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Chiu, Readman, Ka Ming Nip, and Inanc Birol. "Fusion-Bloom: fusion detection in assembled transcriptomes." Bioinformatics 36, no. 7 (December 2, 2019): 2256–57. http://dx.doi.org/10.1093/bioinformatics/btz902.
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Abstract Summary Presence or absence of gene fusions is one of the most important diagnostic markers in many cancer types. Consequently, fusion detection methods using various genomics data types, such as RNA sequencing (RNA-seq) are valuable tools for research and clinical applications. While information-rich RNA-seq data have proven to be instrumental in discovery of a number of hallmark fusion events, bioinformatics tools to detect fusions still have room for improvement. Here, we present Fusion-Bloom, a fusion detection method that leverages recent developments in de novo transcriptome assembly and assembly-based structural variant calling technologies (RNA-Bloom and PAVFinder, respectively). We benchmarked Fusion-Bloom against the performance of five other state-of-the-art fusion detection tools using multiple datasets. Overall, we observed Fusion-Bloom to display a good balance between detection sensitivity and specificity. We expect the tool to find applications in translational research and clinical genomics pipelines. Availability and implementation Fusion-Bloom is implemented as a UNIX Make utility, available at https://github.com/bcgsc/pavfinder and released under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. Supplementary information Supplementary data are available at Bioinformatics online.
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Lin, Hao, Yujie Liu, Ruitao Zhou, Yutao Feng, Huiya Cao, Peisu Suo, JIA Guo, and Shifu Chen. "Noncanonical RET fusions in Chinese patients with non-small cell lung cancer from DNA-based next-generation sequencing." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): e20000-e20000. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.e20000.
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e20000 Background: The FDA has approved selpercatinib and pralsetinib for the treatment of metastatic RET fusion-positive non-small cell lung cancer in adult patients. Although the overall response rate is high and the response is durable, the outcomes may vary due to different fusion types of the same driver gene. Methods: We retrospectively collected and analyzed 14062 samples (tumour tissue or plasma) from Chinese lung cancer patients who underwent tissue-based or ctDNA-based next-generation sequencing (NGS) assays at HaploX Genomic Sequencing Center from May 18, 2020, to January 11, 2024. All samples with a RET gene fusion were included and classified based on the fusion partner gene and breakpoint position. Results: A total of 157 (1.1%) samples with DNA-based NGS harbored a RET gene fusion. Among the samples with a RET gene fusion, the most common RET fusion partners at the DNA level were KIF5B (73.2%) and CCDC6 (21.0%). We categorized RET fusions into canonical fusions and noncanonical fusions based on fusion partner and breakpoint position, and the proportions of canonical fusions and noncanonical fusions were 88.5% (139/157) and 11.5% (18/157) respectively. Among the samples with a noncanonical RET fusion, 5 samples harbored a RET fusion with an uncommon fusion partner, it remains unclear whether these fusions lead to RET activation. Conclusions: In this retrospective study, we identify different types of RET fusions in Chinese lung cancer patients. The majority are canonical fusions, which can benefit from tyrosine kinase inhibitors in clinical, the rest are noncanonical fusions, and their role in precision therapy needs further verification by RNA-based NGS or other assays. All in all, our research helps guide precision therapy in clinical settings. [Table: see text]
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Thomson, Ashlee J., Jacqueline A. Rehn, Susan L. Heatley, Laura N. Eadie, Elyse C. Page, Caitlin Schutz, Barbara J. McClure, et al. "Reproducible Bioinformatics Analysis Workflows for Detecting IGH Gene Fusions in B-Cell Acute Lymphoblastic Leukaemia Patients." Cancers 15, no. 19 (September 26, 2023): 4731. http://dx.doi.org/10.3390/cancers15194731.
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B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by diverse genomic alterations, the most frequent being gene fusions detected via transcriptomic analysis (mRNA-seq). Due to its hypervariable nature, gene fusions involving the Immunoglobulin Heavy Chain (IGH) locus can be difficult to detect with standard gene fusion calling algorithms and significant computational resources and analysis times are required. We aimed to optimize a gene fusion calling workflow to achieve best-case sensitivity for IGH gene fusion detection. Using Nextflow, we developed a simplified workflow containing the algorithms FusionCatcher, Arriba, and STAR-Fusion. We analysed samples from 35 patients harbouring IGH fusions (IGH::CRLF2 n = 17, IGH::DUX4 n = 15, IGH::EPOR n = 3) and assessed the detection rates for each caller, before optimizing the parameters to enhance sensitivity for IGH fusions. Initial results showed that FusionCatcher and Arriba outperformed STAR-Fusion (85–89% vs. 29% of IGH fusions reported). We found that extensive filtering in STAR-Fusion hindered IGH reporting. By adjusting specific filtering steps (e.g., read support, fusion fragments per million total reads), we achieved a 94% reporting rate for IGH fusions with STAR-Fusion. This analysis highlights the importance of filtering optimization for IGH gene fusion events, offering alternative workflows for difficult-to-detect high-risk B-ALL subtypes.
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Zhou, Xinliang, Liyuan He, Zhisong Fan, Jing Zuo, Li Feng, Long Wang, Jing Han, et al. "ALK fusion typing and response to crizotinib in ALK+ lung cancer-naive patients." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e21008-e21008. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e21008.
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e21008 Background: Anaplastic lymphoma kinase (ALK) is one of the major oncogenic driver genes in lung cancer, and fusion as the main mutation type, of which EML4 is the most common fusion ligand. With the development of next-generation sequencing (NGS), some other rare fusion ligands and complex fusions have been discovered. The prognosis of patients with EML4-ALK fusion, non EML4-ALK fusion and multiple ALK fusion was different. Methods: We retrospectively analyzed NGS (including tissue, blood, or other body fluid samples) in 61 patients with ALK[+] lung cancer, including 59 patients with NSCLC and 2 patients with SCLC. Grouping was determined according to whether it was EML4-ALK fusion and multiple fusion. Results: In our data, the partner fused to the ALK gene are diverse, including EML4, KIF5B, TSN and others. Among them, EML4 was the most common ligand in ALK[+] NSCLC, accounting for 93.2% (55/59). Among the different fusion sites of EML4-ALK, V1 (E13:A20) and V3 (E6:A20) mutations were the most common, accounting for 45.5% (25/55) and 41.8% (23/55), respectively. Several novel ALK fusion partners were discovered in this study, including MCFD2, LINC01251, MVP17, CREG2, LINCO1498 and so on. In addition, the incidence of intergenic sequence-ALK fusions was 16.4% (10/61), such as ANXA4-ALK(A[intergenic]:A20), CREG2-ALK (C[intergenic]:A20), HCN1-ALK(H[intergenic]:A20), TSN-ALK(T[intergenic]:A20), RSAD2-ALK(R [intergenic]:A20) and so on. 19.0% (12/61) of the patient had multiple fusion, of which only one patient had multiple fusion of EML4-ALK (V2+V5'+V3a/b), and the remaining patients had co-fusion of EML4-ALK and non EML4-ALK (Table). V3 were more likely to coexist with non EML4-ALK fusions than V1 or other variants (P = 0.047). Multiple fusions were more likely to occur with non EML4-ALK fusions (P < 0.000). Compared with EML4-ALK fusion, mPFS treated with crizotinib in non EML4-ALK fusion were significantly shorter (18.2 vs. 8.5 months, P = 0.035). In the context of crizotinib treatment, multiple fusions were associated with worse mPFS compared with single fusions (13.8 vs. 8.4 months, P = 0.008). In addition, For SCLC patients with ALK fusion (n = 2), the PFS of crizotinib treatment were 8.0 and 30.6 months, respectively. Conclusions: Due to the heterogeneity of tumor development resulting in the diversity of ALK fusions, non EML4-ALK fusions and multiple fusions imply a poorer response to crizotinib. ALK gene status prior to ALK-TKI therapy helps predict drug efficacy and patient prognosis.[Table: see text]
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Zhou, Xinliang, Liyuan He, Zhisong Fan, Jing Zuo, Li Feng, Long Wang, Jing Han, et al. "ALK fusion typing and response to crizotinib in ALK+ lung cancer-naive patients." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e21008-e21008. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e21008.
