title: Impact of the Multi-Gene ThyroSeq Next-Generation Sequencing Assay on Cancer Diagnosis in Thyroid Nodules with Atypia of Undetermined Significance/Follicular Lesion of Undetermined Significance Cytology.
abstract: BACKGROUND
  Fine-needle aspiration (FNA) cytology is a common approach to evaluate thyroid nodules. It offers definitive diagnosis of a benign or malignant nodule in the majority of cases. However, 10-25% of nodules yield one of three indeterminate cytologic diagnoses, leading to suboptimal management of these patients. Atypia of undetermined significance/follicular lesion of undermined significance (AUS/FLUS) is a common indeterminate diagnosis, with the cancer risk ranging from 6% to 48%. This study assessed whether a multi-gene next-generation sequencing (NGS) assay can offer significant improvement in diagnosis in AUS/FLUS nodules.
  
  
  METHODS
  From May 2014 to March 2015, 465 consecutive FNA samples with the cytologic diagnosis of AUS/FLUS underwent prospective molecular testing using the ThyroSeq v2.1 panel. The panel included 14 genes analyzed for point mutations and 42 types of gene fusions occurring in thyroid cancer. In addition, eight genes were assessed for expression in order to evaluate the cell composition of FNA samples. Ninety-eight (21%) of these nodules had definitive surgical (n = 96) or nonsurgical (n = 2) follow-up and were used to determine the assay performance.
  
  
  RESULTS
  Among 465 AUS/FLUS nodules, three were found to be composed of parathyroid cells and 462 of thyroid follicular cells. Of the latter, 31 (6.7%) were positive for mutations. The most frequently mutated genes were NRAS and HRAS, and overall point mutations in seven different genes and five types of gene fusions were identified in these nodules. Among 98 nodules with known outcome, histologic analysis revealed 22 (22.5%) cancers. ThyroSeq v2.1 was able to classify 20/22 cancers correctly, showing a sensitivity of 90.9% [confidence interval (CI) 78.8-100], specificity of 92.1% [CI 86.0-98.2], positive predictive value of 76.9% [CI 60.7-93.1], and negative predictive value of 97.2% [CI 78.8-100], with an overall accuracy of 91.8% [CI 86.4-97.3].
  
  
  CONCLUSIONS
  The results of the study demonstrate that the ThyroSeq v2.1 multi-gene NGS panel of molecular markers provides both high sensitivity and high specificity for cancer detection in thyroid nodules with AUS/FLUS cytology, which should allow improved management for these patients.
authors.affiliation: 1 Department of Pathology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Yuri E
authors.initials: YE
authors.lastname: Nikiforov
authors.affiliation: 2 Division of Endocrine Surgery, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Sally E
authors.initials: SE
authors.lastname: Carty
authors.affiliation: 1 Department of Pathology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Simon I
authors.initials: SI
authors.lastname: Chiosea
authors.affiliation: 3 Division of Endocrinology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Christopher
authors.initials: C
authors.lastname: Coyne
authors.affiliation: 4 Department of Otolaryngology, Head Neck Surgery, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Umamaheswar
authors.initials: U
authors.lastname: Duvvuri
authors.affiliation: 4 Department of Otolaryngology, Head Neck Surgery, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Ferris
authors.affiliation: 5 Biostatisctics Facility, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: William E
authors.initials: WE
authors.lastname: Gooding
authors.affiliation: 3 Division of Endocrinology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Shane O
authors.initials: SO
authors.lastname: LeBeau
authors.affiliation: 1 Department of Pathology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: N Paul
authors.initials: NP
authors.lastname: Ohori
authors.affiliation: 1 Department of Pathology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Raja R
authors.initials: RR
authors.lastname: Seethala
authors.affiliation: 6 Department of Radiology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania.
authors.forename: Mitchell E
authors.initials: ME
authors.lastname: Tublin
authors.affiliation: 2 Division of Endocrine Surgery, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Linwah
authors.initials: L
authors.lastname: Yip
authors.affiliation: 1 Department of Pathology, University of Pittsburgh Cancer Institute , Pittsburgh, Pennsylvania.
authors.forename: Marina N
authors.initials: MN
authors.lastname: Nikiforova
mesh_terms: D044963:Biopsy, Fine-Needle; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D011446:Prospective Studies; D012680:Sensitivity and Specificity; D013961:Thyroid Gland / Q000473:pathology*; D013964:Thyroid Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D016606:Thyroid Nodule / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology