High prevalence of gene fusions and copy number alterations in pediatric radiation therapy-induced papillary and follicular thyroid carcinomas

Thyroid ◽  
2021 ◽  
Author(s):  
Jennifer Hess ◽  
Dorothee K Newbern ◽  
Kristen L Beebe ◽  
Alexandra M Walsh ◽  
Kristian T Schafernak
Keyword(s):  
Radiation Therapy ◽  
Copy Number ◽  
Gene Fusions ◽  
Copy Number Alterations ◽  
Thyroid Carcinomas ◽  
High Prevalence

scholarly journals Development of an RNA sequencing panel to detect gene fusions in thyroid cancer

2021 ◽  
Vol 19 (4) ◽  
pp. e41
Author(s):  
Dongmoung Kim ◽  
Seung-Hyun Jung ◽  
Yeun-Jun Chung
Keyword(s):  
Quality Control ◽  
Thyroid Cancer ◽  
Rna Sequencing ◽  
Copy Number ◽  
Gene Fusion ◽  
Sanger Sequencing ◽  
Limit Of Detection ◽  
Housekeeping Genes ◽  
Gene Fusions ◽  
Copy Number Alterations

In addition to mutations and copy number alterations, gene fusions are commonly identified in cancers. In thyroid cancer, fusions of important cancer-related genes have been commonly reported; however, extant panels do not cover all clinically important gene fusions. In this study, we aimed to develop a custom RNA-based sequencing panel to identify the key fusions in thyroid cancer. Our ThyChase panel was designed to detect 87 types of gene fusion. As quality control of RNA sequencing, five housekeeping genes were included in this panel. When we applied this panel for the analysis of fusions containing reference RNA (HD796), three expected fusions (EML4-ALK, CCDC6-RET, and TPM3-NTRK1) were successfully identified. We confirmed the fusion breakpoint sequences of the three fusions from HD796 by Sanger sequencing. Regarding the limit of detection, this panel could detect the target fusions from a tumor sample containing a 1% fusion-positive tumor cellular fraction. Taken together, our ThyChase panel would be useful to identify gene fusions in the clinical field.

scholarly journals OR21-02 Impact of Nodule Size on the Probability of Hurthle Cell Carcinoma and Other Cancers in Thyroid Nodules with Multiple Chromosomal Copy Number Alterations

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Marina N Nikiforova ◽  
Alyaksandr Nikitski ◽  
Jessica Tebbets ◽  
Lindsey Tolino ◽  
Pooja Manroa ◽  
...  
Keyword(s):  
Copy Number ◽  
Thyroid Nodules ◽  
Surgical Pathology ◽  
Copy Number Alterations ◽  
Nodule Size ◽  
Thyroid Carcinomas ◽  
Hürthle Cell ◽  
Chromosomal Copy Number ◽  
Chromosomal Copy ◽  
Probability Of Cancer

Abstract Fine-needle aspiration (FNA) of thyroid nodules yields indeterminate cytological diagnosis in ~20% of cases, confounding patient management. This includes Hurthle cell nodules, which typically yield Bethesda IV and III cytology. Chromosomal copy number alterations (CNA) are known to occur in thyroid tumors, particularly in Hurthle cell carcinomas (HCC) as well as in other typically follicular-patterned tumors including papillary thyroid carcinomas (PTC) and poorly differentiated thyroid carcinomas (PDTC). The aim of this study was to evaluate thyroid nodules tested positive for CNA but negative for all other genomic alterations using ThyroSeq v3 NGS assay in order to establish the probability of cancer in these nodules and find whether it is influenced by the pattern of CNA and nodule size. We evaluated 111 nodules with multiple CNA detected by ThyroSeq in FNA samples and available surgical pathology outcome. Of those, 69 (62%) nodules showed CNA changes consistent with genome near-haploidization (GNH) whereas 42 (38%) nodules had multiple chromosomal losses and gains (CLG). Nodule size ranged from 0.5-10.2 cm; cytology was Bethesda III in 54%, Bethesda IV in 43%, and Bethesda V-VI in 3% of cases, with Hurthle cells mentioned in the cytology report in 64% of cases. On surgical pathology, 38 (34%) of these nodules were malignant (including 24 HCC, 8 PTC, and 5 oncocytic PDTC) and 73 (66%) were benign (including 43 Hurthle cell and 18 follicular adenomas). No significant difference was observed in probability of malignancy between the two patterns of CNA (p=0.41). However, a significant correlation between the nodule size and probability of cancer was found (p=0.006). In specific CNA groups, correlation between cancer and nodule size remained significant for nodules with GNH pattern (P=0.0002), but not with CLG pattern (p=0.449). Specifically, cancer probability in nodules with GNH pattern and <2 cm in size was 14% (all cancers minimally-invasive), 2.0-2.9 cm was 33%, 3.0-3.9 cm was 50%, 4-4.9 cm was 67%, and ≥5 cm was 80%. Among high-risk cancers (widely-invasive or angioinvasive HCC, PDTC), all 10 tumors had the GNH pattern (p=0.01) and average nodule size of 4.9 cm (range, 2.1-8.5 cm). These findings suggest that CNA of both types are frequently found in Hurthle cell tumors, and probability of cancer in nodules with CNA and no other mutations increases with larger nodule size. This may help to refine the pre-operative assessment of cancer probability and risk of more aggressive disease and offer more tailored management to these patients.

