® and ThyGeNEXT®, are oncogenic driver mutation panels 4,5 . Strong driver mutations that are highly predictive of malignancy, such as BRAF V600E mutations, RET fusions, and TERT promoter mutations, have proven useful in surgical decision making 6‐13 .…”

Section: Introductionmentioning

confidence: 99%

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Multiplatform molecular test performance in indeterminate thyroid nodules

Lupo¹,

Walts

Sistrunk

et al. 2020

Diagnostic Cytopathology

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Background: Approximately 25% of thyroid nodule fine-needle aspirates (FNAs) have cytology that is indeterminate for malignant disease. Accurate risk stratification of these FNAs with ancillary testing would reduce unnecessary thyroid surgery. Methods: We evaluated the performance of an ancillary multiplatform test (MPTX) that has three diagnostic categories (negative, moderate, and positive). MPTX includes the combination of a mutation panel (ThyGeNEXT ®) and a microRNA risk classifier (ThyraMIR ®). A blinded, multicenter study was performed using consensus histopathology diagnosis among three pathologists to validate test performance. Results: Unanimous consensus diagnosis was reached in 197 subjects with indeterminate thyroid nodules; 36% had disease. MPTX had 95% sensitivity (95% CI,86%-99%) and 90% specificity (95% CI,84%-95%) for disease in prevalence adjusted nodules with Bethesda III and IV cytology. Negative MPTX results ruledout disease with 97% negative predictive value (NPV; 95% CI,91%-99%) at a 30% disease prevalence, while positive MPTX results ruledin high risk disease with 75% positive predictive value (PPV; 95% CI,60%-86%). Such results are expected in four out of five Bethesda III and IV nodules tested, including RAS positive nodules in which the microRNA classifier was useful in rulingin disease. 90% of mutation panel false positives were due to analytically verified RAS mutations detected in benign adenomas. Moderate MPTX results had a moderate rate of disease (39%, 95% CI,23%-54%), primarily due to RAS mutations, wherein the possibility of disease could not be excluded. Conclusions: Our results emphasize that decisions for surgery should not solely be based on RAS or RAS-like mutations. MPTX informs management decisions while accounting for these challenges.

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“…37 Targeted next-generation sequencing mutation analyses to detect oncogenic RNA fusion transcripts and DNA mutation variants were performed using ThyGeNEXT as described previously. 38 All tests prescribed by physicians as part of the standard of care were performed at Interpace Diagnostics clinical laboratories (Pittsburgh, Pennsylvania and New Haven, Connecticut) according to standard clinical practices. Clinical FNA samples included cytology slides or dedicated needle passes placed directly into RNARetain preservative solution.…”

Section: Molecular Testingmentioning

confidence: 99%

Analytical and clinical validation of pairwise microRNA expression analysis to identify medullary thyroid cancer in thyroid fine‐needle aspiration samples

Ciarletto¹,

Narick²,

Malchoff

et al. 2020

Cancer Cytopathology

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BACKGROUND: Medullary thyroid carcinoma (MTC) is an aggressive malignancy originating from the parafollicular C cells. Preoperatively, thyroid nodule fine-needle aspiration cytology (FNAC) and pathogenic gene mutations are definitive in approximately one-half of cases. MicroRNAs (miRNAs) are endogenous, noncoding, single-stranded RNAs that regulate gene expression, a characteristic that confers the potential for identifying malignancy. In the current study, the authors hypothesized that differential pairwise (diff-pair) analysis of miRNA expression levels would reliably identify MTC in FNA samples. METHODS: The relative abundance of 10 different miRNAs in total nucleic acids was obtained from ThyraMIR test results. Diff-pair analysis was performed by subtracting the critical threshold value of one miRNA from the critical threshold values of other miRNAs. Next-generation sequencing with the ThyGeNEXT panel identified oncogenic gene alterations. The discovery cohort consisted of 30 formalin-fixed, paraffin-embedded benign and malignant thyroid neoplasms, including 4 cases of MTC. After analytical validation, clinical validation was performed using 3 distinct cohorts (total of 7557 specimens). RESULTS: In the discovery cohort, 9 diff-pairs were identified as having significant power using the Kruskal-Wallis test (P < .0001) to distinguish MTC samples from non-MTC samples. The assay correctly classified all MTC and non-MTC samples in the analytical validation study and in the 3 clinical validation cohorts. The overall test accuracy was 100% (95% confidence interval, 99%-100%). In indeterminate FNAC samples, the sensitivity of the diff-pair analysis was greater than that of the MTC-specific mutation analysis (100% vs 25%; P = .03). CONCLUSIONS: Pairwise miRNA expression analysis of ThyraMIR results were found to accurately predict MTC in thyroid FNA samples, including those with indeterminate FNAC findings.

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Development and Analytical Validation of an Expanded Mutation Detection Panel for Next-Generation Sequencing of Thyroid Nodule Aspirates

Cited by 25 publications

References 26 publications

miRNA expression can classify pediatric thyroid lesions and increases the diagnostic yield of mutation testing

miRNA expression can classify pediatric thyroid lesions and increases the diagnostic yield of mutation testing

Multiplatform molecular test performance in indeterminate thyroid nodules

Analytical and clinical validation of pairwise microRNA expression analysis to identify medullary thyroid cancer in thyroid fine‐needle aspiration samples

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