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e21008 Background: Anaplastic lymphoma kinase (ALK) is one of the major oncogenic driver genes in lung cancer, and fusion as the main mutation type, of which EML4 is the most common fusion ligand. With the development of next-generation sequencing (NGS), some other rare fusion ligands and complex fusions have been discovered. The prognosis of patients with EML4-ALK fusion, non EML4-ALK fusion and multiple ALK fusion was different. Methods: We retrospectively analyzed NGS (including tissue, blood, or other body fluid samples) in 61 patients with ALK[+] lung cancer, including 59 patients with NSCLC and 2 patients with SCLC. Grouping was determined according to whether it was EML4-ALK fusion and multiple fusion. Results: In our data, the partner fused to the ALK gene are diverse, including EML4, KIF5B, TSN and others. Among them, EML4 was the most common ligand in ALK[+] NSCLC, accounting for 93.2% (55/59). Among the different fusion sites of EML4-ALK, V1 (E13:A20) and V3 (E6:A20) mutations were the most common, accounting for 45.5% (25/55) and 41.8% (23/55), respectively. Several novel ALK fusion partners were discovered in this study, including MCFD2, LINC01251, MVP17, CREG2, LINCO1498 and so on. In addition, the incidence of intergenic sequence-ALK fusions was 16.4% (10/61), such as ANXA4-ALK(A[intergenic]:A20), CREG2-ALK (C[intergenic]:A20), HCN1-ALK(H[intergenic]:A20), TSN-ALK(T[intergenic]:A20), RSAD2-ALK(R [intergenic]:A20) and so on. 19.0% (12/61) of the patient had multiple fusion, of which only one patient had multiple fusion of EML4-ALK (V2+V5'+V3a/b), and the remaining patients had co-fusion of EML4-ALK and non EML4-ALK (Table). V3 were more likely to coexist with non EML4-ALK fusions than V1 or other variants (P = 0.047). Multiple fusions were more likely to occur with non EML4-ALK fusions (P < 0.000). Compared with EML4-ALK fusion, mPFS treated with crizotinib in non EML4-ALK fusion were significantly shorter (18.2 vs. 8.5 months, P = 0.035). In the context of crizotinib treatment, multiple fusions were associated with worse mPFS compared with single fusions (13.8 vs. 8.4 months, P = 0.008). In addition, For SCLC patients with ALK fusion (n = 2), the PFS of crizotinib treatment were 8.0 and 30.6 months, respectively. Conclusions: Due to the heterogeneity of tumor development resulting in the diversity of ALK fusions, non EML4-ALK fusions and multiple fusions imply a poorer response to crizotinib. ALK gene status prior to ALK-TKI therapy helps predict drug efficacy and patient prognosis.[Table: see text]
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Karan, Canan, Elaine Tan, Humaira Sarfraz, Christine Marie Walko, Richard D. Kim, Todd C. Knepper, and Ibrahim Halil Sahin. "Clinical and molecular characterization of fusion genes in colorectal cancer." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e15568-e15568. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e15568.
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e15568 Background: Next-generation sequencing (NGS) based molecular profiling technologies have revealed several oncogenic fusion genes that are actionable with small molecule inhibitors leading to practice change, particularly in lung cancer. The molecular and clinical characteristics of these gene fusions are not well defined in colorectal cancer patients (CRC). In this study, we aimed to define clinical and molecular characteristics of fusion genes in patients with CRC who underwent molecular profiling. Methods: Molecular characteristics of tissue confirmed 917 CRC patients were retrieved from the Moffit Cancer Center Clinical Genomics Action Committee database. Patients’ demographic and clinicopathological features and treatment history were collected from the database. All fusion genes were shown by hybridization-based NGS computational algorithms that determined cancer‐related genes, including single‐nucleotide variations, indels, microsatellite instability (MSI) status. Results: Among a total of 917 patients, 24 patients with CRC (2.6%) were found to have at least one fusion gene with a total number of 26 pathogenic fusions. The gene fusions are shown in Table. The most common, potentially targetable, fusion genes in our cohort were (1) RET fusions 0.5% (5/917), (2) ALK fusions 0.4% (4/917), (3) ROS1 fusions 0.2% (2/917), (4) NTRK1 fusion 0.1% (1/917), (5) NRG1 fusion 0.1% (1/917). Fusion genes were more common in MSI-H CRC (N = 27), and 3 (11.1%) patients with MSI-H CRC were found to have fusion genes [(RET (2) and NTRK(1)]. Fusion genes were present in both RAS wild-type (54%; 13/24) and RAS mutant (46%; 11/24) tumors. Most patients were older than 50 years (75%, 18/24) and had left-sided tumor (61.1%) tumor. Conclusions: Fusion genes are rare events in CRC. While fusion genes seem to be more prevalent in MSI-H CRC, RAS status does not correlate with the frequency of fusion genes. Actionable RET and ALK/ROS gene fusion are more common than NTRK fusion genes in this cohort of CRC patients.[Table: see text]
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Zhu, Bowen, Xinlin Zhen, Zeqing Gao, Suo Peisu, Jing Zhang, and Wenzhe Fan. "The frequency of rare ALK fusions and their clinical significance in NSCLC." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e21012-e21012. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e21012.
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e21012 Background: ALK fusion is one of the key driver mechanisms in non-small cell lung cancer. In some case reports, some rare mutant forms have also been found to be active and drug-susceptible. There are few reports on the detection and verification methods of rare ALK fusions. Here, we counted the rare fusions of ALK detected by NGS and verified them by other methods. Methods: We analyzed 184 patients with NSCLC harboring ALK-rearrangement detected by NGS from January 2020 to January 2022. We counted the rare ALK fusion forms, and selected two of them for verification by RNA sequencing or immunohistochemistry. Results: Of the 184 patients with ALK fusion that we included, 105 were female and 79 were male (medium age 53). Most female were non-smokers except one while nearly 50% male were smokers. EML4-ALK fusion accounted for the highest proportion (170, 92.4%), 5 were ALK fusions with other 5’ partners ( C2orf44, KCNG3, KIF5B, KDM5A, DCTN1), 6 were intergenic region- ALK rearrangements, 2 were fusions without transcription initiation region, and 1 was LOC399815 -ALK and ALK-EML4 double fusion. Rare fusion forms accounted for less than 10%. We further verified two of these rare fusion mutations by RNA sequencing or immunohistochemistry. Interestingly, one of the patients with a KCNG3-exon1- ALK-exon20 fusion detected by DNA sequencing was confirmed to be an EML4-ALK fusion by RNA sequencing, and another patient with an intergenic region- ALK fusion was confirmed positive by immunohistochemistry. Conclusions: The vast majority of ALK fusions are EML4-ALK fusions, but there are a small number of other forms of fusions. DNA sequencing, RNA sequencing and ICH may give different conclusions for ALK fusions, which may be limited by the detection method. For some rare fusion forms, a variety of methods can be used to detect whether it is an active ALK fusion form.
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Haferlach, Claudia, Wencke Walter, Manja Meggendorfer, Constance Baer, Anna Stengel, Stephan Hutter, Niroshan Nadarajah, Wolfgang Kern, and Torsten Haferlach. "The Diverse Landscape of Fusion Transcripts in 25 Different Hematological Entities." Blood 136, Supplement 1 (November 5, 2020): 16–17. http://dx.doi.org/10.1182/blood-2020-137518.
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Background: Genomic alterations are a hallmark of hematological malignancies and comprise small nucleotide variants, copy number alterations and structural variants (SV). SV lead to the co-localization of remote genomic material resulting in 2 different scenarios: 1. breakpoints are located within 2 genes leading to a chimeric fusion gene and a fusion transcript, 2. breakpoints are located outside of genes, frequently placing one nearby gene under the influence of the regulatory sequences of the partner, leading to a deregulated - usually increased - transcription. Aim: The frequency of fusion transcripts was determined across hematological entities in order to 1) identify recurrent partner genes across entities, 2) evaluate the specificity of fusion transcripts and genes involved in fusions for distinct entities. Cohort and Methods: Whole transcriptome sequencing (WTS) was performed in 3,549 patients in 25 different hematological entities (table). 101 bp paired-end reads were produced on a NovaSeq 6000 system (Illumina, San Diego, CA) with a yield between 35 and 125 million paired reads per sample. Potential fusions were called using 3 different callers (Arriba, STAR-Fusion, Manta), only fusions called by at least 2 callers, validated by whole genome sequencing (data available for all cases) and with at least one protein coding partner were kept for further analyses. Reciprocal fusion transcripts were counted as one fusion event. Results: In total 1,309 fusion transcripts were identified in 932 of 3,549 (26.3%) patients. 221 patients showed > 1 fusion (2 fusions: 150, 3: 36, >3: 35). 806 distinct fusion transcripts were divided into recurrent fusions (n=50) and unique fusions, i.e. found only in 1 case (n=756). Out of 932 patients with at least 1 fusion, 541 (58%) patients harbored a minimum of one recurrent fusion. The proportion of patients harboring any or a recurrent fusion varied substantially between different entities with high frequencies for both in CML (96.5%/96.5%), B-lineage ALL (53.1%/41.3%), AML (42.8%/31.2%), and T-lineage ALL (35.3%/12.6%). In several myeloid entities low fusion frequencies were observed (e.g. PMF, MDS/MPN-U, MDS, figure A). No fusion transcripts were detected in ET. Strikingly, fusions were detected in a substantial proportion of cases with lymphoid neoplasms but only very few occurred recurrently (e.g. T-PLL: 47.8%/4.3%, FL: 39.3%/4.9%, figure A). With regard to age, only patients with AML and T-ALL harboring recurrent fusions were significantly younger than corresponding cases without recurrent fusions (59 vs 71 yrs, p<0.0001; 35 vs 38 yrs, p=0.02). Only in AML patients with unique fusions were older (70 vs 66 yrs, p=0.02), while no age differences were observed between cases with and without unique fusions in other entities. 23/50 (46%) of the recurrent fusions were specific for one entity (12 in myeloid, 11 in lymphatic entities), while the other 54% (27/50) were observed in 2 to 7 different entities. Of these 27 recurrent fusions, only 16 fusions were shared between myeloid and lymphatic entities, while 10 were restricted to myeloid and one fusion to lymphatic entities (figure B). In total 1,270 different genes were involved in the 806 distinct fusions, indicating a broad spectrum of potential functional impact. 54 genes were involved only in recurrent fusions, 27 genes in both recurrent and unique fusions, while 1,189 genes were solely involved in unique fusions. Four genes involved in recurrent fusions and 32 genes involved in unique fusions are FDA approved drug targets (Human Protein Atlas). Only 16% (199/1270) of the genes were involved in more than one fusion: 3 genes (ETV6, KMT2A, RUNX1) in 14 fusions, 2 genes (ABL1, BCR) in 11 fusions, 16 genes in 4 to 10 fusions, 38 genes in 3 fusions, 140 in 2 fusions. Several genes frequently involved in fusions in hematological malignancies (e.g. ABL1, ETV6, KMT2A) and 78/1189 genes only involved in unique fusions were also reported to be partners in fusions in non-hematological malignancies. Conclusions: As known, in CML and acute several leukemias a high proportion of patients harbor fusions of which many occur recurrently, suggesting a substantial pathogenic impact and, thus, requiring detection in a diagnostic work-up. In BCR-ABL1 negative chronic myeloid malignancies few fusions were observed while lymphoma patients carry frequently non-recurrent fusions with so far unknown impact on pathogenesis and prognosis. Disclosures No relevant conflicts of interest to declare.