Targeted deep sequencing as a diagnostic and research method for detecting EGFR and ALK pathway driver genes in FFPE tissue of lung and colorectal carcinomas.

2012 ◽  
Vol 30 (30_suppl) ◽  
pp. 39-39
Author(s):  
Sakari Knuutila ◽  
Katja Merkkiniemi ◽  
Mikko Rönty ◽  
Aino Wirtanen ◽  
Satu Maria Remes ◽  
...  
Keyword(s):  
Colorectal Carcinoma ◽  
Deep Sequencing ◽  
Lung Carcinoma ◽  
Copy Number ◽  
Mutation Screening ◽  
Gene Fusions ◽  
Copy Number Alterations ◽  
Hospital District ◽  
Targeted Deep Sequencing ◽  
Diagnostic Validation

39 Background: Molecular targeted tyrosine kinase inhibitor (TKI) treatments have made it crucial to perform diagnostic tests of multiple molecular targets. In lung carcinoma there are close to ten clinically relevant gene mutations, copy number alterations and/or gene fusions, such as ALK, EGFR, ERBB2, KRAS, BRAF, MET, PTEN, PI3KCA, ROS1 and RET. Presently, several different tests are utilized, requiring a high amount of tumor material and long turnaround time. Next generation sequencing or targeted deep sequencing (TDS) has opened a new era for rapid genome-wide analyses of mutations, copy number alterations and gene fusions. Our aimwas to 1) prove feasibility for applying TDS to FFPE samples, 2) compare mutations detected by prevalent methods & TDS, and 3) mine novel clinically and biologically relevant genes in lung and colorectal carcinoma. Methods: For TDS, we selected 192 lung carcinoma and colorectal carcinoma related genes and microRNA genes, focusing on the EGFR and ALK pathways. In total, 98 FFPE specimens were studied. Agilent SureSelect system and Illumina sequencing was adopted for the analysis. For diagnostic validation the following genes were selected: EGFR, KRAS, BRAF, PTEN, PI3K, RET and ALK. TDS results were confirmed by PCR, FISH and IHC. Results: We focused on the genes selected for diagnostic validation. Successful results were obtained from all specimens. The results from TDS correlated significantly with those obtained from PCR, FISH, and IHC. Importantly, TDS revealed novel mutations not detected by targeted PCR. Conclusions: An enormous advantage of TDS is that multiple mutation screening can be achieved in one analysis (saving time and material), and most importantly, provides enormous amounts of novel information, for example understanding mechanisms for drug resistance. This study was supported by Finnish Academy, Sigrid Jusélius Foundation, Finnish Cancer Organizations, the special governmental subsidy research funds appropriated to the Helsinki and Uusimaa Hospital District (HUS EVO), Pfizer Oy, AstraZeneca AS, Lab21 Ltd, Abbott Molecular Inc.

scholarly journals Whole-genome sequencing of follicular thyroid carcinomas reveal recurrent mutations in microRNA processing subunit DGCR8

