The Endocrine Society's 97th Annual Meeting & Expo:

Next-Generation Genetic Sequencing in Thyroid Cancer

The management of patients with thyroid nodules or cancer—including advanced genetic sequencing—was described by Marina N. Nikiforova, MD, Professor of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA. Dr. Nikiforova presented her review on March 5, 2014, at The Endocrine Society Annual Meeting in San Diego, CA.

The Management of Patients with Thyroid Nodules
On fine-needle cytology, 70% of thyroid nodules are benign, 25% indeterminate, and 5% malignant. Patients with benign nodules are followed, patients with indeterminate nodules undergo diagnostic lobectomy, with 75% disclosing benign disease and 25% malignancy. Malignant disease is treated with total thyroidectomy, suboptimal surgery, and radioactive iodine.

Conventional (Sanger) Genetic Sequencing
Conventional sequencing interrogates one region of the genome, sequencing up to 102–103 bases, at 20–30% sensitivity.

Next-Generation Genetic Sequencing
Next-generation quantitative technology sequences DNA/RNA in massively parallel configuration, detecting multiple mutations at once. Up to 106–109 bases are sequenced at once at 3–5% sensitivity.

Discovery of next-generation sequencing of the genome, exome, and transcriptome is expensive, time-consuming, and requires complex bioinformatics analysis. Targeted DNA/RNA approaches sequence point mutation and copy number alteration, gene fusions, and gene expression. Such approaches, performed in clinical molecular labs, are fast and reliable, and require only small aspirates.

ThyroSeq™Version 2
ThyroSeq is a targeted next-generation sequencing panel of DNA (14 genes, >1000 mutations) and RNA (42 fusions, 16 genes for expression). This panel provides cancer diagnosis, prognostication, and optimal targeted therapy selection.

Evaluations of Mutational Panels
At the University of Pittsburgh Medical Center, a seven-gene, conventional panel was used in 2007, the 15-gene ThyroSeq v. 1 panel in 2013, and the 56-gene ThyroSeq v. 2 panel in 2014. A single-institution study at the University of Pittsburgh Medical Center was published in 2014 (Nikiforov et al, Cancer). The large sample size (143 consecutive fine-needle aspirates with follicular neoplasms/suspicious for follicular neoplasm cytology and known surgical outcome) yielded 90% sensitivity, 93% specificity, 83% positive predictive value, 96% negative predictive value, and 92% accuracy. Cancer prevalence after surgery was 39/143, or 27.3%.

An as-yet uncompleted trial is evaluating the ThyroSeq v. 2 mutation panel in 67 consecutive thyroid nodules with atypia of undetermined significance/follicular lesions of undetermined significance cytology and surgical follow-up. Successful molecular testing of DNA and RNA was achieved in 65 (97%) patients. Cancer prevalence after surgery was 12/65, or 18.5%. Sensitivity was 83.3%, specificity 94.3%, positive predictive value 76.9%, and negative predictive value 96.2%.

ThyroSeq Analysis for Cancer Prognostication
ThyroSeq analysis has identified multiple oncogenic mutations in 4% of well-developed papillary and follicular thyroid cancer. ThyroSeq analysis has implicated TP53 and TERT mutations as causing aggressive disease.

ALK Fusions in RNA Sequencing of Thyroid Cancer
ALK fusions have been identified in 4/256 (2%) cases of papillary, 3/35 (9%) cases of poorly differentiated, and 1/24 (4%) cases of anaplastic thyroid cancer (Kelly et al, NSAS, 2014).

STRN-ALK protein is expressed in thyroid cancer cells and carries ALK kinase. STRN-ALK increases cell proliferation and induces transformation and tumor formation. ALK inhibitors can block STRN-ALK kinase and cell proliferation.

Conclusion
Precision medicine holds great promise for delivering the right treatment to the right patient at the right time. Next-generation genetic sequencing is the tool that has broadened the scope of precision medicine to allow us to attack the rising tide of thyroid cancer.

March 17, 2015

 

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