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Zhang, Xuhui, Dongsheng Chen, Qin Zhang, Qianqian Duan, Qing WANG, Si Li, and Mingzhe Xiao. "Characterization of NTRK gene fusion events in solid tumors among Chinese patients." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): e15040-e15040. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e15040.
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e15040 Background: NTRK fusions are actionable genomic alterations detected across tumor types. NTRK gene fusions involving either NTRK1, NTRK2 or NTRK3 (encoding the neurotrophin receptors TRKA, TRKB and TRKC, respectively) are oncogenic drivers of various adult and paediatric tumour types. Here, we update the detection of NTRK gene fusions across tumor types and further describe fusion partner characteristics among Chinese patients. Methods: Samples submitted for clinical molecular profiling were retrospectively analyzed for NTRK fusion events. Method for identifying NTRK fusions was DNA-based next-generation sequencing that tumour DNA is extracted from formalin-fixed paraffin-embedded tissue. All NTRK fusion partners were identified for intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations. Results: A total of 64 NTRK fusion events (0.26% of 24,451) were identified. NTRK fusions are characteristic in a few rare types of cancer, such as melanoma, glioma and carcinomas of the thyroid, lung and colon, but they are also infrequently seen in some uncommon cancers, such as secretory carcinoma of the breast or salivary gland and infantile fibrosarcoma. Among the fusions, NTRK1 (0.08% of 24,430), NTRK2 (0.02% of 24,445), NTRK3 (0.15% of 24,414) were identified. Twenty-six unique fusion partners were identified, the most common in NTRK1 fusion being TPM3 (23.8%), NTRK2 fusion being AGTPBP1 (33.3%), and NTRK3 fusion being TFG (13.5%). Almost 53.8 % (14 of 26) of all fusion events are expected to include the transmembrane domain contributed by the NTRK fusion partner. The most commonly identified breakpoints occur in exon 14 and exon 17 and in exon 15 and exon 20, in NTRK1, NTRK3, respectively. Conclusions: NTRK fusion products are diverse across tumor types, but the significance of these variations is not clear. The biological and clinical implications of retaining certain domains of NTRK and of fusion partners warrants further investigation.
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Priedigkeit, Nolan, Alinés Lebrón-Torres, Janny Liao, Jean-Baptiste Alberge, Stefania Morganti, Jakob Weiss, Jorge Gomez Tejeda Zanudo, et al. "Abstract GS03-09: Characterization and proposed therapeutic exploitation of fusion RNAs in metastatic breast cancers." Cancer Research 84, no. 9_Supplement (May 2, 2024): GS03–09—GS03–09. http://dx.doi.org/10.1158/1538-7445.sabcs23-gs03-09.
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Abstract BACKGROUND: Large-scale genomic studies such as The Cancer Genome Atlas (TCGA) and Pan-Cancer Analysis of Whole Genomes (PCAWG) show that the breast cancer (BrCa) genome is dominated by structural variation (SV) rather than single base pair mutations, producing a fertile environment for gene fusions. In this study, we implement a rigorous, expression-based approach to create a comprehensive landscape of fusion RNAs in metastatic breast cancer (MBC). We find fusion RNAs—many of which are novel involving known oncogenes—are surprisingly common in the advanced setting and credential their use as base-editing therapeutic targets. METHODS: Two retrospective cohorts of MBC RNA-sequencing data were analyzed— Dana-Farber Cancer Institute CCPM (n = 252 cases, 276 specimens), MichiganCSER (n = 171 cases, 190 specimens)—with a Fusion MetaCaller that integrates 5 unsupervised fusion-finding algorithms. Fusion RNAs identified in at least 2 callers (High-Confidence) and absent in RNA-seq from normal tissue (Cancer-Specific) were classified as HCCS-Fusions. Further removal of common artifactual fusions was performed using public databases. Expression of each HCCS-Fusion was quantified using a supervised method (FusionInspector)—expressed HCCS-Fusions were defined as having a Fusion Fragment Per Million (FFPM) value > 0.1 and at least 10% of read counts mapping to the fusion breakpoint versus the flanking 5’ or 3’ partners’ exons. Normalized gene-level expression abundances were calculated to correlate transcriptomic features (gene expression, PAM50) with fusion RNAs. Recurrent, potentially pathogenic fusion RNAs were annotated using OncoKB and outlier expressed fusions (Q3 FFPM + [1.5 X IQR]) were interrogated. RESULTS: The frequency of HCCS-Fusions differed between subtypes with basal BrCa harboring the most per tumor followed by Her2, LumB and LumA—with a median HCCS-Fusion count of 13, 12, 7, 4 respectively. 64.5% of cases harbored a HCCS-Fusion in an OncoKB cancer-related gene. The most recurrent fusions involving a cancer-related gene were 5’ ESR1 fusions (14 cases)—all with in-frame breakpoints near exon6/7, disrupting ESR1’s ligand binding domain. 13 of 14 ESR1 fusions were called in Luminal B (LumB) metastases (Fisher’s exact enrichment p < 0.005 vs other subtypes)—defining an ESR1 fusion frequency of 6.5% in LumB disease. Beyond ESR1, we identify recurrent, low-frequency (2-4 cases) in-frame kinase fusions involving FGFR2, ADK, TLK2, PRKCA, BRAF, CHKA, CSNK1D, NEK11, TNIK—some potentially targetable with FDA-approved small molecule inhibitors—as well as recurrent, predicted loss-of-function fusion RNAs in NF1, MSI2, USP32, PTEN, and CDH1. Lastly, 33.6% of cases harbored at least one outlier expressed fusion RNA; including highly expressed in-frame fusions involving known BrCa mediators such as ERBB2, BRCA1, ARID1B, RPS6KB1/2, PIK3R3, AXIN1, TGFB1/2, FOXP1, PAK1, and CREBBP. CONCLUSIONS: Taken together, these results demonstrate that fusion RNAs in MBC—some recurrent, many highly expressed and unique to individual tumors—are common. We create the most comprehensive catalog of ESR1 fusions in MBC, better define their frequency, discover their enrichment in LumB-like tumors, and will discuss clinicopathologic and transcriptomic features associated with ESR1 fusion positive disease. We identify druggable fusions that would likely be missed by current testing standards, find recurrent loss-of-function fusion RNAs, and show that over one-third of metastatic cases harbor at least one outlier expressed fusion—many of which involve BrCa-related genes. In summary, we propose that fusion RNAs are a driving and perhaps overlooked mechanism of tumor evolution in therapy-resistant disease and postulate fusion transcripts present a compelling therapeutic opportunity in MBC. Preliminary data targeting fusion RNA breakpoints using a novel RNA base-editing approach will be discussed. Citation Format: Nolan Priedigkeit, Alinés Lebrón-Torres, Janny Liao, Jean-Baptiste Alberge, Stefania Morganti, Jakob Weiss, Jorge Gomez Tejeda Zanudo, Albert Grinshpun, Melissa Hughes, Karla Helvie, Kerry Sendrick, Kyleen Nguyen, Sarah Strauss, Janet Files, Maxwell Lloyd, Nikhil Wagle, Chip Stewart, Eric Winer, Bruce Johnson, Yvonne Li, Rinath Jeselsohn, Sara Tolaney, Daniel Abravanel, Nancy Lin, Heather Parsons, Gad Getz, Steffi Oesterreich, Adrian Lee, Todd Golub. Characterization and proposed therapeutic exploitation of fusion RNAs in metastatic breast cancers [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr GS03-09.
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Dulai, H. S., W. S. Bartynski, W. S. Rothfus, and P. C. Gerszten. "Provocation Lumbar Diskography at Previously Fused Levels." Interventional Neuroradiology 16, no. 3 (September 2010): 326–35. http://dx.doi.org/10.1177/159101991001600317.
