Concordance of BRAF V600E mutation between immunohistochemistry and genomic testing for thyroid cancer

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Although targeted therapy for this mutation requires genomic testing in Japan, turnaround time (TAT) is often unacceptably long, especially for certain conditions, such as ATC, which is one of the most aggressive cancers. Here, we evaluated concordance between immunohistochemistry (IHC) with a relatively short TAT of a few days and genomic testing in thyroid cancer. Methods Immunohistochemical staining was performed with BRAF (VE1) antibody (Ventana) using the OptiView method on samples already undergoing genomic testing. A pathologist blindly annotated each staining expression with a cut-off of 1% in the cytoplasm. We then calculated the positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA). Results We identified 62 samples, including 12 of ATC, that underwent genomic testing using different methods: Oncomine Dx Target Test (ODxTT) (n = 32), MEBGEN BRAF 3 Kit (MEBGEN3) (n = 14), FoundationOne CDx (F1CDx) (n = 13), and GenMineTOP (TOP) (n = 1). Annotation results of IHC were positive for 31, negative for 29, and undeterminable for 2 samples due to low tumor content. PPA, NPA, and OPA were 100%, 91.7%, 96.9% for ODxTT; 100%, 100%, 100% for MEBGEN3; 100%, 80.0%, 93.9% for F1CDx; and incalculable, 100%, 100% for TOP, respectively. Discordance was found in the two undeterminable samples only. Conclusion Concordance between IHC and genomic testing in assessing BRAF V600E was encouragingly high; its reliability and potentially short TAT should benefit patients, especially those with ATC. IHC CDx Thyroid cancer Anaplastic thyroid cancer Targeted therapy BRAF plus MEK inhibitors Figures Figure 1 Figure 2 Figure 3 Figure 4 Introduction The incidence of thyroid cancer, the most common malignancy originating from the endocrine system, continues to increase throughout the world [ 1 ]. This includes Japan, where the annual incidence has now reached 14 per 100,000 people [ 2 ]. Follicular cell-derived thyroid cancer is categorized by histological subtype into papillary thyroid cancer (PTC), follicular thyroid cancer (FTC), poorly differentiated thyroid cancer (PDTC), and anaplastic thyroid cancer (ATC). Standard treatment is surgery for all histological subtypes, while radioactive iodine treatment and thyroid-stimulating hormone suppression treatment are provided as adjuvant therapy or cancer treatment for PTC, FTC, and PDTC [ 3 ]. However, the eighth edition of the American Joint Committee on Cancer staging systems manual reports that ATC – known to be one of the most aggressive cancers – is consistently classified as stage IV at diagnosis [ 4 ]. Despite advances in multimodal treatment, the most recent retrospective national database analysis in the United States reports a median overall survival (OS) of ATC of only three months [ 5 ]. Systemic therapy consisting of multi-kinase inhibitors and targeted therapy for specific genomic alterations is considered for patients who are refractory to or ineligible for the above treatment for all histological subtypes. In this context, BRAF V600E mutation is the most common treatable genomic alteration in thyroid cancer, with a reported prevalence of approximately 75% in PTC, 3% in FTC, 20% in PDTC, and 50% in ATC in the Japanese population [ 6 – 8 ]. BRAF plus MEK inhibitors, namely dabrafenib plus trametinib and encorafenib plus binimetinib, have demonstrated a favorable balance between efficacy and safety in clinical phase II trials for recurrent and/or metastatic thyroid cancer in patients with BRAF V600E mutation who were ineligible for multi-kinase inhibitors [ 9 , 10 ]. Based on these results, these therapies were recently approved in Japan and now play an increasingly important role in the treatment of recurrent and/or metastatic thyroid cancer patients with BRAF V600E mutation. In this situation, because multi-kinase inhibitors showed limited clinical activity, the combination of BRAF plus MEK inhibitors demonstrated the most promising clinical activity for ATC patients with BRAF V600E mutation as well: in phase II trials, dabrafenib plus trametinib showed an objective response rate of 55.5%, 1-y progression-free survival (PFS) of 43.2%, and 1-y OS of 51.7%, while encorafenib plus binimetinib showed an objective response rate of 80.0%, 1-y PFS of 75.0%, and 1-y OS of 100% for unresectable or metastatic ATC patients with BRAF V600E mutation [ 10 , 11 ]. The two combination treatments also showed tolerable safety profiles. Accordingly, BRAF plus MEK inhibitors are considered the most promising treatment for ATC patients with BRAF V600E mutation. In current clinical practice in Japan, initiation of treatment with BRAF plus MEK inhibitors requires the confirmation of mutation by genomic testing, which consists of the results of certified companion diagnostics (CDx) or official recommendations based on the results of comprehensive genomic profiling (CGP). However, the confirmation process takes from two weeks to two months, which is often unacceptably long, especially for ATC, which generally progresses rapidly. In contrast, immunohistochemistry (IHC) takes only a few days and can be performed relatively promptly, even within institutions. However, while IHC testing for BRAF V600E mutation has been approved as an in vitro diagnostic for colorectal cancer in Japan, it has not been established for thyroid cancer, likely due to a lack of reliable data on concordance between IHC and genomic testing, such as that introduced above. Here, we aimed to evaluate the concordance of BRAF V600E mutation between IHC and genomic testing of CDx and CGP for thyroid cancer. Material and Methods 1. Sample selection We retrospectively reviewed the medical records of patients with thyroid cancer treated from June 2019, the time of introduction of genomic testing under the Japanese insurance system, to June 2024 at National Cancer Center Hospital East, Japan. Inclusion criteria were (1) histologically proven PTC, FTC, PDTC, or ATC, (2) previous genomic testing with Oncomine™ Dx Target Test MultiCDx System (ODxTT), MEBGEN™ BRAF 3 Kit (MEBGEN3), FoundationOne® CDx (F1CDx), or GenMineTOP Cancer Genome Profiling System (TOP) as a clinical order, (3) availability of an formalin-fixed paraffin-embedded (FFPE) block for research in our hospital, and (4) consent to the use of clinical residual samples for research purposes. Sample characteristics were collected from medical and pathological records. The genomic tests evaluated in this study are characteristically distinct, and each is covered by the Japanese insurance system. Briefly, ODxTT (Thermo Fisher Scientific, Waltham, MA, USA) is a DNA- and RNA-based next-generation sequencing hot spot panel test that includes 46 genes from tumor tissue samples, and was approved as CDx in 2022 for thyroid cancers. MEBGEN3 (Medical and Biological Laboratories Co., Ltd., Tokyo, Japan) is a DNA-based PCR sequencing test that detects a single spot of BRAF V600E mutation from tumor tissue samples, and was approved as CDx in 2023. F1CDx (Foundation Medicine Inc., Cambridge, MA, USA) is a DNA-based next-generation sequencing panel test that includes 324 genes from tumor tissue samples, and was approved as CGP in 2019. TOP (Konica Minolta, Inc., Tokyo, Japan) is a DNA-based and RNA-based next-generation sequencing panel test that includes 737 genes from paired tumor tissue samples and non-tumor blood samples, and was approved as CGP in 2023. 2. Sample preparation and immunohistochemical examination Two sections were freshly cut from the residual FFPE blocks by microtome at a 4-µm thickness in a single session. All blocks had been previously used for genomic testing. On the Ventana BenchMark ULTRA automated slide strainer (Roche Tissue Diagnostics, Tucson, AZ, USA), one section was stained with hematoxylin and eosin (HE) and another section with VENTANA® anti-BRAF V600E (VE1) Mouse Monoclonal Primary Antibody (Catalog Number. 760–5095; Roche Tissue Diagnostics, Tucson, AZ, USA), with cell conditioning at 100°C for 64 minutes, and pre-peroxidase inhibition and primary antibody incubation at 36°C for 16 minutes. The OptiView DAB IHC Detection Kit (Roche Tissue Diagnostics, Tucson, AZ, USA) was applied for optimal visualization. These processes were performed in July 2024. 