![]() * Correspondence: Veracyte, Inc., South San Francisco, CA, USA Keywords: Molecular testing, Variants, Fusions, RNA seq, Genomic alterations, Thyroid nodules, FNA Due to the finding that variants are also found in benign nodules, testing only GEC suspicious nodules may be helpful in avoiding false positives and altering the extent of treatment when selected mutations are found. The largest set of such mutations known to date detects only a portion of thyroid carcinomas in preoperative FNAs in our cohort and thus is not sufficient to rule out cancer. The specificity based only on genetic alterations was 84 %, compared to 77 % specificity with the GEC.Ĭonclusions: While the genomic landscape of all thyroid neoplasm subtypes will inevitably be elucidated, caution should be used in the early adoption of published mutations as the sole predictor of malignancy in thyroid. In a direct comparison of the same FNA also tested by an RNA-based gene expression classifier (GEC), the sensitivity of genetic alterations alone was 42 %, compared to the 91 % sensitivity achieved by the GEC. Of the TSHR variants detected, (6/7, 86 %) were in benign nodules. Frequently mutated genes in malignant samples included BRAF (20/76, 26 %) and RAS (9/76, 12 %). Additionally, follicular adenoma, a benign subtype of thyroid neoplasm, was also found to harbor mutations (12/29,41 %). The most frequently mutated malignant subtypes were medullary thyroid carcinoma (9/12, 75 %) and PTC (14/30,47 %). Overall, after adding a cohort of tissue samples, 38/76 (50 %) of histopathology malignant samples were found to harbor a genetic alteration, while 15/75 (20 %) of benign samples were also mutated. Results: In FNAs, genetic alterations were detected in 19/44 malignant samples (43 % sensitivity) and in 7/44 histopathology benign samples (84 % specificity). This is the first clinical evaluation of a large panel of TCGA-reported genomic alterations in thyroid FNAs. ![]() We sought to investigate the prevalence of these and other genetic alterations in diverse subtypes of thyroid nodules beyond PTC, including a variety of samples with benign histopathology. Recent work by The Cancer Genome Atlas (TCGA) Research Network has expanded the number of genetic alterations detected in papillary thyroid carcinomas (PTC). 11-13 January 2016īackground: Thyroid carcinomas are known to harbor oncogenic driver mutations and advances in sequencing technology now allow the detection of these in fine needle aspiration biopsies (FNA). Kennedy*įrom The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016) San Francisco, CA, USA. ![]() The diagnostic application of RNA sequencing in patients with thyroid cancer an analysis of 851 variants and 133 fusions in 524 genes
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