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Recurrent or persistent low back pain (LBP) after lumbar fusion can be related to many factors. We reviewed the provocation lumbar diskogram (PLD) features and redo-fusion outcome in our patients evaluated for recurrent/persistent LBP after technically successful fusion. LD was performed in 27 patients with recurrent/persistent LBP after prior successful lumbar surgical fusion (31 fused levels: single-level fusion-23; two-level fusion-4). PLD response and imaging characteristics at fused and non-fused levels were assessed including: intra-diskal lidocaine response, diskogram-image/post-diskogram CT appearance, presence/absence of diskographic contrast leakage, and evidence of fusion integrity or hardware failure. Outcomes in patients having redo-fusion were assessed. Concordant pain was encountered at 15 out of 23 (65%) single-level fusions, non-concordant pain in one fusion with non-painful response in seven. Adjacent-level concordant pain was identified in seven out of 23 (30%) patients (three of 15 with painful fused levels; four of seven with non-painful fusions). In two-level fusions, concordant pain was encountered at one fused level in each patient. In painful fused levels, leaking and contained disks were encountered with partial or complete pain elimination after intra-diskal lidocaine injection. In anterior fusions, space or contrast surrounding the cage was noted at five of 11 levels. Pseudoarthrosis was noted only with trans-sacral screw fusions. Redo-fusion in 13 patients resulted in significant improvement in nine and moderate improvement in one. Patients with recurrent/persistent LBP after technically successful fusion may have a diskogenic pain source at the surgically fused or adjacent level confirmed by lidocaine-assisted PLD.
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lin, qiuju, and Zhichao Fu. "Abstract 5845: The fusion gene landscape in Chinese patients with non-small cell lung cancer." Cancer Research 82, no. 12_Supplement (June 15, 2022): 5845. http://dx.doi.org/10.1158/1538-7445.am2022-5845.
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Abstract Background: Gene fusion is one of the common types of pathogenic mutation in non-small cell lung cancer(NSCLC). Numerous fusion genes have been identified as important biomarkers and therapeutic targets in NSCLC. The identification and analysis of fusion genes will provide important insights into the mechanisms of NSCLC development and devise novel therapeutic strategies. Here, our primary objective was to describe the landscape of fusion in Chinese patients with NSCLC to explore the new treatment option in NSCLC. Methods: A total of 1192 pathologically confirmed NSCLC samples were collected. The fusion genes were detected using next-generation sequence(NGS). Results: A total of 168 fusion events (14.1%) were identified in 1,192 patients with NSCLC. The most common type of fusion was ALK (64.9%), RET (25%), ROS (8.93%), NTRK1 (3.57%), and FGFR3 (3.57%). In these cases, 109 patients exhibited ALK fusion, including EML4/ALK (97.2%), KIF5B/ALK (0.92%), KLC1/ALK (0.92%), and STRN/ALK (0.92%). A total of 42 patients had RET fusions, of which 83.3%, 11.9%, 2.38%, and 2.38% with KIF5B, CCDC6, GOPC, and TET1 respectively. Notably, RET gene fusions with GOPC (GOPC/RET1), TET1 (TET1/RET1) were first reported in NSCLC and the two novel fusions retained the complete kinase domain of RET. We also found three types of ROS fusions in 15 patients, CD74/ROS1(66.7%) and EZR/ROS1(20%) were the common fusions. Additionally, a new fusion LRIG3/ROS1 which retained the complete kinase domain was identified for the first time in NSCLC patients. Conclusions: We conducted a comprehensive review of fusion genes in Chinese patients with NSCLC. With the exception of common gene fusions, we found three cases of rare fusion mutations, which help to understand the potential pathogenic mechanisms of NSCLC and translate into therapeutic applications. Citation Format: qiuju lin, Zhichao Fu. The fusion gene landscape in Chinese patients with non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5845.
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Brukman, Nicolas G., Berna Uygur, Benjamin Podbilewicz, and Leonid V. Chernomordik. "How cells fuse." Journal of Cell Biology 218, no. 5 (April 1, 2019): 1436–51. http://dx.doi.org/10.1083/jcb.201901017.
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Cell–cell fusion remains the least understood type of membrane fusion process. However, the last few years have brought about major advances in understanding fusion between gametes, myoblasts, macrophages, trophoblasts, epithelial, cancer, and other cells in normal development and in diseases. While different cell fusion processes appear to proceed via similar membrane rearrangements, proteins that have been identified as necessary and sufficient for cell fusion (fusogens) use diverse mechanisms. Some fusions are controlled by a single fusogen; other fusions depend on several proteins that either work together throughout the fusion pathway or drive distinct stages. Furthermore, some fusions require fusogens to be present on both fusing membranes, and in other fusions, fusogens have to be on only one of the membranes. Remarkably, some of the proteins that fuse cells also sculpt single cells, repair neurons, promote scission of endocytic vesicles, and seal phagosomes. In this review, we discuss the properties and diversity of the known proteins mediating cell–cell fusion and highlight their different working mechanisms in various contexts.
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Farooq, Maria, Havell Markus, Bradon McDonald, Jan B. Egan, Tania Contente-Cuomo, Ahuva Odenheimer, Martin Fernandez-Zapico, Mitesh J. Borad, and Muhammed Murtaza. "Detection of FGFR fusions in intrahepatic cholangiocarcinoma using targeted RNA sequencing." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): e16185-e16185. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e16185.
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e16185 Background: Comprehensive sequencing efforts have identified fibroblast growth factor receptor (FGFR) translocations in numerous cancers. FGFR2 fusions were recently identified as an actionable therapeutic target in ̃17% of cholangiocarcinoma patients, predominantly found in patients with intrahepatic cholangiocarcinoma. Genomic partners for FGFR fusions are variable. In addition, obtaining high yield tissue biopsies for CCA remains challenging and tumor tissue available for molecular analyses is scarce. When combined, these two factors make detection of FGFR fusions in CCA challenging. An accurate molecular assay to detect FGFR fusions in CCA could improve utilization of FGFR-targeted therapies. Methods: The objective of our study was to develop an approach for targeted RNA analysis to improve sensitivity for FGFR fusion detection from limited tumor material. We adapted the sensitive targeted digital sequencing (TARDIS) approach recently developed in our lab for analysis of RNA. This approach utilizes a combination of open-ended targeted amplification followed by ligation, enabling detection of tyrosine kinase fusions without prior knowledge of the precise sequence of the fusion breakpoint or identity of the fusion partner. For evaluation of analytical performance, we analyzed RNA from a CCA organoid model with a known FGFR2 fusion, and Seraseq Fusion RNA Mix v3 Reference Material with two known FGFR3 fusions. Results: Without prior knowledge the partner or coordinates of the fusion breakpoint, we detected an FGFR2-KIF5C fusion in RNA from a CCA organoid model. The fusion breakpoint coordinates predicted by TARDIS-RNA were validated by comparison with RNA-Seq. To assess sensitivity and quantitative performance of the assay, we analyzed a serial dilution of the reference RNA sample from Seraseq with concentration of RNA molecules representing candidate fusions verified by digital PCR. Using TARDIS-RNA to analyze replicates with 5 ng RNA input, we were able to detect candidate fusions represented by as few as 2.7 fusion molecules on average. Concentrations of fusion molecules measured using the two methods were highly correlated (R = 0.96). Conclusions: These results demonstrate sensitivity and quantitative performance of a targeted RNA sequencing assay to detect and quantify FGFR fusions in tumor specimen from intrahepatic cholangiocarcinoma. On-going work is focused on further evaluating assay performance and characterizing FGFR fusions using additional tissue specimen.
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Dong, Zhouhuan, Jie Gao, Fengwei Zhu, Fei Gai, Wenqing Su, Zhixin Liang, Xiaodong Tian, and Huaiyin Shi. "Analysis of genomic alterations in pan-cancer from a large real-world Chinese population." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 10568. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.10568.
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10568 Background: Effective targeted therapy sorely depends on comprehensive and precise genomic profiling. Besides, single nucleotide variations (SNVs) and InDels, gene fusions, as drivers and therapeutic targets of great importance, are not yet well characterized in Chinese patients. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor tissues from 1,384 pan-cancer patients were collected and sequenced using next-generation sequencing (NGS) targeting 40 cancer genes including SNV, fusion and assessing copy number variation (CNV) (AmoyDx HANDLE Classic Panel). qPCR and fluorescence in situ hybridization (FISH) were further applied to verify NGS detected fusion genes. Results: 1,384 patients were recruited including 890 lung cancers, 272 colorectal cancers, 174 gastric cancers, and 48 endometrial cancers. The prevalence of fusion genes (5.49%), including ALK-fusion (2.67%), ROS1-fusion (0.94%), RET-fusion (0.72%), NRG1-fusion (0.29%), and NTRK-fusion (0.07%), was nearly double the frequency of previously reported data from East Asians. Prevalence of fusion genes varied in different types of cancers. For instance, ALK (3.7%), ROS1 (1.5%), RET (1.0%) and NRG1 (0.2%) fusions were largely found in patients with non-small cell lung cancer (NSCLC), and were rarely detected in other cancer types. Further analysis of genomic alterations in fusion-positive patients revealed that, TP53 (21%) was the most frequently co-occurred mutated gene with ALK fusion, while RET fusions and ROS1 fusions were rarely accompanied by other mutated genes. In addition, two patients with RBPMS- NRG1 fusion were accompanied by BRAF and RB1 mutations, whereas no co-occurred mutation was found in patients with other partners of NRG1. Patients with inconsistent results of RNA-based NGS and FISH validation fusions are still being followed for treatment and survival, updated data will be available at the time of the presentation. Conclusions: Genomic alterations in real-world Chinese populations have specific characteristics, especially fusion genes. Further characterization of these variants is essential for clinics to guide appropriate targeted therapies.
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Dong, Zhouhuan, Jie Gao, Fengwei Zhu, Fei Gai, Wenqing Su, Zhixin Liang, Xiaodong Tian, and Huaiyin Shi. "Analysis of genomic alterations in pan-cancer from a large real-world Chinese population." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 10568. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.10568.