3. Concordance analysis One pathologist blindly annotated each staining expression of IHC with a cut-off of 1% in the cytoplasm as positive, negative, or undetermined using light microscopy. After evaluation of IHC expression, the slides were digitalized by scanning at × 40 magnification using a NanoZoomer2.0HT digital slide scanner (Hamamatsu Photonics, Hamamatsu, Japan) to preserve the image. Another researcher independently documented BRAF V600E mutation status from the respective genomic test report. We then calculated sensitivity, specificity,positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) between IHC and genomic testing results. Slides annotated as undetermined were classified as false negative to avoid overestimating the usefulness of the IHC stain. Statistical analyses were performed using pandas, version 1.5.3; NumPy, version 1.24.2; SciPy, version 1.10.0; stats models, version 2.13.5; and lifelines, version 0.27.4 (Python Data Analysis Library). Results 1. Sample characteristics We identified 62 samples from 59 patients; of these, 6 were duplicates from 3 individuals (Table 1). Histologic subtype was PTC in 40 (64.5%) samples, FTC in 6 (9.7%), PDTC in 4 (6.5%), and ATC in 12 (19.4%). By method, 44 (71.0%) samples were obtained at surgery and 18 (29.0%) on biopsy. By location, samples were from the primary thyroid lesion in 33 (53.2%), lymph node metastasis in 20 (32.3%), lung metastasis in 7 (11.3%), bone metastasis in 1 (1.6%), and pleural metastasis in 1 (1.6%). Genomic testing was by ODxTT in 32 (51.6%) samples, MEBGEN3 in 14 (22.6%), F1CDx in 30 (48.4%), and TOP in 1 (1.6%). Of the 77 tests, 67 (87.7%) were performed within three years of sampling (Fig. 1). The confirmed BRAF mutation status by genomic testing was 51 positive (46 for PTC, 1 for PDTC, and 4 for ATC) and 26 negative (4 for PTC, 8 for FTC, 3 for PDTC, and 11 for ATC). Positive and negative status was identified using ODxTT (19/2), MEBGEN3 (9/1), and F1CDx (18/1) for PTC samples; ODxTT (0/5), MEBGEN3 (0/2), and F1CDx (1/1) for FTC samples; ODxTT (0/2) and F1CDx (1/1) for PDTC samples; ODxTT (1/3), MEBGEN3 (0/2), F1CDx (3/5), and TOP (0/1) for ATC samples. 2. Results of BRAF-IHC For all samples, BRAF-IHC was positive in 31, negative in 29, and undeterminable in 2 due to low tumor content in the section from the residual FFPE block. Fig. 2 shows the results by IHC status, genomic testing status, and sample characteristics. In addition, three representative samples (two BRAF-IHC-positive samples and one BRAF-IHC-negative sample) are shown in Fig. 3 (1, HE, low magnification; 2, HE, high magnification; 3, IHC, low magnification; and 4, IHC, high magnification in each figure). Fig. 3A is a true positive sample of PTC, and was the oldest sample in this research, obtained 18 years ago. Fig. 3A4 shows strong IHC expression in the cytoplasm. Fig. 3B is a true positive sample of ATC originating from PTC in which both areas were stained, and Fig. 3B4 shows strong IHC expression in the ATC area. Fig. 3C is a true negative sample of ATC, and Fig. 3B4 shows the lack of IHC expression. The two undeterminable samples are shown in Fig. 4 (1, HE, low magnification; 2, HE, high magnification; 3, IHC, low magnification; 4, IHC, high magnification; 5, IHC, low magnification; 5, IHC, high magnification, in each figure). Fig. 4A is an undeterminable surgical sample with low PTC content. Fig. 4A4 shows moderate IHC expression; however, the area shown by the black arrows in Fig. 4A6 shows a lack of IHC expression. Fig. 4B is an undeterminable biopsy sample with low PTC content. Fig. 4B4 shows moderate IHC expression; however, the area shown by the black arrows in Fig. 4B6 shows a lack of IHC expression. 3. Concordance between BRAF-IHC and genomic test Table 2 shows the concordance between IHC and the genomic tests for all histologic subtypes. PPA, NPA, and OPA were 100% (20/20), 91.7% (11/12), and 96.9% (31/32) for ODxTT; 100% (9/9), 100% (5/5), and 100% (14/14) for MEBGEN3; 100% (20/20), 80.0% (8/10), and 93.9% (28/30) for F1CDx; and incalculable, 100% (1/1), and 100% (1/1) for TOP, respectively. Discordance was found in the two undeterminable samples only. The results of concordance for ATC are shown in Table 3. All calculable PPA, NPA, and OPA results in ATC samples were 100% for each genomic test. Discussion Here, we demonstrate for the first time a high concordance for BRAF status between IHC using anti-BRAF V600E (VE1) antibody and genomic tests certified as CDx and CGP and covered by the Japanese insurance system. Notably, we found that the results were completely reproduced in ATC samples, a fact which has been little known worldwide. These results support the early detection of subjects with the BRAF V600E mutation and a shorter TAT, and consequently the introduction of BRAF plus MEK inhibitors for them. This approach will greatly benefit patients who require treatment immediately due to the disease’s characteristics of aggressive and rapid disease progression. Recently, the clinical significance of BRAF-targeted therapy in thyroid cancer has been increasingly noted. Several clinical studies have shown prominent clinical activity, particularly for ATC, for which even lenvatinib, a multi-kinase inhibitor uniquely approved for ATC in Japan, has shown limited efficacy and raised concerns about safety [ 12 ]. A prospective observational study of lenvatinib reported an ORR of 11% as well as grade 3 adverse events of fistula (2.0%), perforation of the gastrointestinal tract (1.2%), and bleeding (1.6%), probably due to an incompatibility between its strong inhibition of vascular endothelial growth factor receptor and the disease’s highly invasive features [ 13 ]. Further, although a number of other specific genetic alterations could be used (e.g., RET fusion-positive, NTRK fusion-positive) [ 14 – 16 ], their prevalence is rare (e.g., 2% in ATC) [ 6 , 7 ]. Nevertheless, insurance regulations in Japan require the prescription of target therapy on confirmation of the presence of BRAF mutation using specific platforms, namely CDx (ODxTT, MEBGEN3) and CGP. This often leads to a delay in treatment initiation, which is disadvantageous to the patient. From a global context, the National Comprehensive Cancer Network guidelines, the American Thyroid Association guidelines, and the Endocrine Pathology Society state that IHC testing is recommended owing to its shorter TAT compared to genomic testing, especially in ATC, for which early treatment initiation is strongly desirable [ 3 , 17 , 18 ]. All investigations to date of the concordance between BRAF-IHC as a tool for prompt detection of target alterations and corresponding gene testing have been conducted abroad. A recent meta-analysis showed that the sensitivity and specificity of IHC by VE1 clone against the direct sequence and PCR-based sequence were 100%, 84%, 98%, and 89%, respectively, in PTC [ 19 ]. Our present study is thus the first to evaluate the relationship between CDx platforms approved in Japan (ODxTT and MEBGEN3). Furthermore, the search for concordance with hybridization capture-based sequences adopted in CGP (F1CDx and TOP) could reveal equivalent agreement with these previous reports. Fewer studies have reported concordance for ATC than for PTC. The largest study to date with 53 samples reported the sensitivity, specificity, and OPA of IHC using an exact clone (VE1) for PCR-based sequence on BRAF status of 100%, 96.65%, and 86.4%, respectively [ 20 ]. Our present study affirms these findings and newly demonstrates that they were independent of sampling location or method. Given the difficulties in tissue sampling for ATC, including procedure-related complications (e.g., bleeding) due to invasiveness to surrounding organs, these findings are valuable in clinical practice, particularly in the preoperative setting in ATC, where successful initiation of the combination of BRAF and MEK inhibitors could confer a substantial benefit on patient survival (1-year overall survival rate of 93.6% in patients treated with BRAF plus MEK inhibitors followed by surgery) [ 21 ]. Several points of this study should be noted. First, we encountered two samples in which the BRAF V600E mutation was detected by genomic testing, whereas assessment on BRAF-IHC was undeterminable (Fig. 4 A and Fig. 4 B). We considered that this was due to low tumor content and crush artifacts in tissue sampling. These samples simultaneously contained areas both with and without IHC expression but – due to our goal of assessing concordance in the same block – we were unable to avoid artifacts of residual sampling. This difficulty highlights the need for careful determination in samples with limited tumor cells in order to both prevent the loss of valuable therapeutic opportunities and to facilitate discussion aimed at an appropriate assessment of the IHC sample. Second, the anti-BRAF V600E (VE1) antibody, which is designed to detect the change of amino acid peptide from 596 to 606 (GLATEKSRWSG), might be reactive to mutations other than the BRAF V600E mutation, resulting in a false positive in detecting the target [ 22 ]. However, BRAF non-V600E mutations are extremely rare in thyroid cancer [ 23 , 24 ], and a study of lung cancers for BRAF non-V600E mutation found that no sample was stained by an anti-BRAF V600E (VE1) antibody [ 25 ]. Third, although we obtained significant agreement between IHC and insurance-certified platforms (CDx) that would be beneficial to the patient population, any application of our results to clinical settings in Japan requires further discussion, including prospective study or equivalence testing. Conclusion IHC and genomic testing in the assessment of BRAF status in thyroid cancer have clinically sufficient concordance. IHC – which is primarily characterized by a short TAT – will benefit patients, particularly those whose cancers show aggressive clinical features requiring the prompt initiation of treatment. Declarations Acknowledgments The authors thank Yuka Nakamura (Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center) for technical assistance and Guy Harris D.O. of Dmed () for editing drafts of this manuscript. However, the ultimate responsibility for opinions, conclusions, and data interpretation lies with the authors. Conflict of Interest MT reports grants and personal fees from Ono Pharmaceutical and Bayer, and personal fees from MSD, BMS, Merck Biopharma, Novartis, Pfizer, Rakuten Medical, Lilly, Boehringer Ingelheim, Eisai, Chugai Pharmaceutical, Daiichi-Sankyo, Janssen Pharmaceutical, Genmab, Astra Zeneca, Abbvie and Astellas, outside the submitted work. SO reports personal fees from Ono Pharmaceutical, MSD, BMS, and Merck Biopharma outside the submitted work. TF reports honoraria for lectures from Amelieff Co. Ltd. GI reports grants from Takeda Pharmaceutical Company Limited, Noile-Immune Biotech, Indivumed GmbH, Sumitomo Dainippon Pharma Co., Ltd. Nihon Medi-Physics CO., Ltd. ONO PHARMACEUTICAL CO., LTD. DAIICHI SANKYO, INC. