Molecular markers are a rapidly developing field despite the current limitations. Veracyte and CBL Path have begun to address the challenges discussed here. In 2017, Veracyte launched the Afirma® Genomic Sequencing Classifier (GSC), its newest product which tests a total of 10,196 genes. The Afirma® GSC test system is composed of a series of classifiers including parathyroid (mRNA expression), MTC (mRNA expression), BRAF (mRNA expression + variants), and RET/PTC fusion (fusion transcripts). GSC also includes a follicular content index (mRNA expression), HC index (mRNA expression and mitochondrial transcripts), and Hürthle neoplasm index (mRNA expression and chromosomal level loss of heterozygosity). The reliance on mRNA could prevent detection of mutations undetectable in transcriptome-based assays, such as telomerase reverse transcriptase (hTERT) promoter mutations. Veracyte states that GSC addresses the weaknesses of GEC by significantly increasing molecular test specificity, using a validation cohort with 15 NIFTP samples, and improving the diagnostic performance among HC lesions. Among Bethesda Type III and IV nodules, Veracyte quotes a Se, Sp, NPV, and PPV of 91, 68, 96, and 50%, respectively, when compared with the GEC parameters of 89 50, 93, and 46%, respectively. Among HC lesions, Sp has increased from 11.8 to 58.8%.