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10568 Background: Effective targeted therapy sorely depends on comprehensive and precise genomic profiling. Besides, single nucleotide variations (SNVs) and InDels, gene fusions, as drivers and therapeutic targets of great importance, are not yet well characterized in Chinese patients. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor tissues from 1,384 pan-cancer patients were collected and sequenced using next-generation sequencing (NGS) targeting 40 cancer genes including SNV, fusion and assessing copy number variation (CNV) (AmoyDx HANDLE Classic Panel). qPCR and fluorescence in situ hybridization (FISH) were further applied to verify NGS detected fusion genes. Results: 1,384 patients were recruited including 890 lung cancers, 272 colorectal cancers, 174 gastric cancers, and 48 endometrial cancers. The prevalence of fusion genes (5.49%), including ALK-fusion (2.67%), ROS1-fusion (0.94%), RET-fusion (0.72%), NRG1-fusion (0.29%), and NTRK-fusion (0.07%), was nearly double the frequency of previously reported data from East Asians. Prevalence of fusion genes varied in different types of cancers. For instance, ALK (3.7%), ROS1 (1.5%), RET (1.0%) and NRG1 (0.2%) fusions were largely found in patients with non-small cell lung cancer (NSCLC), and were rarely detected in other cancer types. Further analysis of genomic alterations in fusion-positive patients revealed that, TP53 (21%) was the most frequently co-occurred mutated gene with ALK fusion, while RET fusions and ROS1 fusions were rarely accompanied by other mutated genes. In addition, two patients with RBPMS- NRG1 fusion were accompanied by BRAF and RB1 mutations, whereas no co-occurred mutation was found in patients with other partners of NRG1. Patients with inconsistent results of RNA-based NGS and FISH validation fusions are still being followed for treatment and survival, updated data will be available at the time of the presentation. Conclusions: Genomic alterations in real-world Chinese populations have specific characteristics, especially fusion genes. Further characterization of these variants is essential for clinics to guide appropriate targeted therapies.
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Kou, Furong, Lin Shen, Jian Li, Zhenghang Wang, Ting Xu, Juanjuan Qian, Enli Zhang, Lisha Cui, Lijun Zhang, and Xicheng Wang. "Incidence and genomic characteristics of gene fusions in a large Chinese colorectal cancer cohort." Journal of Clinical Oncology 42, no. 3_suppl (January 20, 2024): 192. http://dx.doi.org/10.1200/jco.2024.42.3_suppl.192.
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192 Background: Gene fusion is rare in colorectal cancer (CRC). With the advent of fusion-targeted therapeutics, such as entrectinib for NTRK fusion and selpercatinib for RET fusion, the identification of gene fusions holds clinical significance. Reports providing a comprehensive description of fusions in CRC are limited, and understanding the molecular characteristics of CRC with fusions will contribute to efficient fusion screening. Here, we investigate the incidence and genomic features of gene fusions in a large Chinese CRC population. Methods: We systematically analyzed next-generation sequencing results of tumor tissue from 5534 CRC patients between January 2020 and August 2023. The sequencing panel covers 769 cancer-related genes and can detect fusions, single nucleotide variants and indels, and microsatellite instability (MSI). Statistical significance was determined using chi-square test. Results: Overall, the median age of patients was 62 years (inter-quartile range [IQR]: 53-70), and 40% were female. Gene fusions were detected in 4.4% (242/5534) of all the patients. The incidence is 0.98% (54/5534) if only reported clinically actionable fusions are considered. The median age of the 242 fusion-positive patients was 64 years (IQR: 54-70), and 43% were female. The most highly detected potentially actionable gene fusions were NTRK (0.89%) and FGFR (0.81%), accounting for 39% of the fusion-positive patients. The other fusion genes were ERBB2 (0.52%), RET (0.38%), BRAF (0.31%), EGFR (0.27%), ALK (0.22%), MET (0.09%) and ROS1 (0.07%). Consistent with previous reports, patients with MSI-High were more likely to have fusions compared with those with microsatellite stability (MSS) or MSI-Low (9.9% vs 4.0%, p < 0.001). Besides, RAS or BRAF mutated patients accounted for 59% of the cohort, of whom 2.5% (83/3273) had fusions detected, while 7.0% (159/2261) of the RAS and BRAF wildtype patients had positive fusions ( p < 0.001). Moreover, 404 (7.3%) patients had RNF43 splice or truncating mutations, and gene fusions were detected in 12.9% of these patients. Combining these markers increased the detection rate of fusions, with 28% (33/118) of the RAS/ BRAF wildtype and MSI-H patients having fusions detected. Furthermore, in patients with wildtype RAS/BRAF and MSI-H and RNF43 splice or truncating mutations, the fusion detection rate was as high as 49% (32/65), including 24 patients with actionable fusions of definite clinical significance. Conclusions: Gene fusions were detected in 4.4% of the Chinese CRC population and tended to occur in patients with wildtype RAS/BRAF, MSI-H, or RNF43 mutations. Combining the mutational status of RAS, BRAF, and RNF43 along with MSI status can improve the fusion detection rate and help select candidates for fusion testing and targeted therapy.
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Ma, Yan, Ranjana Ambannavar, James Stephans, Jennie Jeong, Andrew Dei Rossi, John Morlan, Mei-Lan Liu, et al. "Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues and its relation to tumor progression." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 11018. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.11018.
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11018 Background: While several recently discovered gene fusions already play an important role in personalized cancer treatment, many cancer gene fusions remain to be discovered. Next generation sequencing has enabled identification of many rare gene fusion events in fresh or frozen solid tumors. There is a need to detect gene fusions in transcriptomes of formalin-fixed paraffin-embedded (FFPE) tumor tissue, for which there is long-term clinical outcome data. We therefore sought to develop bioinformatics methods to detect fusion transcripts in FFPE tissue and to characterize their association with clinical outcomes. Methods: RNA sequencing libraries were created and sequenced from tumor biopsy tissues (Plos One 2012 7(7): e40092) of two ER+ breast cancer cohorts consisting of 136 and 77 patients, for which clinical outcomes were available. The fusion junctions were nominated by the RNA-seq aligner GSNAP and further filtered to consider discontinuous expression patterns at exon/intron levels. Results: A total of 108 candidate fusion transcripts were detected and RT-PCR assays confirmed 89% of the top ranking fusion transcript candidates. The majority (82%) of identified fusion gene partners are listed in the COSMIC database of known cancer sequence variations. Of note, several patients expressed multiple fusion transcripts that are significantly associated with tumor progression (P<0.001), including genes associated with cell proliferation and cellular metabolism. Furthermore, these patients also harbored inter-chromosomal gene fusions. It is noteworthy that several gene fusions were present in multiple patients. In one of these recurrent fusions the estrogen receptor gene acts as the fusion pair donor. Conclusions: Novel bioinformatics approaches developed here demonstrate the ability to detect fusion transcripts as biomarkers from archival FFPE tissues that associate with breast cancer progression. Some gene fusions were common in multiple patients and deserved further study.
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Zhao, Xiaonan, Chelsea Kotch, Elizabeth Fox, Lea F. Surrey, Gerald B. Wertheim, Zubair W. Baloch, Fumin Lin, et al. "NTRK Fusions Identified in Pediatric Tumors: The Frequency, Fusion Partners, and Clinical Outcome." JCO Precision Oncology, no. 5 (January 2021): 204–14. http://dx.doi.org/10.1200/po.20.00250.
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PURPOSE Neurotrophic tyrosine receptor kinase (NTRK) fusions have been described as oncogenic drivers in a variety of tumors. However, little is known about the overall frequency of NTRK fusion in unselected pediatric tumors. Here, we assessed the frequency, fusion partners, and clinical course in pediatric patients with NTRK fusion–positive tumors. PATIENTS AND METHODS We studied 1,347 consecutive pediatric tumors from 1,217 patients who underwent tumor genomic profiling using custom-designed DNA and RNA next-generation sequencing panels. NTRK fusions identified were orthogonally confirmed. RESULTS AND DISCUSSION NTRK fusions were identified in 29 tumors from 27 patients with a positive yield of 2.22% for all patients and 3.08% for solid tumors. Although NTRK2 fusions were found exclusively in CNS tumors and NTRK1 fusions were highly enriched in papillary thyroid carcinomas, NTRK3 fusions were identified in all tumor categories. The most canonical fusion was ETV6-NTRK3 observed in 10 patients with diverse types of tumors. Several novel NTRK fusions were observed in rare tumor types, including KCTD16-NTRK1 in ganglioglioma and IRF2BP2-NTRK3 in papillary thyroid carcinomas. The detection of an NTRK fusion confirmed the morphologic diagnosis including five cases where the final tumor diagnosis was largely based on the discovery of an NTRK fusion. In one patient, the diagnosis was changed because of the identification of an ETV6-NTRK3 fusion. One patient with infantile fibrosarcoma was treated with larotrectinib and achieved complete pathologic remission. CONCLUSION NTRK fusions are more frequently seen in pediatric tumors than in adult tumors and involve a broader panel of fusion partners and a wider range of tumors than previously recognized. These results highlight the importance of screening for NTRK fusions as part of the tumor genomic profiling for patients with pediatric cancer.
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Zakharov, L. E. "LiWALL FUSION — THE NEW CONCEPT OF MAGNETIC FUSION." Problems of Atomic Science and Technology, Ser. Thermonuclear Fusion 34, no. 1 (2011): 29–38. http://dx.doi.org/10.21517/0202-3822-2011-34-1-29-38.