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Ethics Statement This study protocol was approved by the Institutional Ethical Committee of the National Cancer Center Hospital East (reference number 2024-066). Written informed consent for participation was not required for this study, in accordance with national legislation and institutional requirements. Patients and their families were provided an opportunity to opt-out of the study in accordance with the policy of the Japanese government. The study was conducted in accordance with the principles laid down in the Declaration of Helsinki. Data availability The data that support the fundings of this study is available from the corresponding author upon reasonable request. Author Contributions Ryutaro Onaga: Methodology, Formal analysis, Investigation, Data Curation, Writing - Original Draft, Writing - Review & Editing. Tomohiro Enokida: Methodology, Formal analysis, Investigation, Data Curation, Writing - Original Draft, Writing - Review & Editing. Shingo Sakashita: Conceptualization, Validation, Data Curation, Writing - Review & Editing. Susumu Okano: Writing - Review & Editing. Takao Fujisawa: Writing - Review & Editing. Nobukazu Tanaka: Writing - Review & Editing. Yuta Hoshi: Writing - Review & Editing. Takuma Kishida: Writing - Review & Editing. Ryo Kuboki: Writing - Review & Editing. Hiroshi Nishino: Writing - Review & Editing. Makoto Ito: Writing - Review & Editing. Genichiro Ishii: Writing - Review & Editing. Shumpei Ishikawa: Writing - Review & Editing. Makoto Tahara: Conceptualization, Writing - Review & Editing, Supervision, Project administration. References Siegel RL, Giaquinto AN, Jemal A (2024) Cancer statistics, 2024. CA Cancer J Clin 74:12-49. https://doi.org/10.3322/caac.21820 (2016-2020) Cancer Statistics. Cancer Information Service, National Cancer Center, Japan. 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Sample characteristics Total samples n=62 † (%) Patient age at sampling Mean age, years [SD] Median age, years [range] 68.3 [10.0] 71.5 [47-84] Gender Female Male 34 (54.8) 28 (45.2) Histologic subtype Papillary thyroid cancer Follicular thyroid cancer Poorly differentiated thyroid cancer Anaplastic thyroid cancer 40 (64.5) 6 (9.7) 4 (6.5) 12 (19.4) Sampling method Surgery Biopsy 44 (71.0) 18 (29.0) Location of sampling Primary thyroid lesion Lymph node metastasis Lung metastasis Bone metastasis Pleural metastasis 33 (53.2) 20 (32.3) 7 (11.3) 1 (1.6) 1 (1.6) Type of testing ‡ ODxTT MEBGEN3 F1CDx TOP 32 (51.6%) 14 (22.6%) 30 (48.4%) 1 (1.6%) Note: † Three patients each provided two different samples, ‡ Some samples underwent multiple types of testing. Abbreviations: SD; standard deviation, ODxTT; Oncomine™ Dx Target Test MultiCDx System, MEBGEN3; MEBGEN™ BRAF 3 Kit, F1CDx; FoundationOne ® CDx, TOP; GenMineTOP Cancer Genome Profiling System. Table 2. Concordance evaluation of IHC in comparison with genomic testing in all cases ODxTT (n=32) MEBGEN3 (n=14) F1CDx (n=30) TOP (n=1) Subject nucleic acid DNA, RNA DNA DNA DNA, RNA Enrichment method PCR PCR HC HC True positive 20 9 20 0 False positive 0 0 0 0 True negative 11 5 8 1 False negative † 1 0 2 0 Sensitivity 95.2% 100 % 90.9 % NA Specificity 100 % 100 % 100 % 100 % Positive percent agreement 100 % 100 % 100 % NA Negative percent agreement 91.7% 100 % 80.0% 100 % Overall percent agreement 96.9% 100 % 93.3% 100 % Note: † False negatives consisted of two undeterminable samples only. Abbreviations: PCR; polymerase chain reaction-based sequence, HC; hybridization capture-based sequence, ODxTT; Oncomine™ Dx Target Test MultiCDx System, MEBGEN3; MEBGEN™ BRAF 3 Kit, F1CDx; FoundationOne ® CDx, TOP; GenMineTOP Cancer Genome Profiling System, NA; Not Applicable. Table 3. Concordance evaluation of IHC in comparison with genomic testing for anaplastic thyroid cancer ODxTT (n=4) MEBGEN3 (n=2) F1CDx (n=8) TOP (n=1) Subject nucleic acid DNA, RNA DNA DNA DNA, RNA Enrichment method PCR PCR HC HC True positive 1 0 3 0 False positive 0 0 0 0 True negative 3 2 5 1 False negative 0 0 0 0 Sensitivity 100% NA 100% NA Specificity 100% 100% 100% 100% Positive percent agreement 100% NA 100% NA Negative percent agreement 100% 100% 100% 100% Overall percent agreement 100% 100% 100% 100% Abbreviations: PCR; polymerase chain reaction-based sequence, HC; hybridization capture-based sequence, ODxTT; Oncomine™ Dx Target Test MultiCDx System, MEBGEN3; MEBGEN™ BRAF 3 Kit, F1CDx; FoundationOne ® CDx, TOP; GenMineTOP Cancer Genome Profiling System, NA; Not Applicable. Cite Share Download PDF Status: Published Journal Publication published 10 Apr, 2025 Read the published version in International Journal of Clinical Oncology → Version 1 posted Editorial decision: Accept 29 Mar, 2025 Reviewers agreed at journal 29 Mar, 2025 Reviewers invited by journal 27 Mar, 2025 Editor assigned by journal 26 Mar, 2025 First submitted to journal 25 Mar, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5969512","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":434706846,"identity":"bf9bcf51-24cb-44ce-b9da-e701563f9f66","order_by":0,"name":"Ryutaro Onaga","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5ElEQVRIiWNgGAWjYPACG1SuARFa0oCYmTQth1G14AXm7b0HP36pOS/H33/+AHNBjR2DvHsDQ3EBHi0yZ84lS8scu20scSOZgXnGsWQGwzMHGIxn4NEiIZFjIC3Bdjux4QYzAzNvwwEGwxkJDMY8+LUY/5b4d65+/vnDxGsxk/zYdiDB4EAyRIu8BCEtPGfMrBn7kg033kg2OMxzLJnHgOdgA36/sPcY3/zxzU5e7vzBh495auzk5NubjxnjCzEQYIY54wAQ8xgcYGwzJqCDgfEHMk++gYH5MSEto2AUjIJRMKIAAKK6RUo/+ycRAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-6422-4033","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":true,"prefix":"","firstName":"Ryutaro","middleName":"","lastName":"Onaga","suffix":""},{"id":434706847,"identity":"d72e68c9-cb02-4474-b881-c1754fe560cf","order_by":1,"name":"Tomohiro Enokida","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Tomohiro","middleName":"","lastName":"Enokida","suffix":""},{"id":434706848,"identity":"3cfc5971-cc79-4ce2-ae33-da9e76a203dc","order_by":2,"name":"Shingo Sakashita","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Shingo","middleName":"","lastName":"Sakashita","suffix":""},{"id":434706849,"identity":"14578ac9-7a21-4007-932d-40ec2705f929","order_by":3,"name":"Nobukazu Tanaka","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Nobukazu","middleName":"","lastName":"Tanaka","suffix":""},{"id":434706850,"identity":"1e9d50ee-33c1-4580-b85a-48a9950bd8b6","order_by":4,"name":"Yuta Hoshi","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Yuta","middleName":"","lastName":"Hoshi","suffix":""},{"id":434706851,"identity":"60221abd-82c2-47df-a6f9-2ae22b622058","order_by":5,"name":"Takuma Kishida","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Takuma","middleName":"","lastName":"Kishida","suffix":""},{"id":434706852,"identity":"2f8ff21e-4ab4-49ae-b55c-33e83f9d99ba","order_by":6,"name":"Ryo Kuboki","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Ryo","middleName":"","lastName":"Kuboki","suffix":""},{"id":434706853,"identity":"3cf25619-0fc1-49fc-b049-97439ba1cdbd","order_by":7,"name":"Takao Fujisawa","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Takao","middleName":"","lastName":"Fujisawa","suffix":""},{"id":434706854,"identity":"53d44e3d-d31a-4fc4-9bcc-3d55e2fb4140","order_by":8,"name":"Susumu Okano","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Susumu","middleName":"","lastName":"Okano","suffix":""},{"id":434706855,"identity":"ce1a2edd-4ce7-4c14-bd72-b61f08cd1acd","order_by":9,"name":"Hiroshi Nishino","email":"","orcid":"","institution":"Jichi Medical University: Jichi Ika Daigaku","correspondingAuthor":false,"prefix":"","firstName":"Hiroshi","middleName":"","lastName":"Nishino","suffix":""},{"id":434706856,"identity":"fa40862c-6a91-4f06-a602-082ff96ebd50","order_by":10,"name":"Makoto Ito","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Makoto","middleName":"","lastName":"Ito","suffix":""},{"id":434706857,"identity":"eb8597ba-c63a-41d1-978e-7d4c4bb90951","order_by":11,"name":"Genichiro Ishii","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Genichiro","middleName":"","lastName":"Ishii","suffix":""},{"id":434706858,"identity":"dee02c9e-5d21-4b25-8e80-706e44cf00fb","order_by":12,"name":"Shumpei Ishikawa","email":"","orcid":"","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Shumpei","middleName":"","lastName":"Ishikawa","suffix":""},{"id":434706859,"identity":"06451649-1f54-4809-97b4-19a4259929a1","order_by":13,"name":"Makoto Tahara","email":"","orcid":"https://orcid.org/0000-0001-9035-3106","institution":"National Cancer Center-Hospital East: Kokuritsu Gan Center Higashi Byoin","correspondingAuthor":false,"prefix":"","firstName":"Makoto","middleName":"","lastName":"Tahara","suffix":""}],"badges":[],"createdAt":"2025-02-06 03:09:39","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5969512/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5969512/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s10147-025-02760-y","type":"published","date":"2025-04-10T16:05:54+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":79550932,"identity":"37bb899b-5285-4199-b11c-45d61ac8fc68","added_by":"auto","created_at":"2025-03-31 06:37:08","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":4499277,"visible":true,"origin":"","legend":"\u003cp\u003eTime from sampling to genomic testing\u003c/p\u003e\n\u003cp\u003eAbbreviations: ODxTT; Oncomine™ Dx Target Test MultiCDx System, MEBGEN3; MEBGEN™ BRAF 3 Kit, F1CDx; FoundationOne\u003csup\u003e®\u003c/sup\u003eCDx, TOP; GenMineTOP Cancer Genome Profiling System.\u003c/p\u003e","description":"","filename":"1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-5969512/v1/3a46bfdc8e092acde42a7658.jpg"},{"id":79550940,"identity":"bb373ecf-7657-4436-a58e-ffe3bfee2161","added_by":"auto","created_at":"2025-03-31 06:37:08","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1939545,"visible":true,"origin":"","legend":"\u003cp\u003eComprehensive results containing IHC status, genomic testing status, and sample characteristics\u003c/p\u003e\n\u003cp\u003eNote: In the rows for IHC, ODxTT, MEBGEN3, F1CDx, and TOP, the numbers represent the no. of years from sampling to testing. The same patients from X, Y, Z were tested using two modalities of genomic testing for different samples.\u003c/p\u003e\n\u003cp\u003eAbbreviations: IHC; immunohistochemistry, ODxTT; Oncomine™ Dx Target Test MultiCDx System, MEBGEN3; MEBGEN™ BRAF 3 Kit, F1CDx; FoundationOne\u003csup\u003e®\u003c/sup\u003eCDx, TOP; GenMineTOP Cancer Genome Profiling System.\u003c/p\u003e","description":"","filename":"2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-5969512/v1/1882586757c5b1b7d5bb9fbe.jpg"},{"id":79550945,"identity":"c3e5b982-e87f-421a-a75c-70f818f498eb","added_by":"auto","created_at":"2025-03-31 06:37:08","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1160828,"visible":true,"origin":"","legend":"\u003cp\u003eRepresentative sample presentations of HE and IHC using VENTANA OptiView BRAF V600E (VE1) antibody\u003c/p\u003e\n\u003cp\u003e(A) True positive sample of PTC, which was the oldest sample in this research, obtained 18 years ago; (B) true positive sample of ATC originating from PTC in which both areas were stained; and (C) a true negative sample of ATC.\u003c/p\u003e\n\u003cp\u003eNote: 1, HE, low magnification; 2, IHC, low magnification; 3, HE, high magnification focused on the black boxed area in 1; 4, IHC, high magnification focused on the black boxed area in 2, in each figure. Abbreviations: HE; Hematoxylin and eosin, IHC; immunohistochemistry, ATC; Anaplastic thyroid cancer, PTC; Papillary thyroid cancer.\u003c/p\u003e","description":"","filename":"3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-5969512/v1/41a31b86eb45cd38b97bcd18.jpg"},{"id":79550929,"identity":"4fd5186b-45e7-4a88-82fa-be128540540f","added_by":"auto","created_at":"2025-03-31 06:37:08","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1244424,"visible":true,"origin":"","legend":"\u003cp\u003eUndeterminable sample presentation of HE and IHC using VENTANA OptiView BRAF V600E (VE1) antibody\u003c/p\u003e\n\u003cp\u003e(A) Undeterminable surgical sample with low PTC content, and (B) undeterminable biopsy sample with low PTC content. Although a small portion of the tumor showed staining, some areas highlighted with black arrows show a lack of IHC expression. We evaluated the overall status as undeterminable.\u003c/p\u003e\n\u003cp\u003eNote: 1, HE, low magnification; 2, IHC, low magnification; 3, HE, high magnification focused on the black boxed area in 1; 4, IHC, high magnification focused on the black boxed area in 2; 5, HE, high magnification focused on the blue boxed area in 1; 6, IHC, high magnification focused on the blue boxed area in 2, in each figure. Abbreviations: HE; Hematoxylin and eosin, IHC; immunohistochemistry, PTC; Papillary thyroid cancer.\u003c/p\u003e","description":"","filename":"4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-5969512/v1/a6bddfcebcc2a80da352f5f8.jpg"},{"id":80558678,"identity":"bad55493-e8c8-44a7-b3ef-f7901e5b05d6","added_by":"auto","created_at":"2025-04-14 16:16:01","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":9648768,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5969512/v1/20ce7443-b43e-43c6-928a-d153bd29db79.pdf"}],"financialInterests":"","formattedTitle":"Concordance of BRAF V600E mutation between immunohistochemistry and genomic testing for thyroid cancer","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe incidence of thyroid cancer, the most common malignancy originating from the endocrine system, continues to increase throughout the world [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. This includes Japan, where the annual incidence has now reached 14 per 100,000 people [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Follicular cell-derived thyroid cancer is categorized by histological subtype into papillary thyroid cancer (PTC), follicular thyroid cancer (FTC), poorly differentiated thyroid cancer (PDTC), and anaplastic thyroid cancer (ATC). Standard treatment is surgery for all histological subtypes, while radioactive iodine treatment and thyroid-stimulating hormone suppression treatment are provided as adjuvant therapy or cancer treatment for PTC, FTC, and PDTC [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. However, the eighth edition of the American Joint Committee on Cancer staging systems manual reports that ATC \u0026ndash; known to be one of the most aggressive cancers \u0026ndash; is consistently classified as stage IV at diagnosis [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Despite advances in multimodal treatment, the most recent retrospective national database analysis in the United States reports a median overall survival (OS) of ATC of only three months [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eSystemic therapy consisting of multi-kinase inhibitors and targeted therapy for specific genomic alterations is considered for patients who are refractory to or ineligible for the above treatment for all histological subtypes. In this context, \u003cem\u003eBRAF\u003c/em\u003e V600E mutation is the most common treatable genomic alteration in thyroid cancer, with a reported prevalence of approximately 75% in PTC, 3% in FTC, 20% in PDTC, and 50% in ATC in the Japanese population [\u003cspan additionalcitationids=\"CR7\" citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. BRAF plus MEK inhibitors, namely dabrafenib plus trametinib and encorafenib plus binimetinib, have demonstrated a favorable balance between efficacy and safety in clinical phase II trials for recurrent and/or metastatic thyroid cancer in patients with \u003cem\u003eBRAF\u003c/em\u003e V600E mutation who were ineligible for multi-kinase inhibitors [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Based on these results, these therapies were recently approved in Japan and now play an increasingly important role in the treatment of recurrent and/or metastatic thyroid cancer patients with \u003cem\u003eBRAF\u003c/em\u003e V600E mutation. In this situation, because multi-kinase inhibitors showed limited clinical activity, the combination of BRAF plus MEK inhibitors demonstrated the most promising clinical activity for ATC patients with \u003cem\u003eBRAF\u003c/em\u003e V600E mutation as well: in phase II trials, dabrafenib plus trametinib showed an objective response rate of 55.5%, 1-y progression-free survival (PFS) of 43.2%, and 1-y OS of 51.7%, while encorafenib plus binimetinib showed an objective response rate of 80.0%, 1-y PFS of 75.0%, and 1-y OS of 100% for unresectable or metastatic ATC patients with \u003cem\u003eBRAF\u003c/em\u003e V600E mutation [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. The two combination treatments also showed tolerable safety profiles. Accordingly, BRAF plus MEK inhibitors are considered the most promising treatment for ATC patients with \u003cem\u003eBRAF\u003c/em\u003e V600E mutation.\u003c/p\u003e \u003cp\u003eIn current clinical practice in Japan, initiation of treatment with BRAF plus MEK inhibitors requires the confirmation of mutation by genomic testing, which consists of the results of certified companion diagnostics (CDx) or official recommendations based on the results of comprehensive genomic profiling (CGP). However, the confirmation process takes from two weeks to two months, which is often unacceptably long, especially for ATC, which generally progresses rapidly. In contrast, immunohistochemistry (IHC) takes only a few days and can be performed relatively promptly, even within institutions. However, while IHC testing for \u003cem\u003eBRAF\u003c/em\u003e V600E mutation has been approved as an in vitro diagnostic for colorectal cancer in Japan, it has not been established for thyroid cancer, likely due to a lack of reliable data on concordance between IHC and genomic testing, such as that introduced above.\u003c/p\u003e \u003cp\u003eHere, we aimed to evaluate the concordance of \u003cem\u003eBRAF\u003c/em\u003e V600E mutation between IHC and genomic testing of CDx and CGP for thyroid cancer.