Whole Genome and Targeted Next Generation Sequencing in Thyroid Cancer
Yuri Nikiforov, Lindsey Kelly, Mary Beth Durso, Pengyuan Liu, Jianhua Luo, Marina Nikiforova. University of Pittsburgh, Pittsburgh, PA; Medical College of Wisconsin, Milwaukee, WI
Background: Thyroid cancer is the most common type of endocrine malignancy. Somatic mutations in BRAF, RAS, RET/PTC, and PAX8/PPARg are the most common genetic alterations in thyroid cancer and important in diagnostics and prognostication. However, around 30% of thyroid tumors do not harbor any known mutations and another 10% carry rare type of mutations which is difficult to detect using conventional techniques. Next generation sequencing can be used for discovery of novel genetic alterations and for cost-efficient detection of rare mutation types, and both of these approaches were evaluated in thyroid cancer in this study.
Design: Nine mutation-negative papillary thyroid carcinomas (PTC) and corresponding normal thyroid samples were studied using whole genome sequencing (WGS) or whole transcriptome sequencing (RNA-Seq) on the Illumina HiSeq2000. In addition, 60 thyroid samples including 25 PTC, 2 follicular carcinomas (FC), 6 anaplastic carcinomas (AC), 3 normal tissues and 24 FNA samples were analyzed for mutations in 739 hot spots of 46 cancer-related genes on Ion Torrent PGM (Life Technologies).
Results: WGS had an average coverage of 49 reads and yielded 3-19 nonsynonymous single nucleotide variations (SNV) and 3-35 structural variations (SV) per tumor. One metastatic FVPTC tumor revealed a fusion between TMP3 and NTRK1 with a novel breakpoint, and other tumors revealed several novel interchromosomal rearrangements and promising SNVs. Targeted NGS on Ion Torrent allowed to test all samples for extensive number of mutations using small amount of DNA (10 ng) in a cost-efficient way by barcoding 8-10 samples per run. The platform detected all common point mutations (BRAF, RAS) and rare mutation types including RET M918T, KRAS Q61R, PIK3CA E707K TP53 L194R, ATM V410A, and MET E168D in thyroid surgical and FNA specimens.
Conclusions: Whole genome sequencing and RNA-Seq analysis of PTC revealed a TPM3/NTRK1 fusion with a novel breakpoint, as well as several promising novel chromosomal rearrangement and SNVs, which may allow better characterization of the biology and clinical behavior of PTC. Targeted NGS on Ion Torrent platform allows testing for a broad spectrum of mutations and may further improve the diagnostic accuracy of molecular analysis in thyroid surgical and FNA samples.
Wednesday, March 6, 2013 1:00 PM
Poster Session VI # 50, Wednesday Afternoon