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Jonna, Sushma, Rebecca Feldman, Sai-Hong Ignatius Ou, Misako Nagasaka, Jeffrey Swensen, Wolfgang Michael Korn, Hossein Borghaei, et al. "Characterization of NRG1 gene fusion events in solid tumors." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): 3113. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.3113.
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3113 Background: NRG1 fusions are actionable genomic alterations detected across tumor types. The NRG1 gene encode for neuregulin, which serves as a ligand for ERBB3 and ERBB4 receptors and activates downstream signaling through the MAPK and PI3K pathways. Here, we update the detection of NRG1 gene fusions across tumor types and further describe fusion characteristics. Methods: Samples submitted for clinical molecular profiling that included RNA-sequencing (Archer Dx or Caris MI transcriptome) were retrospectively analyzed for NRG1 fusion events. All NRG1 fusions with ≥ 3 junction reads were identified for manual review and for characterization of fusion class, intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations by NGS. Results: A total of 82 NRG1 fusion events (0.2% of 44,570) were identified. Among the fusions identified, the distribution across tumor types was as follows: non-small cell lung cancer (NSCLC, 54%), breast cancer (11%), ovarian cancer (7%), pancreatic cancer (7%), cholangiocarcinoma (6%), colorectal cancer (5%), and other (10%). Forty-two unique fusion partners were identified, the most common being CD74 (23%), ATP1B1 (9%), SLC3A2 (7%), RBPMS (6%) and SDC4 (4%). Almost half (47%) of all fusion events are expected to include the transmembrane domain contributed by the NRG1 fusion partner. Lung and pancreatobilliary cancers had the highest rates of transmembrane domain retention from their fusion partners (63.6% and 54.5%, respectively). In all other tumor groups, most fusion partners lacked transmembrane domains. In 15% of cases, the chimeric transcripts are predicted to lead to increased expression of NRG1. The most commonly reported breakpoints in NRG1 occur in exon 6 and exon 2. While fusions with the NRG1 breakpoint at exon 2 retain the immunoglobulin (Ig) domain and all downstream portions (including EGF-like domain), those at exon 6 do not contain the Ig portion and result in shorter chimeric proteins. The breakpoints in all CD74:NRG1 fusions, the most common fusions in NSCLC, occur at exon 5 or 6 and cause truncation of domains upstream of the EGF-like domain. In ATP1B1:NRG1 fusions, the most common fusions in pancreatobilliary cancers, the breakpoints are at exon 1 or 2 and retain the Ig domain. Conclusions: NRG1 fusion products are diverse across tumor types, but the significance of these variations is not clear. The biological and clinical implications of retaining certain domains of NRG1 (such as the Ig domain) and of fusion partners warrants further investigation.
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Barnett, Reagan, Sante Gnerre, Jason Willis, Michael J. Overman, Kanwal Pratap Singh Raghav, Christine Megerdichian Parseghian, Arvind Dasari, et al. "ctDNA-based fusion detection for advanced colorectal cancer with a partner-agnostic assay." Journal of Clinical Oncology 41, no. 4_suppl (February 1, 2023): 186. http://dx.doi.org/10.1200/jco.2023.41.4_suppl.186.
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186 Background: Actionable mutations can predict therapeutic benefit in patients with advanced malignancies, though clinical relevance of fusion testing for advanced colorectal cancer (aCRC) remains undefined. Identification of fusions from circulating tumor DNA (ctDNA) has previously been restricted to defined oncogenic fusion partners. To improve the sensitivity for fusion detection, we evaluated a partner-agnostic fusion analysis from ctDNA of patients with aCRC. Methods: De-identified data from Guardant Health was reviewed for 18,558 patients with aCRC who underwent ctDNA NGS testing by Guardant360 (Redwood City, CA) between 2017-2022. Fusion results were analyzed with a partner-agnostic bioinformatic approach. A fusion was defined as “clonal” if the variant allele frequency (VAF) ratio exceed ≥50% of highest somatic VAF, and “subclonal” if < 50% maxVAF. Microsatellite instability (MSI) status [MSI-high (bMSI-H) or microsatellite stable (bMSS)] and anti-EGFR exposure signature were determined using prior methods. Associations between fusion occurrence and coexisting alterations were performed using Fisher’s exact test. Results: Fusions were detected in 221 (1.2%) of patients with aCRC. 258 activating fusions were detected in 187 patients; FGFR3 (N = 59, 23%), RET N = 55, 21%), BRAF (N = 43, 17%), and ALK (N = 41, 16%) were most frequent. There were 71 previously unreported fusions in 28 additional patients; RET (N = 16; 23%), MET (N = 15, 21%), and BRAF (N = 11; 15%) were most prevalent. Clonal fusions occurred in 7% (18/258) of all activating fusions; RET (5/18, 28%) and FGFR3 (3/18, 17%) were most common and associated with bMSI-H status relative to bMSS (27% vs 4%, OR 8.165, 95% CI 2.332-33.99; p = 0.0076). Clonal fusions occurred less commonly in samples with a prior EGFR signature (OR 0.22, 95% CI 0.05-0.997, p = 0.049). Most detected fusions were subclonal including ALK, FGFR1-3, MET, RET and ROS1. Conclusions: Highly specific partner-agnostic fusion detection is feasible to increase sensitivity of ctDNA assay performance. Oncogenic fusions occurred in ~1% of all patients with aCRC. Clonal fusions as oncogenic drivers were infrequent and associated with bMSI-H status. Subclonal fusions were more common and occur in a setting consistent with prior exposure to anti-EGFR therapies. Reporting fusion partners and clonality from ctDNA may guide oncologists on the appropriate context for consideration of fusion-directed treatments.
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Song, Yang, Yongjun Zhu, Ning Wu, Fei Xu, Ting Ma, and Zhiming Chen. "Landscape of gene fusions and METex14 skipping in non-small cell lung carcinoma among the Chinese population: Insights from targeted RNA sequencing." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): e20041-e20041. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.e20041.
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e20041 Background: Targeted RNA Sequencing is crucial for detecting gene fusions and exon-skipping mutations in non-small cell lung carcinoma (NSCLC). This study delineates the landscape of RNA-based fusion and METex14 skipping in the Chinese NSCLC population, compares the consistency with DNA-based fusion detection, and further explores the relationship between fusion-positive cases and immune markers. Methods: We profiled 294 NSCLC tumor tissues using targeted RNA sequencing, focusing on 29 fusion genes and 6 reference genes. Of these, 229 samples were concurrently assessed for fusions using a DNA panel. Patients with gene fusions or METex14 skipping were categorized as 'FUSION-POS'. Additionally, the expression of PD-L1 was evaluated. Results: In 294 NSCLC patients, 33 types of fusions and METex14 skipping were detected from 45 patients based on RNA detection. Actionable gene fusions/METex14 skipping were present in 11.22% (33/294) of patients, with the most prevalent being ALK (4.4%), METex14 skipping (2.7%), ROS1 (1.4%), and RET (1.0%). The partners of ALK, RET and ROS1 were EML4 (n= 12)/ LCLAT1(n=1), KIF5B (n=3) /PARD3(n=1) and CD74(n=2)/LRIG3(n=1)/EZR (n=1), respectively. Notably, we also identified two patients harboring FGFR2-ATE1 fusion and CD74-NRG1 fusion, respectively. Except for MET 14skipping, ST7-MET fusion was detected in 2 patients. Comparing the consistency of actionable fusions/METex14 skipping between RNA and DNA assessments in 229 NSCLC patients, RNA detection yielded a higher number of cases (24 patients vs 15 patients, 10.5% vs 6.5%), with all 15 fusions/ METex14 skipping detected by DNA also identified by RNA. Furthermore, we observed that PD-L1 expression was significantly elevated in the FUSION-POS group within lung adenocarcinoma patients (TPS: P=0.015). Conclusions: Our findings indicate that 11.22% of Chinese LUAD patients possess actionable fusions and METex14 skipping. The detection rate of fusions/ METex14 skipping via RNA is higher than that via DNA, with RNA detection fully encompassing all fusions/ METex14 skipping identified by DNA. Meanwhile, the association between fusions and PD-L1 expression suggests potential synergies for combining targeted therapy and immunotherapy in NSCLC.
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Tao, Zhonghua, Xichun Hu, Wen-Ming Cao, Jianxia Liu, Ting Li, Hong Xu, Kai Chen, et al. "Profiling receptor tyrosine kinase fusions in Chinese breast cancers." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): e15092-e15092. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e15092.