\u003c/p\u003e"},{"header":"Material and Methods","content":"\u003cp\u003e1. Sample selection\u003c/p\u003e \u003cp\u003eWe retrospectively reviewed the medical records of patients with thyroid cancer treated from June 2019, the time of introduction of genomic testing under the Japanese insurance system, to June 2024 at National Cancer Center Hospital East, Japan. Inclusion criteria were (1) histologically proven PTC, FTC, PDTC, or ATC, (2) previous genomic testing with Oncomine\u0026trade; Dx Target Test MultiCDx System (ODxTT), MEBGEN\u0026trade; BRAF 3 Kit (MEBGEN3), FoundationOne\u0026reg; CDx (F1CDx), or GenMineTOP Cancer Genome Profiling System (TOP) as a clinical order, (3) availability of an formalin-fixed paraffin-embedded (FFPE) block for research in our hospital, and (4) consent to the use of clinical residual samples for research purposes. Sample characteristics were collected from medical and pathological records.\u003c/p\u003e \u003cp\u003eThe genomic tests evaluated in this study are characteristically distinct, and each is covered by the Japanese insurance system. Briefly, ODxTT (Thermo Fisher Scientific, Waltham, MA, USA) is a DNA- and RNA-based next-generation sequencing hot spot panel test that includes 46 genes from tumor tissue samples, and was approved as CDx in 2022 for thyroid cancers. MEBGEN3 (Medical and Biological Laboratories Co., Ltd., Tokyo, Japan) is a DNA-based PCR sequencing test that detects a single spot of \u003cem\u003eBRAF\u003c/em\u003e V600E mutation from tumor tissue samples, and was approved as CDx in 2023. F1CDx (Foundation Medicine Inc., Cambridge, MA, USA) is a DNA-based next-generation sequencing panel test that includes 324 genes from tumor tissue samples, and was approved as CGP in 2019. TOP (Konica Minolta, Inc., Tokyo, Japan) is a DNA-based and RNA-based next-generation sequencing panel test that includes 737 genes from paired tumor tissue samples and non-tumor blood samples, and was approved as CGP in 2023.\u003c/p\u003e \u003cp\u003e2. Sample preparation and immunohistochemical examination\u003c/p\u003e \u003cp\u003eTwo sections were freshly cut from the residual FFPE blocks by microtome at a 4-\u0026micro;m thickness in a single session. All blocks had been previously used for genomic testing. On the Ventana BenchMark ULTRA automated slide strainer (Roche Tissue Diagnostics, Tucson, AZ, USA), one section was stained with hematoxylin and eosin (HE) and another section with VENTANA\u0026reg; anti-BRAF V600E (VE1) Mouse Monoclonal Primary Antibody (Catalog Number. 760\u0026ndash;5095; Roche Tissue Diagnostics, Tucson, AZ, USA), with cell conditioning at 100\u0026deg;C for 64 minutes, and pre-peroxidase inhibition and primary antibody incubation at 36\u0026deg;C for 16 minutes. The OptiView DAB IHC Detection Kit (Roche Tissue Diagnostics, Tucson, AZ, USA) was applied for optimal visualization. These processes were performed in July 2024.\u003c/p\u003e \u003cp\u003e3. Concordance analysis\u003c/p\u003e \u003cp\u003eOne pathologist blindly annotated each staining expression of IHC with a cut-off of 1% in the cytoplasm as positive, negative, or undetermined using light microscopy. After evaluation of IHC expression, the slides were digitalized by scanning at \u0026times; 40 magnification using a NanoZoomer2.0HT digital slide scanner (Hamamatsu Photonics, Hamamatsu, Japan) to preserve the image. Another researcher independently documented \u003cem\u003eBRAF\u003c/em\u003e V600E mutation status from the respective genomic test report. We then calculated sensitivity, specificity,positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) between IHC and genomic testing results. Slides annotated as undetermined were classified as false negative to avoid overestimating the usefulness of the IHC stain. Statistical analyses were performed using pandas, version 1.5.3; NumPy, version 1.24.2; SciPy, version 1.10.0; stats models, version 2.13.5; and lifelines, version 0.27.4 (Python Data Analysis Library).\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e1. Sample characteristics\u003c/p\u003e\n\u003cp\u003eWe identified 62 samples from 59 patients; of these, 6 were duplicates from 3 individuals (Table 1). Histologic subtype was PTC in 40 (64.5%) samples, FTC in 6 (9.7%), PDTC in 4 (6.5%), and ATC in 12 (19.4%). By method, 44 (71.0%) samples were obtained at surgery and 18 (29.0%) on biopsy. By location, samples were from the primary thyroid lesion in 33 (53.2%), lymph node metastasis in 20 (32.3%), lung metastasis in 7 (11.3%), bone metastasis in 1 (1.6%), and pleural metastasis in 1 (1.6%). Genomic testing was by ODxTT in 32 (51.6%) samples, MEBGEN3 in 14 (22.6%), F1CDx in 30 (48.4%), and TOP in 1 (1.6%). Of the 77 tests, 67 (87.7%) were performed within three years of sampling (Fig. 1). The confirmed\u003cem\u003e\u0026nbsp;BRAF\u003c/em\u003e mutation status by genomic testing was 51 positive (46 for PTC, 1 for PDTC, and 4 for ATC) and 26 negative (4 for PTC, 8 for FTC, 3 for PDTC, and 11 for ATC). Positive and negative status was identified using ODxTT (19/2), MEBGEN3 (9/1), and F1CDx (18/1) for PTC samples; ODxTT (0/5), MEBGEN3 (0/2), and F1CDx (1/1) for FTC samples; ODxTT (0/2) and F1CDx (1/1) for PDTC samples; ODxTT (1/3), MEBGEN3 (0/2), F1CDx (3/5), and TOP (0/1) for ATC samples.\u003c/p\u003e\n\u003cp\u003e2. Results of BRAF-IHC\u003c/p\u003e\n\u003cp\u003eFor all samples, BRAF-IHC was positive in 31, negative in 29, and undeterminable in 2 due to low tumor content in the section from the residual FFPE block. Fig. 2 shows the results by IHC status, genomic testing status, and sample characteristics. In addition, three representative samples (two BRAF-IHC-positive samples and one BRAF-IHC-negative sample) are shown in Fig. 3 (1, HE, low magnification; 2, HE, high magnification; 3, IHC, low magnification; and 4, IHC, high magnification in each figure). Fig. 3A is a true positive sample of PTC, and was the oldest sample in this research, obtained 18 years ago. Fig. 3A4 shows strong IHC expression in the cytoplasm. Fig. 3B is a true positive sample of ATC originating from PTC in which both areas were stained, and Fig. 3B4 shows strong IHC expression in the ATC area. Fig. 3C is a true negative sample of ATC, and Fig. 3B4 shows the lack of IHC expression. The two undeterminable samples are shown in Fig. 4 (1, HE, low magnification; 2, HE, high magnification; 3, IHC, low magnification; 4, IHC, high magnification; 5, IHC, low magnification; 5, IHC, high magnification, in each figure). Fig. 4A is an undeterminable surgical sample with low PTC content. Fig. 4A4 shows moderate IHC expression; however, the area shown by the black arrows in Fig. 4A6 shows a lack of IHC expression. Fig. 4B is an undeterminable biopsy sample with low PTC content. Fig. 4B4 shows moderate IHC expression; however, the area shown by the black arrows in Fig. 4B6 shows a lack of IHC expression.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e3. Concordance between BRAF-IHC and genomic test\u003c/p\u003e\n\u003cp\u003eTable 2 shows the concordance between IHC and the genomic tests for all histologic subtypes. PPA, NPA, and OPA were 100% (20/20), 91.7% (11/12), and 96.9% (31/32) for ODxTT; 100% (9/9), 100% (5/5), and 100% (14/14) for MEBGEN3; 100% (20/20), 80.0% (8/10), and 93.9% (28/30) for F1CDx; and incalculable, 100% (1/1), and 100% (1/1) for TOP, respectively. Discordance was found in the two undeterminable samples only. The results of concordance for ATC are shown in Table 3. All calculable PPA, NPA, and OPA results in ATC samples were 100% for each genomic test.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eHere, we demonstrate for the first time a high concordance for \u003cem\u003eBRAF\u003c/em\u003e status between IHC using anti-BRAF V600E (VE1) antibody and genomic tests certified as CDx and CGP and covered by the Japanese insurance system. Notably, we found that the results were completely reproduced in ATC samples, a fact which has been little known worldwide. These results support the early detection of subjects with the \u003cem\u003eBRAF\u003c/em\u003e V600E mutation and a shorter TAT, and consequently the introduction of BRAF plus MEK inhibitors for them. This approach will greatly benefit patients who require treatment immediately due to the disease\u0026rsquo;s characteristics of aggressive and rapid disease progression.