2021 ◽  
Author(s):  
Johan O Paulsson ◽  
Nima Rafati ◽  
Sebastian DiLorenzo ◽  
Yi Chen ◽  
Felix Haglund ◽  
...  
Keyword(s):  
Copy Number ◽  
Somatic Mutations ◽  
Whole Genome ◽  
Cancer Genes ◽  
Copy Number Alterations ◽  
Thyroid Carcinomas ◽  
Future Studies ◽  
Recurrent Mutations ◽  
Microrna Processing ◽  
Widely Invasive

Abstract Background The genomic and transcriptomic landscape of widely invasive follicular thyroid carcinomas (wiFTCs) and Hürthle cell carcinoma (HCC) are poorly characterized and subsets of these tumors lack information on genetic driver events. The aim of this study was to bridge this gap. Methods We performed whole-genome and RNA sequencing and subsequent bioinformatic analyses of 11 wiFTCs and 2 HCCs with a particularly poor prognosis, and matched normal tissue. Results All wiFTCs exhibited one or several mutations in established thyroid cancer genes, including TERT (n=4), NRAS (n=3), HRAS, KRAS, AKT, PTEN, PIK3CA, MUTYH, TSHR and MEN1 (n=1 each). MutSig2CV analysis revealed recurrent somatic mutations in FAM72D (n=3, in two wiFTCs and in a single HCC), TP53 (n=3, in two wiFTCs and a single HCC) and EIF1AX (n=3), with DGCR8 (n=2) as borderline significant. The DGCR8 mutations were recurrent p.E518K missense alterations, known to cause familial multinodular goiter via disruption of microRNA processing. Expression analyses showed reduced DGCR8 mRNA expression in FTCs in general, and the two DGCR8 mutants displayed a distinct miRNA profile compared to DGCR8 wildtypes. Copy number analyses revealed recurrent gains on chromosomes 4, 6 and 10, and fusiongene analyses revealed 27 high-quality events. Both HCCs displayed hyperploidy, which was fairly unusual in the FTC cohort. Based on the transcriptome data tumors amassed in two principal clusters. Conclusion We describe the genomic and transcriptomic landscape in wiFTCs and HCCs and identify novel recurrent mutations and copy number alterations with possible driver properties and lay the foundation for future studies.

scholarly journals Analytical and Clinical Validation of an Amplicon-based Next Generation Sequencing Assay for Ultrasensitive Detection of Circulating Tumor DNA

2021 ◽  
Author(s):  
Jonathan Poh ◽  
Kao Chin Ngeow ◽  
Michelle Pek ◽  
Kian-Hin Tan ◽  
Jing Shan Lim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Point Mutations ◽  
Circulating Tumor Dna ◽  
Clinical Validation ◽  
Gene Fusions ◽  
Copy Number Alterations ◽  
Next Generation ◽  
Tumor Dna ◽  
Generation Sequencing

Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA. The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (EBV and HBV) and microsatellite instability. Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF, with high specificity even at 0.1% VAF (99.11% per-base). The limit of detection for copy number alterations, EBV, HBV, and microsatellite instability were also empirically determined. Orthogonal comparison of EGFR variant calls made by LiquidHALLMARK and a reference allele-specific PCR method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% alteration-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.

scholarly journals Copy Number Alterations in Papillary Thyroid Carcinomas: Does Loss of SESN2 Have a Role in Age-related Different Prognoses?

2020 ◽  
Vol 17 (5) ◽  
pp. 643-648
Author(s):  
DEISE CIBELE N. DE ALMEIDA ◽  
MICHEL PLATINI CALDAS DE SOUZA ◽  
CAROLINA KOURY NASSAR AMORIM ◽  
JERSEY HEITOR DA SILVA MAUÉS ◽  
FERNANDA DO E. SANTO SAGICA ◽  
...  
Keyword(s):  
Copy Number ◽  
Papillary Thyroid ◽  
Copy Number Alterations ◽  
Thyroid Carcinomas ◽  
Age Related

scholarly journals Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome

2020 ◽  
Vol 144 (12) ◽  
pp. 1535-1546
Author(s):  
Kyung Park ◽  
Hung Tran ◽  
Kenneth W. Eng ◽  
Sinan Ramazanoglu ◽  
Rebecca M. Marrero Rolon ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Precision Oncology ◽  
Gene Fusions ◽  
Copy Number Alterations ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Sequencing Platform ◽  
Generation Sequencing

Context.— An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. Objective.— To describe the validation studies as per New York State–Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) trial. Design.— Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. Results.— High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. Conclusions.— This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH.

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