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e15092 Background: Receptor tyrosine kinases (RTKs) are a class of tyrosine kinases that regulate cell-to-cell communication and control a variety of complex biological functions. Dysregulation of RTK signaling partly due to chromosomal rearrangements leads to novel tyrosine kinase fusion oncoproteins which are possibly driver alterations to cancers. Targeting some RTK fusions with specific tyrosine kinases inhibitors (TKIs) is an effective therapeutic strategy across a spectrum of RTK fusion-related cancers. However, there is still a paucity of extensive RTK fusion investigations in breast cancer. We aimed to characterize RTK fusions in Chinese breast cancer patients. Methods: An in-house sequencing database of 1440 Chinese breast cancer patients using a 520-gene NGS sequencing panel was thoroughly reviewed. RTK fusion was defined as an in-frame fusion with the tyrosine kinase domain of the RTK completely retained with the only exception of ERBB2 fusion which was not counted due to its unclear significance. Concomitant mutations and TMB were also analyzed and calculated. Patients’ clinical characteristics were retrieved from case records. Results: 27 RTK fusion-positive breast cancers (12 tissues + 15 plasmas) were identified, patients had a median age of 52 years. Triple-negative breast cancer subtype comprised 37% with luminal and HER2 positive subtypes being 40.8% and 22.2%, respectively. 77.8% of patients were at stage IV and 22.2% at stage I-III. Ten were treatment naïve. RTK fusions occurred in 2% of breast cancers in our database, compared with the prevalence of 0.6% and 1.3% in MSKCC and TCGA, respectively. In the subset of stage IV patients, our database showed a significantly higher RTK fusion frequency than that in MSKCC (3.2% vs. 0.6%, p = 0.013). FGFR2 fusions were seen most commonly (n = 7), followed by RET (n = 4), ROS1 (n = 3), NTRK3 (n = 3), BRAF (n = 2), and NTRK1 (n = 2). Other RTK fusions including ALK, EGFR, FGFR1, FGFR3, MET, and NTRK2 were identified in one patient each. Of note, the normalized abundance of RTK fusion (fusion AF/max AF) correlated negatively with TMB (r = -0.48, p = 0.017). Patients with TMB < 4 (Muts/Mb) displayed a higher fusion abundance than those with TMB ≥ 4 (Muts/Mb) (p = 0.018), suggesting a higher likelihood of subclonal nature for RTK fusions in TMB-high patients. Moreover, CREBBP mutation only co-occurred with FGFR2 fusion (p = 0.012), while NTRK3 fusion and TP53 mutation were mutually exclusive (p = 0.019). Conclusions: This is the first study comprehensively delineating the prevalence and spectrum of RTK fusions in Chinese breast cancers. Further study is ongoing to identify the enriched subpopulation which may benefit from RTK fusion inhibitors.
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Wei, Ting, Ji Lu, Tao Ma, Haojie Huang, Jean-Pierre Kocher, and Liguo Wang. "Re-Evaluate Fusion Genes in Prostate Cancer." Cancer Informatics 20 (January 2021): 117693512110275. http://dx.doi.org/10.1177/11769351211027592.
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Background: Thousands of gene fusions have been reported in prostate cancer, but their authenticity, incidence, and tumor specificity have not been thoroughly evaluated, nor have their genomic characteristics been carefully explored. Methods: We developed FusionVet to dedicatedly validate known fusion genes using RNA-seq alignments. Using FusionVet, we re-assessed 2727 gene fusions reported from 36 studies using the RNA-seq data generated by The Cancer Genome Atlas (TCGA). We also explored their genomic characteristics and interrogated the transcriptomic and DNA methylomic consequences of the E26 transformation-specific (ETS) fusions. Results: We found that nearly two-thirds of reported fusions are intra-chromosomal, and 80% of them were formed between 2 protein-coding genes. Although most (76%) genes were fused to only 1 partner, we observed many fusion hub genes that have multiple fusion partners, including ETS family genes, androgen receptor signaling pathway genes, tumor suppressor genes, and proto-oncogenes. More than 90% of the reported fusions cannot be validated by TCGA RNA-seq data. For those fusions that can be validated, 5% were detected from tumor and normal samples with similar frequencies, and only 4% (120 fusions) were tumor-specific. The occurrences of ERG, ETV1, and ETV4 fusions were mutually exclusive, and their fusion statuses were tightly associated with overexpressions. Besides, we found ERG fusions were significantly co-occurred with PTEN deletion but mutually exclusive with common genomic alterations such as SPOP mutation and FOXA1 mutation. Conclusions: Most of the reported fusion genes cannot be validated by TCGA samples. The ETS family and androgen response genes were significantly enriched in prostate cancer–specific fusion genes. Transcription activity was significantly repressed, and the DNA methylation was significantly increased in samples carrying ERG fusion.
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Guo, Mengbiao, Zhen-Dong Xiao, Zhiming Dai, Ling Zhu, Hang Lei, Li-Ting Diao, and Yuanyan Xiong. "The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers." Nucleic Acids Research 48, no. 22 (December 4, 2020): 12618–31. http://dx.doi.org/10.1093/nar/gkaa1119.
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Abstract The majority of the human genome encodes long noncoding RNA (lncRNA) genes, critical regulators of various cellular processes, which largely outnumber protein-coding genes. However, lncRNA-involved fusions have not been surveyed and characterized yet. Here, we present a systematic study of the lncRNA fusion landscape across cancer types and identify >30 000 high-confidence tumor-specific lncRNA fusions (using 8284 tumor and 6946 normal samples). Fusions positively correlated with DNA damage and cancer stemness and were specifically low in microsatellite instable (MSI)-High or virus-infected tumors. Moreover, fusions distribute differently among cancer molecular subtypes, but with shared enrichment in tumors that are microsatellite stable (MSS), with high somatic copy number alterations (SCNA), and with poor survival. Importantly, we find a potentially new mechanism, mediated by enhancer RNAs (eRNA), which generates secondary fusions that form densely connected fusion networks with many fusion hubs targeted by FDA-approved drugs. Finally, we experimentally validate functions of two tumor-promoting chimeric proteins derived from mRNA-lncRNA fusions, KDM4B–G039927 and EPS15L1–lncOR7C2–1. The EPS15L1 fusion protein may regulate (Gasdermin E) GSDME, critical in pyroptosis and anti-tumor immunity. Our study completes the fusion landscape in cancers, sheds light on fusion mechanisms, and enriches lncRNA functions in tumorigenesis and cancer progression.
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Chang, Ya-Sian, Siang-Jyun Tu, Ju-Chen Yen, Ya-Ting Lee, Hsin-Yuan Fang, and Jan-Gowth Chang. "The Fusion Gene Landscape in Taiwanese Patients with Non-Small Cell Lung Cancer." Cancers 13, no. 6 (March 16, 2021): 1343. http://dx.doi.org/10.3390/cancers13061343.
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Background: Analyzing fusion gene transcripts may yield an effective approach for selecting cancer treatments. However, few comprehensive analyses of fusions in non-small cell lung cancer (NSCLC) patients have been performed. Methods: We enrolled 54 patients with NSCLC, and performed RNA-sequencing (RNA-Seq). STAR (Spliced Transcripts Alignment to a Reference)-Fusion was used to identify fusions. Results: Of the 218 fusions discovered, 24 had been reported and the rest were novel. Three fusions had the highest occurrence rates. After integrating our gene expression and fusion data, we found that samples harboring fusions containing ASXL1, CACNA1A, EEF1A1, and RET also exhibited increased expression of these genes. We then searched for mutations and fusions in cancer driver genes in each sample and found that nine patients carried both mutations and fusions in cancer driver genes. Furthermore, we found a trend for mutual exclusivity between gene fusions and mutations in the same gene, with the exception of DMD, and we found that EGFR mutations are associated with the number of fusion genes. Finally, we identified kinase gene fusions, and potentially druggable fusions, which may play roles in lung cancer therapy. Conclusion: The clinical use of RNA-Seq for detecting driver fusion genes may play an important role in the treatment of lung cancer.
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Jing, Yu, Yan-Fen Li, Hua Wan, and Dai-Hong Liu. "Detection of EP300-ZNF384 fusion in patients with acute lymphoblastic leukemia using RNA fusion gene panel sequencing." Annals of Hematology 99, no. 11 (September 26, 2020): 2611–17. http://dx.doi.org/10.1007/s00277-020-04251-8.
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Abstract EP300-ZNF384 fusion is a rare recurrent cytogenetic abnormality associated with B cell acute lymphoblastic leukemia (B-ALL), which was rarely studied in Chinese patient cohort. Here, we used a customized RNA fusion gene panel to investigate gene fusions in 56 selected acute leukemia patients without conventional genetic abnormalities. Two EP300-ZNF384 fusion forms were detected in ten cases, which were in-frame fusions of EP300 exon 6 fused with exon 3 or 2 of ZNF384. The fusions led to the lack of most functional domains of EP300. We firstly reported EP300-ZNF384 fusion in a mixed-phenotype acute leukemia (MPAL) patient whose CD33 and CD13 were negative. The rest nine B-ALL patients with EP300-ZNF384 fusion expressed CD33 and/or CD13. Fifty-six percent of B-ALL patients (5/9) with EP300-ZNF384 fusion were positive with CD10. After the diagnosis of EP300-ZNF384 fusion, 70% of the patients achieved remission after chemotherapy. Our observations indicated that EP300-ZNF384 fusion consists of a distinct subgroup of B-ALL with a characteristic immunophenotype. These patients are sensitive to current chemotherapy regimen and have an excellent outcome.
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Nielsen, Jeffery J., Stewart A. Low, Christopher Chen, Xinlan Li, Ephraim Mbachu, Lina Trigg, Siyuan Sun, Madeline Tremby, Rahul Hadap, and Philip S. Low. "Targeted Delivery of Abaloparatide to Spinal Fusion Site Accelerates Fusion Process in Rats." Biomedicines 12, no. 3 (March 8, 2024): 612. http://dx.doi.org/10.3390/biomedicines12030612.