\u003c/p\u003e \u003cp\u003eRecently, the clinical significance of BRAF-targeted therapy in thyroid cancer has been increasingly noted. Several clinical studies have shown prominent clinical activity, particularly for ATC, for which even lenvatinib, a multi-kinase inhibitor uniquely approved for ATC in Japan, has shown limited efficacy and raised concerns about safety [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. A prospective observational study of lenvatinib reported an ORR of 11% as well as grade 3 adverse events of fistula (2.0%), perforation of the gastrointestinal tract (1.2%), and bleeding (1.6%), probably due to an incompatibility between its strong inhibition of vascular endothelial growth factor receptor and the disease\u0026rsquo;s highly invasive features [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. Further, although a number of other specific genetic alterations could be used (e.g., \u003cem\u003eRET\u003c/em\u003e fusion-positive, \u003cem\u003eNTRK\u003c/em\u003e fusion-positive) [\u003cspan additionalcitationids=\"CR15\" citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e], their prevalence is rare (e.g., 2% in ATC) [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Nevertheless, insurance regulations in Japan require the prescription of target therapy on confirmation of the presence of \u003cem\u003eBRAF\u003c/em\u003e mutation using specific platforms, namely CDx (ODxTT, MEBGEN3) and CGP. This often leads to a delay in treatment initiation, which is disadvantageous to the patient. From a global context, the National Comprehensive Cancer Network guidelines, the American Thyroid Association guidelines, and the Endocrine Pathology Society state that IHC testing is recommended owing to its shorter TAT compared to genomic testing, especially in ATC, for which early treatment initiation is strongly desirable [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e, \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eAll investigations to date of the concordance between BRAF-IHC as a tool for prompt detection of target alterations and corresponding gene testing have been conducted abroad. A recent meta-analysis showed that the sensitivity and specificity of IHC by VE1 clone against the direct sequence and PCR-based sequence were 100%, 84%, 98%, and 89%, respectively, in PTC [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. Our present study is thus the first to evaluate the relationship between CDx platforms approved in Japan (ODxTT and MEBGEN3). Furthermore, the search for concordance with hybridization capture-based sequences adopted in CGP (F1CDx and TOP) could reveal equivalent agreement with these previous reports. Fewer studies have reported concordance for ATC than for PTC. The largest study to date with 53 samples reported the sensitivity, specificity, and OPA of IHC using an exact clone (VE1) for PCR-based sequence on BRAF status of 100%, 96.65%, and 86.4%, respectively [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. Our present study affirms these findings and newly demonstrates that they were independent of sampling location or method. Given the difficulties in tissue sampling for ATC, including procedure-related complications (e.g., bleeding) due to invasiveness to surrounding organs, these findings are valuable in clinical practice, particularly in the preoperative setting in ATC, where successful initiation of the combination of BRAF and MEK inhibitors could confer a substantial benefit on patient survival (1-year overall survival rate of 93.6% in patients treated with BRAF plus MEK inhibitors followed by surgery) [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eSeveral points of this study should be noted. First, we encountered two samples in which the \u003cem\u003eBRAF\u003c/em\u003e V600E mutation was detected by genomic testing, whereas assessment on BRAF-IHC was undeterminable (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eA and Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eB). We considered that this was due to low tumor content and crush artifacts in tissue sampling. These samples simultaneously contained areas both with and without IHC expression but \u0026ndash; due to our goal of assessing concordance in the same block \u0026ndash; we were unable to avoid artifacts of residual sampling. This difficulty highlights the need for careful determination in samples with limited tumor cells in order to both prevent the loss of valuable therapeutic opportunities and to facilitate discussion aimed at an appropriate assessment of the IHC sample. Second, the anti-BRAF V600E (VE1) antibody, which is designed to detect the change of amino acid peptide from 596 to 606 (GLATEKSRWSG), might be reactive to mutations other than the \u003cem\u003eBRAF\u003c/em\u003e V600E mutation, resulting in a false positive in detecting the target [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. However, \u003cem\u003eBRAF\u003c/em\u003e non-V600E mutations are extremely rare in thyroid cancer [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e, \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e], and a study of lung cancers for \u003cem\u003eBRAF\u003c/em\u003e non-V600E mutation found that no sample was stained by an anti-BRAF V600E (VE1) antibody [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]. Third, although we obtained significant agreement between IHC and insurance-certified platforms (CDx) that would be beneficial to the patient population, any application of our results to clinical settings in Japan requires further discussion, including prospective study or equivalence testing.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eIHC and genomic testing in the assessment of BRAF status in thyroid cancer have clinically sufficient concordance. IHC \u0026ndash; which is primarily characterized by a short TAT \u0026ndash; will benefit patients, particularly those whose cancers show aggressive clinical features requiring the prompt initiation of treatment.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors thank Yuka Nakamura (Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center) for technical assistance and Guy Harris D.O. of Dmed (\u0026lt;http://www.dmed.co.jp/\u0026gt;) for editing drafts of this manuscript. However, the ultimate responsibility for opinions, conclusions, and data interpretation lies with the authors.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of Interest\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eMT reports grants and personal fees from Ono Pharmaceutical and Bayer, and personal fees from MSD, BMS, Merck Biopharma, Novartis, Pfizer, Rakuten Medical, Lilly, Boehringer Ingelheim, Eisai, Chugai Pharmaceutical, Daiichi-Sankyo, Janssen Pharmaceutical, Genmab, Astra Zeneca, Abbvie and Astellas, outside the submitted work. SO reports personal fees from Ono Pharmaceutical, MSD, BMS, and Merck Biopharma outside the submitted work. TF reports honoraria for lectures from Amelieff Co. Ltd. GI reports grants from Takeda Pharmaceutical Company Limited, Noile-Immune Biotech, Indivumed GmbH, Sumitomo Dainippon Pharma Co., Ltd. Nihon Medi-Physics CO., Ltd. ONO PHARMACEUTICAL CO., LTD. DAIICHI SANKYO, INC. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study protocol was approved by the Institutional Ethical Committee of the National Cancer Center Hospital East (reference number 2024-066). Written informed consent for participation was not required for this study, in accordance with national legislation and institutional requirements. Patients and their families were provided an opportunity to opt-out of the study in accordance with the policy of the Japanese government. The study was conducted in accordance with the principles laid down in the Declaration of Helsinki.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe data that support the fundings of this study is available from the corresponding author upon reasonable request.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eRyutaro Onaga: Methodology, Formal analysis, Investigation, Data Curation, Writing - Original Draft, Writing - Review \u0026amp; Editing. Tomohiro Enokida: Methodology, Formal analysis, Investigation, Data Curation, Writing - Original Draft, Writing - Review \u0026amp; Editing. Shingo Sakashita: Conceptualization, Validation, Data Curation, Writing - Review \u0026amp; Editing. Susumu Okano: Writing - Review \u0026amp; Editing. Takao Fujisawa: Writing - Review \u0026amp; Editing. Nobukazu Tanaka: Writing - Review \u0026amp; Editing. Yuta Hoshi: Writing - Review \u0026amp; Editing. Takuma Kishida: Writing - Review \u0026amp; Editing. Ryo Kuboki: Writing - Review \u0026amp; Editing. Hiroshi Nishino: Writing - Review \u0026amp; Editing. Makoto Ito: Writing - Review \u0026amp; Editing. Genichiro Ishii: Writing - Review \u0026amp; Editing. Shumpei Ishikawa: Writing - Review \u0026amp; Editing. Makoto Tahara: Conceptualization, Writing - Review \u0026amp; Editing, Supervision, Project administration.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eSiegel RL, Giaquinto AN, Jemal A (2024) Cancer statistics, 2024. CA Cancer J Clin 74:12-49. https://doi.org/10.3322/caac.21820\u003c/li\u003e\n\u003cli\u003e(2016-2020) Cancer Statistics. Cancer Information Service, National Cancer Center, Japan. National Cancer Registry, Ministry of Health, Labour and Welfare\u003c/li\u003e\n\u003cli\u003eNational comprehensive cancer network clinical practice guidelines in oncology, Thyroid Carcinoma, version 4.2024.