title: The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes.
abstract: BACKGROUND
  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). Recent work by The Cancer Genome Atlas (TCGA) Research Network has expanded the number of genetic alterations detected in papillary thyroid carcinomas (PTC). 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. This is the first clinical evaluation of a large panel of TCGA-reported genomic alterations in thyroid FNAs.
  
  
  RESULTS
  In FNAs, genetic alterations were detected in 19/44 malignant samples (43% sensitivity) and in 7/44 histopathology benign samples (84% specificity). 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. The most frequently mutated malignant subtypes were medullary thyroid carcinoma (9/12, 75%) and PTC (14/30, 47%). Additionally, follicular adenoma, a benign subtype of thyroid neoplasm, was also found to harbor mutations (12/29, 41%). Frequently mutated genes in malignant samples included BRAF (20/76, 26%) and RAS (9/76, 12%). Of the TSHR variants detected, (6/7, 86%) were in benign nodules. 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. The specificity based only on genetic alterations was 84%, compared to 77% specificity with the GEC.
  
  
  CONCLUSIONS
  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. 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. 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.
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Moraima
authors.initials: M
authors.lastname: Pagan
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Richard T
authors.initials: RT
authors.lastname: Kloos
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Chu-Fang
authors.initials: CF
authors.lastname: Lin
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Travers
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Hajime
authors.initials: H
authors.lastname: Matsuzaki
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Ed Y
authors.initials: EY
authors.lastname: Tom
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Su Yeon
authors.initials: SY
authors.lastname: Kim
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Mei G
authors.initials: MG
authors.lastname: Wong
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Stewart
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Huang
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: P Sean
authors.initials: PS
authors.lastname: Walsh
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Monroe
authors.affiliation: Veracyte, Inc., South San Francisco, CA, USA. giulia@veracyte.com.
authors.forename: Giulia C
authors.initials: GC
authors.lastname: Kennedy
mesh_terms: D018263:Adenocarcinoma, Follicular / Q000175:diagnosis* / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics; D044963:Biopsy, Fine-Needle; D002277:Carcinoma / Q000175:diagnosis* / Q000235:genetics; D018278:Carcinoma, Neuroendocrine / Q000175:diagnosis* / Q000235:genetics; D002291:Carcinoma, Papillary; D050939:Gene Fusion / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011446:Prospective Studies; D012372:ROC Curve; D017423:Sequence Analysis, RNA / Q000379:methods; D000077273:Thyroid Cancer, Papillary; D013964:Thyroid Neoplasms / Q000175:diagnosis* / Q000235:genetics; D016606:Thyroid Nodule / Q000175:diagnosis / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor
references.citation: Clin Endocrinol (Oxf). 1999 Apr;50(4):529-35
references.pmid: 10468914
references.citation: J Clin Endocrinol Metab. 2002 Aug;87(8):3947-52
references.pmid: 12161538
references.citation: Stat Med. 2007 May 10;26(10):2170-83
references.pmid: 16927452
references.citation: Cancer. 2007 Dec 25;111(6):508-16
references.pmid: 17999413
references.citation: Expert Rev Mol Diagn. 2008 Jan;8(1):83-95
references.pmid: 18088233
references.citation: Diagn Cytopathol. 2008 Jun;36(6):425-37
references.pmid: 18478609
references.citation: Am J Clin Pathol. 2009 Nov;132(5):658-65
references.pmid: 19846805
references.citation: Thyroid. 2009 Nov;19(11):1167-214
references.pmid: 19860577
references.citation: Thyroid. 2009 Dec;19(12):1351-61
references.pmid: 19895341
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D652-7
references.pmid: 19906727
references.citation: Genome Res. 2010 Sep;20(9):1297-303
references.pmid: 20644199
references.citation: J Clin Endocrinol Metab. 2011 Nov;96(11):3390-7
references.pmid: 21880806
references.citation: N Engl J Med. 2012 Aug 23;367(8):705-15
references.pmid: 22731672
references.citation: Acta Cytol. 2012;56(4):333-9
references.pmid: 22846422
references.citation: Thyroid. 2012 Oct;22(10):996-1001
references.pmid: 22873825
references.citation: Bioinformatics. 2013 Jan 1;29(1):15-21
references.pmid: 23104886
references.citation: J Clin Endocrinol Metab. 2013 May;98(5):E914-22
references.pmid: 23539734
references.citation: J Clin Endocrinol Metab. 2013 May;98(5):E962-72
references.pmid: 23543667
references.citation: Lancet. 2013 Mar 23;381(9871):1058-69
references.pmid: 23668556
references.citation: J Clin Endocrinol Metab. 2013 Sep;98(9):E1562-6
references.pmid: 23833040
references.citation: Thyroid. 2014 Feb;24(2):305-13
references.pmid: 23837487
references.citation: J Natl Cancer Inst. 2013 Nov 6;105(21):1617-27
references.pmid: 24136889
references.citation: J Clin Endocrinol Metab. 2014 Jan;99(1):119-25
references.pmid: 24152684
references.citation: Endocr Pract. 2014 Apr;20(4):364-9
references.pmid: 24246351
references.citation: J Clin Endocrinol Metab. 2014 Nov;99(11):4069-77
references.pmid: 24780044
references.citation: Thyroid. 2014 Oct;24(10):1479-87
references.pmid: 24811481
references.citation: Hum Pathol. 2014 Jul;45(7):1339-47
references.pmid: 24830619
references.citation: Ann Surg. 2014 Jul;260(1):163-8
references.pmid: 24901361
references.citation: Nat Rev Endocrinol. 2014 Oct;10(10):616-23
references.pmid: 25069464
references.citation: Cancer Cytopathol. 2014 Dec;122(12):866-72
references.pmid: 25078420
references.citation: Cancer Cytopathol. 2014 Oct;122(10):737-44
references.pmid: 25123499
references.citation: Cancer. 2014 Dec 1;120(23):3627-34
references.pmid: 25209362
references.citation: Bioinformatics. 2014 Dec 15;30(24):3556-7
references.pmid: 25286921
references.citation: Cell. 2014 Oct 23;159(3):676-90
references.pmid: 25417114
references.citation: Oncogene. 2015 Sep 10;34(37):4845-54
references.pmid: 25500544
references.citation: Hum Mol Genet. 2015 Apr 15;24(8):2318-29
references.pmid: 25576899
references.citation: Thyroid. 2015 Apr;25(4):401-9
references.pmid: 25629769
references.citation: Ann Surg Oncol. 2015 Nov;22(12):3996-4001
references.pmid: 25862581
references.citation: Cancer Cytopathol. 2015 Jun;123(6):356-61
references.pmid: 25926393
references.citation: J Clin Endocrinol Metab. 2015 Jul;100(7):2743-50
references.pmid: 25965083
references.citation: N Engl J Med. 2015 Jun 4;372(23):2235-42
references.pmid: 26014595
references.citation: Thyroid. 2015 Jul;25(7):760-8
references.pmid: 26058403
references.citation: BMC Med. 2015 Aug 07;13:184
references.pmid: 26253102
references.citation: Laryngoscope. 2016 Feb;126(2):524-7
references.pmid: 26343268
references.citation: J Clin Endocrinol Metab. 2015 Nov;100(11):E1477-83
references.pmid: 26353010
references.citation: Thyroid. 2015 Nov;25(11):1217-23
references.pmid: 26356635
references.citation: Oncogene. 1996 Aug 15;13(4):687-93
references.pmid: 8761289