Multiplatform molecular test performance in indeterminate thyroid nodules

Abstract

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.

Thyroseq v3, Afirma GSC, and microRNA Panels Versus Previous Molecular Tests in the Preoperative Diagnosis of Indeterminate Thyroid Nodules: A Systematic Review and Meta-Analysis

“…In the current MPT, designated MPTX, an analytically validated expanded NGS test (ThyGeNEXT), is combined with ThyraMIR. This multiplatform test demonstrated a high PPV of 75% and NPV of 97%, comparable with other marketed tests (14,16,23). RosettaGX Reveal (Rosetta Genomics) is a thyroid miRNAs classifier for the stratification of ITNs by evaluating the expression of 24 up and down-regulated miRNAs species, using the routinely stained cytology smears as testing substrate (24).…”

“…However, this relative superiority is countered by the limited number of studies for these assays. Also, miRNA-based panel Interpace has shown the lowest risk of bias concerning index test, as in two of three studies the molecular testing was performed blind to histological diagnosis (23,67). For other criteria, the quality concerns were similarly high for all tests.…”

“…The most recent version of the Interpace platform ThyraMIR/ ThyGeNEXT (MPTX) was approached by Lupo et al, on 197 patients enrolled from 2013 to 2019 (23). In a similar two-step approach, MPTX is reported as negative when no mutations (ThyGeNEXT) are detected and the miRNA (ThyraMIR) test is negative; as positive when a strong driver mutation is detected or when the miRNA test is positive; and as moderate when a weak driver mutation is detected and the miRNA test is negative or moderate, or when no mutations are detected and the miRNA test is moderate.…”

Reply to Letter to the Editor by William Gooding and Simion Chiosea: Alternate diagnostic test interpretation in a retrospective convenience cohort and clinical application of MPTX

“…[8][9][10] As described in the Methods of our manuscript, MPTX is resulted as negative when no mutations are detected and the microRNA test is negative; as positive when a strong driver mutation is detected or when the microRNA test is positive; and as moderate for the remaining molecular scenarios. 3 We disagree with Gooding and Chiosea's view that only one diagnostic threshold should be used in data analysis of…”

Advancements in the treatment of differentiated thyroid cancer

“… 47 Molecular profiling is commonly performed using commercially available testing services such as the ThyroSeq v3 Genomic Classifier, a DNA/RNA next generation sequencing assay evaluating 112 candidate genes providing information on >12,000 mutation hotspots and >150 gene fusion types (CBLPath, Inc., Rye Brook, NY, USA), Afirma Genomic Sequencing Classifier (GSC), designed based on the RNA expression profiles of 1115 core genes, with the Xpression Atlas extension measuring variants and fusions in 593 genes (Veracyte, Inc., South San Francisco, CA, USA), and ThyGeNEXT ® + ThyraMIR ® , a multiplatform test comprised of the ThyGeNEXT ® mutation panel and ThyraMIR ® microRNA risk classifier (Interpace Biosciences, Inc., Parsippany-Troy Hills, NJ, USA). 48 – 52 The MAPK and PI3K-AKT molecular pathways have been implicated in the pathogenesis of DTC, and may provide useful information for risk stratification in DTC. 25 In 2014, The Cancer Genome Atlas (TCGA) project recognized BRAF V600E -like PTCs (BVL-PTCs) and RAS -like PTCs (RL-PTCs) as distinct entities based on their genetic, epigenetic, and protein expression profiles.…”