\u003c/li\u003e\n\u003cli\u003eAmerican Joint Committee on C, Amin MB (2017) AJCC cancer staging manual, 8th edn. Springer\u003c/li\u003e\n\u003cli\u003eTitanji BN, Earley M, Kebebew E (2024) Trends in Mortality for Anaplastic Thyroid Cancer: Have We Made Progress? J Surg Res 302:476-483. https://doi.org/10.1016/j.jss.2024.07.075\u003c/li\u003e\n\u003cli\u003eYamazaki H, Kunisaki C, Sugimori M, et al (2024) Genetic landscape of 482 thyroid carcinomas: analysis with the national datacenter for cancer genomic medicine in Japan. Endocrine 85:766-776. https://doi.org/10.1007/s12020-024-03738-y\u003c/li\u003e\n\u003cli\u003eToda S, Hiroshima Y, Iwasaki H, et al (2024) Genomic Landscape and Clinical Features of Advanced Thyroid Carcinoma: A National Database Study in Japan. J Clin Endocrinol Metab 109:2784-2792. https://doi.org/10.1210/clinem/dgae271\u003c/li\u003e\n\u003cli\u003eSaito Y, Kage H, Kobayashi K, et al (2024) Comprehensive genomic profiling from C-CAT database unveiled over 80% presence of oncogenic drivers in anaplastic thyroid carcinoma including BRAF, RAS family, NF1, and FGFR1. Clin Endocrinol (Oxf) 101:170-179. https://doi.org/10.1111/cen.15098\u003c/li\u003e\n\u003cli\u003eBusaidy NL, Konda B, Wei L, et al (2022) Dabrafenib Versus Dabrafenib + Trametinib in BRAF-Mutated Radioactive Iodine Refractory Differentiated Thyroid Cancer: Results of a Randomized, Phase 2, Open-Label Multicenter Trial. Thyroid\u0026reg; 32:1184-1192. https://doi.org/10.1089/thy.2022.0115\u003c/li\u003e\n\u003cli\u003eTahara M, Kiyota N, Imai H, et al (2024) A Phase 2 Study of Encorafenib in Combination with Binimetinib in Patients with Metastatic BRAF-Mutated Thyroid Cancer in Japan. Thyroid 34:467-476. https://doi.org/10.1089/thy.2023.0547\u003c/li\u003e\n\u003cli\u003eSubbiah V, Kreitman RJ, Wainberg ZA, et al (2022) Dabrafenib plus trametinib in patients with BRAF V600E-mutant anaplastic thyroid cancer: updated analysis from the phase II ROAR basket study. Ann Oncol 33:406-415. https://doi.org/10.1016/j.annonc.2021.12.014\u003c/li\u003e\n\u003cli\u003eTahara M, Kiyota N, Yamazaki T, et al (2017) Lenvatinib for Anaplastic Thyroid Cancer. Front Oncol 7:25. https://doi.org/10.3389/fonc.2017.00025\u003c/li\u003e\n\u003cli\u003eTahara M, Takami H, Ito Y, et al (2024) A Prospective Cohort Study Exploring the Effect of Lenvatinib Planned Drug Holidays in Treatment of Differentiated Thyroid Cancer. Thyroid 34:566-574. https://doi.org/10.1089/thy.2023.0553\u003c/li\u003e\n\u003cli\u003eWirth LJ, Sherman E, Robinson B, et al (2020) Efficacy of Selpercatinib in RET-Altered Thyroid Cancers. N Engl J Med 383:825-835. https://doi.org/10.1056/NEJMoa2005651\u003c/li\u003e\n\u003cli\u003eDemetri GD, De Braud F, Drilon A, et al (2022) Updated Integrated Analysis of the Efficacy and Safety of Entrectinib in Patients With NTRK Fusion-Positive Solid Tumors. Clin Cancer Res 28:1302-1312. https://doi.org/10.1158/1078-0432.CCR-21-3597\u003c/li\u003e\n\u003cli\u003eWaguespack SG, Drilon A, Lin JJ, et al (2022) Efficacy and safety of larotrectinib in patients with TRK fusion-positive thyroid carcinoma. Eur J Endocrinol 186:631-643. https://doi.org/10.1530/EJE-21-1259\u003c/li\u003e\n\u003cli\u003eBible KC, Kebebew E, Brierley J, et al (2021) 2021 American Thyroid Association Guidelines for Management of Patients with Anaplastic Thyroid Cancer. Thyroid 31:337-386. https://doi.org/10.1089/thy.2020.0944\u003c/li\u003e\n\u003cli\u003eMete O, Boucher A, Schrader KA, et al (2024) Consensus Statement: Recommendations on Actionable Biomarker Testing for Thyroid Cancer Management. Endocr Pathol 35:293-308. https://doi.org/10.1007/s12022-024-09836-x\u003c/li\u003e\n\u003cli\u003eParker KG, White MG, Cipriani NA (2020) Comparison of Molecular Methods and BRAF Immunohistochemistry (VE1 Clone) for the Detection of BRAF V600E Mutation in Papillary Thyroid Carcinoma: A Meta-Analysis. Head Neck Pathol 14:1067-1079. https://doi.org/10.1007/s12105-020-01166-8\u003c/li\u003e\n\u003cli\u003eRushton S, Burghel G, Wallace A, et al (2016) Immunohistochemical detection of BRAF V600E mutation status in anaplastic thyroid carcinoma. Histopathology 69:524-526. https://doi.org/10.1111/his.12964\u003c/li\u003e\n\u003cli\u003eHamidi S, Dadu R, Zafereo ME, et al (2024) Initial Management of BRAF V600E-Variant Anaplastic Thyroid Cancer: The FAST Multidisciplinary Group Consensus Statement. JAMA Oncol 10:1264-1271. https://doi.org/10.1001/jamaoncol.2024.2133\u003c/li\u003e\n\u003cli\u003eCapper D, Preusser M, Habel A, et al (2011) Assessment of BRAF V600E mutation status by immunohistochemistry with a mutation-specific monoclonal antibody. Acta Neuropathol 122:11-19. https://doi.org/10.1007/s00401-011-0841-z\u003c/li\u003e\n\u003cli\u003eDe Leo A, Serban D, Maloberti T, et al (2023) Expanding the Spectrum of BRAF Non-V600E Mutations in Thyroid Nodules: Evidence-Based Data from a Tertiary Referral Centre. Int J Mol Sci 24. https://doi.org/10.3390/ijms24044057\u003c/li\u003e\n\u003cli\u003eHanrahan AJ, Chen Z, Rosen N, et al (2024) BRAF - a tumour-agnostic drug target with lineage-specific dependencies. Nat Rev Clin Oncol 21:224-247. https://doi.org/10.1038/s41571-023-00852-0\u003c/li\u003e\n\u003cli\u003eIlie M, Long E, Hofman V, et al (2013) Diagnostic value of immunohistochemistry for the detection of the BRAFV600E mutation in primary lung adenocarcinoma Caucasian patients. Ann Oncol 24:742-748. https://doi.org/10.1093/annonc/mds534\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Tables","content":"\u003cp\u003e\u003cstrong\u003eTable 1.\u003c/strong\u003e Sample characteristics\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"681\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTotal samples\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003en=62\u003csup\u003e\u0026dagger;\u0026nbsp;\u003c/sup\u003e(%)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ePatient age at sampling\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Mean age, years [SD]\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Median age, years [range]\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e68.3 [10.0]\u003c/p\u003e\n \u003cp\u003e71.5 [47-84]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eGender\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Female\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Male\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e34 (54.8)\u003c/p\u003e\n \u003cp\u003e28 (45.2)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eHistologic subtype\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Papillary thyroid cancer\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Follicular thyroid cancer\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Poorly differentiated thyroid cancer\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Anaplastic thyroid cancer\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e40 (64.5)\u003c/p\u003e\n \u003cp\u003e6 (9.7)\u003c/p\u003e\n \u003cp\u003e4 (6.5)\u003c/p\u003e\n \u003cp\u003e12 (19.4)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSampling method\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Surgery\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Biopsy\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e44 (71.0)\u003c/p\u003e\n \u003cp\u003e18 (29.0)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eLocation of sampling\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Primary thyroid lesion\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Lymph node metastasis\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Lung metastasis\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Bone metastasis\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Pleural metastasis\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e33 (53.2)\u003c/p\u003e\n \u003cp\u003e20 (32.3)\u003c/p\u003e\n \u003cp\u003e7 (11.3)\u003c/p\u003e\n \u003cp\u003e1 (1.6)\u003c/p\u003e\n \u003cp\u003e1 (1.6)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 388px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eType of testing\u003c/strong\u003e\u003csup\u003e\u0026Dagger;\u003c/sup\u003e\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;ODxTT\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;MEBGEN3\u003c/p\u003e\n \u003cp\u003eF1CDx\u003c/p\u003e\n \u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;TOP\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 293px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003cp\u003e32 (51.6%)\u003c/p\u003e\n \u003cp\u003e14 (22.6%)\u003c/p\u003e\n \u003cp\u003e30 (48.4%)\u003c/p\u003e\n \u003cp\u003e1 (1.6%)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003eNote: \u003csup\u003e\u0026dagger;\u003c/sup\u003eThree patients each provided two different samples, \u003csup\u003e\u0026Dagger;\u003c/sup\u003eSome samples underwent multiple types of testing. Abbreviations: SD; standard deviation, ODxTT; Oncomine\u0026trade; Dx Target Test MultiCDx System, MEBGEN3; MEBGEN\u0026trade; BRAF 3 Kit, F1CDx; FoundationOne\u003csup\u003e\u0026reg;\u003c/sup\u003eCDx, TOP; GenMineTOP Cancer Genome Profiling System.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 2.\u003c/strong\u003e Concordance evaluation of IHC in comparison with genomic testing in all cases\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"671\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"bottom\" style=\"width: 221px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eODxTT\u003cbr\u003e\u003c/strong\u003e(n=32)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMEBGEN3\u003cbr\u003e\u003c/strong\u003e(n=14)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eF1CDx\u003cbr\u003e\u003c/strong\u003e(n=30)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTOP\u003cbr\u003e\u003c/strong\u003e(n=1)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSubject nucleic acid\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eDNA, RNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eDNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eDNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eDNA, RNA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eEnrichment method\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003ePCR\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003ePCR\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eHC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eHC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTrue positive\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFalse positive\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTrue negative\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFalse negative\u003c/strong\u003e\u003csup\u003e\u0026dagger;\u003c/sup\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSensitivity\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e95.2%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e90.9 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eNA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSpecificity\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ePositive percent agreement\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eNA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNegative percent agreement\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e91.7%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e80.0%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 221px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eOverall percent agreement\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e96.9%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e93.3%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100 %\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003eNote: \u003csup\u003e\u0026dagger;\u003c/sup\u003eFalse negatives consisted of two undeterminable samples only. Abbreviations: PCR; polymerase chain reaction-based sequence, HC; hybridization capture-based sequence, ODxTT; Oncomine\u0026trade; Dx Target Test MultiCDx System, MEBGEN3; MEBGEN\u0026trade; BRAF 3 Kit, F1CDx; FoundationOne\u003csup\u003e\u0026reg;\u003c/sup\u003eCDx, TOP; GenMineTOP Cancer Genome Profiling System, NA; Not Applicable.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 3.\u003c/strong\u003e Concordance evaluation of IHC in comparison with genomic testing for anaplastic thyroid cancer\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"671\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 222px;\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"bottom\" style=\"width: 112px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eODxTT\u003cbr\u003e\u003c/strong\u003e(n=4)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"bottom\" style=\"width: 113px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMEBGEN3\u003cbr\u003e\u003c/strong\u003e(n=2)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"bottom\" style=\"width: 112px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eF1CDx\u003cbr\u003e\u003c/strong\u003e(n=8)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"bottom\" style=\"width: 112px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTOP\u003cbr\u003e\u003c/strong\u003e(n=1)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSubject nucleic acid\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eDNA, RNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eDNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eDNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eDNA, RNA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eEnrichment method\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003ePCR\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003ePCR\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eHC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eHC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTrue positive\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFalse positive\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eTrue negative\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eFalse negative\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSensitivity\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eNA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSpecificity\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ePositive percent agreement\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003eNA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003eNA\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNegative percent agreement\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 222px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eOverall percent agreement\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 113px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 112px;\"\u003e\n \u003cp\u003e100%\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003eAbbreviations: PCR; polymerase chain reaction-based sequence, HC; hybridization capture-based sequence, ODxTT; Oncomine\u0026trade; Dx Target Test MultiCDx System, MEBGEN3; MEBGEN\u0026trade; BRAF 3 Kit, F1CDx; FoundationOne\u003csup\u003e\u0026reg;\u003c/sup\u003eCDx, TOP; GenMineTOP Cancer Genome Profiling System, NA; Not Applicable.\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"international-journal-of-clinical-oncology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ijco","sideBox":"Learn more about [International Journal of Clinical Oncology](http://link.springer.com/journal/10147)","snPcode":"10147","submissionUrl":"https://www.editorialmanager.com/ijco/default2.aspx","title":"International Journal of Clinical Oncology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"IHC, CDx, Thyroid cancer, Anaplastic thyroid cancer, Targeted therapy, BRAF plus MEK inhibitors","lastPublishedDoi":"10.21203/rs.3.rs-5969512/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5969512/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003e \u003cem\u003eBRAF\u003c/em\u003e V600E mutation is a significant therapeutic target for thyroid cancer, including anaplastic thyroid cancer (ATC). Although targeted therapy for this mutation requires genomic testing in Japan, turnaround time (TAT) is often unacceptably long, especially for certain conditions, such as ATC, which is one of the most aggressive cancers. Here, we evaluated concordance between immunohistochemistry (IHC) with a relatively short TAT of a few days and genomic testing in thyroid cancer.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eImmunohistochemical staining was performed with BRAF (VE1) antibody (Ventana) using the OptiView method on samples already undergoing genomic testing. A pathologist blindly annotated each staining expression with a cut-off of 1% in the cytoplasm. We then calculated the positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA).\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eWe identified 62 samples, including 12 of ATC, that underwent genomic testing using different methods: Oncomine Dx Target Test (ODxTT) (n\u0026thinsp;=\u0026thinsp;32), MEBGEN BRAF 3 Kit (MEBGEN3) (n\u0026thinsp;=\u0026thinsp;14), FoundationOne CDx (F1CDx) (n\u0026thinsp;=\u0026thinsp;13), and GenMineTOP (TOP) (n\u0026thinsp;=\u0026thinsp;1). Annotation results of IHC were positive for 31, negative for 29, and undeterminable for 2 samples due to low tumor content. PPA, NPA, and OPA were 100%, 91.7%, 96.9% for ODxTT; 100%, 100%, 100% for MEBGEN3; 100%, 80.0%, 93.9% for F1CDx; and incalculable, 100%, 100% for TOP, respectively. Discordance was found in the two undeterminable samples only.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eConcordance between IHC and genomic testing in assessing \u003cem\u003eBRAF\u003c/em\u003e V600E was encouragingly high; its reliability and potentially short TAT should benefit patients, especially those with ATC.\u003c/p\u003e","manuscriptTitle":"Concordance of BRAF V600E mutation between immunohistochemistry and genomic testing for thyroid cancer","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-31 06:37:02","doi":"10.21203/rs.3.rs-5969512/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Accept","date":"2025-03-29T22:58:08+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2025-03-29T11:11:05+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-03-27T08:52:27+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-03-27T00:39:36+00:00","index":"","fulltext":""},{"type":"submitted","content":"International Journal of Clinical Oncology","date":"2025-03-25T21:39:50+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"international-journal-of-clinical-oncology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ijco","sideBox":"Learn more about [International Journal of Clinical Oncology](http://link.springer.com/journal/10147)","snPcode":"10147","submissionUrl":"https://www.editorialmanager.com/ijco/default2.aspx","title":"International Journal of Clinical Oncology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"4ec7d919-7e0a-4c64-b09a-ef26a7cba2da","owner":[],"postedDate":"March 31st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-04-14T16:11:08+00:00","versionOfRecord":{"articleIdentity":"rs-5969512","link":"https://doi.org/10.1007/s10147-025-02760-y","journal":{"identity":"international-journal-of-clinical-oncology","isVorOnly":false,"title":"International Journal of Clinical Oncology"},"publishedOn":"2025-04-10 16:05:54","publishedOnDateReadable":"April 10th, 2025"},"versionCreatedAt":"2025-03-31 06:37:02","video":"","vorDoi":"10.1007/s10147-025-02760-y","vorDoiUrl":"https://doi.org/10.1007/s10147-025-02760-y","workflowStages":[]},"version":"v1","identity":"rs-5969512","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5969512","identity":"rs-5969512","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}