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Spinal fusions are performed to treat congenital skeletal malformations, spondylosis, degenerative disk diseases, and other pathologies of the vertebrae that can be resolved by reducing motion between neighboring vertebrae. Unfortunately, up to 100,000 fusion procedures fail per year in the United States, suggesting that efforts to develop new approaches to improve spinal fusions are justified. We have explored whether the use of an osteotropic oligopeptide to target an attached bone anabolic agent to the fusion site might be exploited to both accelerate the mineralization process and improve the overall success rate of spinal fusions. The data presented below demonstrate that subcutaneous administration of a modified abaloparatide conjugated to 20 mer of D-glutamic acid not only localizes at the spinal fusion site but also outperforms the standard of care (topically applied BMP2) in both speed of mineralization (p < 0.05) and overall fusion success rate (p < 0.05) in a posterior lateral spinal fusion model in male and female rats, with no accompanying ectopic mineralization. Because the bone-localizing conjugate can be administered ad libitum post-surgery, and since the procedure appears to improve on standard of care, we conclude that administration of a bone-homing anabolic agent for improvement of spinal fusion surgeries warrants further exploration.
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Leucht, Anna-Kathrin, Andrea N. Veljkovic, Kevin J. Wing, Murray J. Penner, and Alastair S. Younger. "Surgical Outcome of Hindfoot Fusion using a Retrograde Hindfoot Fusion Nail." Foot & Ankle Orthopaedics 7, no. 1 (January 2022): 2473011421S0031. http://dx.doi.org/10.1177/2473011421s00312.
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Category: Hindfoot Introduction/Purpose: TTC fusions are often performed as a salvage procedure in patient with severe hindfoot arthritis or hindfoot deformity. Comorbidities in this patient collective are frequent, leading to increased risk of postoperative complication. The purpose of this study was to evaluate the surgical outcome regarding union rate, reoperation rate and adverse events using a retrograde hindfoot fusion nail. Methods: Patient records of a single center were retrospectively reviewed in which a retrograde hindfoot fusion nail was utilized for hindfoot fusion between July 1st, 2009 and August 31st, 2018. These records included age, gender, BMI, comorbidities, indications for surgery, non-union, re-operation rates and adverse events related to the surgery. The fusions were performed by 4 fellowship trained foot and ankle surgeons at a tertiary care teaching hospital. 58 cases were identified consecutively, in 51 cases a TTC fusion was performed, in 7 cases a tibiotalar fusion with preexisting talocalcaneal fusion. 22 fusions were arthroscopic and 36 open. The average age of patients was 59 years, the average BMI 29. Main indication for the hindfoot fusion were arthritis (55%) and complex hindfoot deformity (43%). Results: An overall union rate of 89.66% was achieved, 5 non-union tibiotalar and 1 non-union tibiotalar + talocalcaneal was documented. In the group of arthroscopic fusion the non-union rate was 9.09%, in the open group 11.11% respectively. The non- union group included patient with elevated BMI (50%), Diabetes mellitus (33%) and smoking (33%). Adverse events were documented in 21%. The reoperation rate was 17%, mostly due to deep infection or wound complication requiring surgical debridement. No patient in the arthroscopic fusion group needed a reoperation due to deep infection or wound complication, whereas in open surgery this rate was 27.78%. Conclusion: A union rate of 89.66% was achieved using a retrograde hindfoot fusion nail in a high risk patient population for non- union. Arthroscopic preparation of the tibiotalar and the subtalar joint seem to prevent postoperative wound complications.
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Schubert, Laura, Andrew Elliott, Robert Charles Doebele, Emil Lou, Hossein Borghaei, Michael J. Demeure, Razelle Kurzrock, et al. "Incidence of ERBB gene fusions (EGFR, ERBB2, ERBB4) across tumor types." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): 3091. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.3091.
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3091 Background: Gene fusions often represent critical therapeutic targets across cancer subtypes. Fusions within the ErbB family of receptor tyrosine kinases, including EGFR, ERBB2 ( HER2) and ERBB4 ( HER4), have been previously described and represent potentially actionable alterations. Here, we report the relative incidence and functional characterization of these rare genomic events. Methods: Tumor samples (n = 64,354; representing > 40 tumors types) submitted to Caris Life Sciences (Phoenix, AZ) were molecularly profiled by next-generation sequencing of DNA (NextSeq, 592-gene panel; or NovaSeq, whole exome) and RNA (whole transcriptome). Gene fusion partners, in/out-of-frame status, retention of ERBB kinase domain, and topology of fusion breakpoints were characterized for each ERBB fusion transcript detected. Fusion prevalence was further examined in public data sets (TCGA, MSK-IMPACT and AACR GENIE). Results: From the Caris database, a total of 64 EGFR fusion isoforms were detected in 59 tumors (incidence 0.09%); 83% were in-frame and 91% retained the EGFR kinase domain. 206 ERBB2 fusion isoforms were detected in 114 tumors (0.18%); 37% were in-frame and 34% retained the ERBB2 kinase domain. 131 ERBB4 fusion isoforms were detected in 108 tumors (0.17%); 62% were in-frame and 51% retained the kinase domain. All fusions were detected at low incidence across all tumor types. EGFR fusions were most common in high grade glioma (1.7%, n = 35), largely driven by recurrent EGFR-SEPT14 fusions (n = 20). ERBB2 fusions were most common in esophageal/gastroesophageal junction carcinoma (1.1%, n = 20), with recurrent fusion to PGAP3 observed in multiple tumor types (n = 37). ERBB4 fusions were most common in ovarian (0.7%, n = 40) and bladder (0.7%, n = 15) cancers, which often resulted from recurrent fusion with IKZF2 (n = 36). EGFR and ERBB2 fusions were generated predominantly (44-48%) from inversion events, while ERBB4 fusions arose more frequently and at similar rates (27-32%) from deletions, duplications, or translocations. Mining of public data sets corroborated the prevalence of ERBB gene fusions: the frequency of EGFR fusions was 0.63%, ERBB2 was 0.14% and ERBB4 was 0.04%. TP53 mutations frequently co-occurred with ERBB2 and ERBB4 fusions ( > 60% average across public data sets), with higher co-mutation rates ( > 70%) observed for samples in the Caris database. Conclusions: ERBB gene fusions are detectable at low frequency in various tumor types and may represent a unique genomic subset of cancer. Identification of novel ERBB gene fusions warrants further investigation to determine the potential pathogenicity and actionability of these fusions.
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Uzosike, Akachimere C., Venkata K. Byrapogu, Alim F. Ramji, Richard L. Skolasky, and Brian J. Neuman. "2447." Journal of Clinical and Translational Science 1, S1 (September 2017): 78–79. http://dx.doi.org/10.1017/cts.2017.277.
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OBJECTIVES/SPECIFIC AIMS: Cervical fusion is commonly performed for the management of degenerative disc disease, which can cause spinal stenosis and radiculopathy. Adjacent segment disease (ASD) is an adverse postsurgical outcome experienced by some patients as new radiculopathy, stenosis, or other symptomatic sequelae. We sought to assess whether fusion extension past the cervicothoracic junction reduces the risk of distal ASD after multilevel fusions ending at C7-T3. METHODS/STUDY POPULATION: We retrospectively reviewed all first-time patients undergoing instrumented cervical fusion of at least 2 spinal levels and whose distal level of fusion ranged from C7-T3, at the Johns Hopkins Medical Institutions, from 1999 to 2013. The primary outcome was reoperation for distal ASD. Using multiple logistic regression, ANOVA, and χ2 analysis, we determined the odds of ASD due to age, gender, distal level of fusion, surgical approach (anterior, posterior, or combined), smoking status, and race. RESULTS/ANTICIPATED RESULTS: Of the 158 patients who met the selection criteria, the mean age was 58.7±13.8 years, and 95 (60.1%) were female. Ten patients (6.3%) underwent reoperation for ASD. Patients whose fusions ended at C7 were significantly more likely to develop ASD and undergo reoperation (70%, p=0.007) than those whose fusions ended at T1. There were no differences in age, proximal fusion level, smoking status, BMI, gender, and patient-reported race between the reoperation and non-reoperation groups. Following a multivariable analysis, extending the distal fusion to T1 was again found to be protective against reoperation (OR=0.07, p=0.020). DISCUSSION/SIGNIFICANCE OF IMPACT: Our study shows that for multilevel instrumented cervical fusions that terminate within the cervicothoracic junction, fusion distal to the C7 vertebra is associated with decreased odds of reoperation for symptomatic ASD. Therefore, this study provides clinical evidence that may help surgeons determine the optimal distal fusion segment for multilevel fusions ending at C7-T3.
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Chen, Jiani, Jinhua Wu, Jeff Schubert, Fumin Lin, Elizabeth H. Denenberg, Alison Muir, Edward J. Romasko, et al. "The spectrum of RAF1 fusion positive solid tumors in children and young adults." Journal of Clinical Oncology 41, no. 16_suppl (June 1, 2023): e22013-e22013. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e22013.
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e22013 Background: The RAF1 gene encodes a kinase protein in the MAPK signaling pathway. Fusions involving RAF1 have been reported in solid tumors with a higher prevalence in melanoma, breast cancer, non-small cell lung cancer, and brain tumors. The fusions typically replace the N-terminal autoinhibitory domain with the 5’ partner genes leading to autonomous activation of RAF1 kinase. The efficacy of MEK inhibitors as a potential treatment for RAF1 fusion positive tumors is under investigation. Here we present a cohort of 8 RAF1 fusions involved in a spectrum of tumors in children and young adults. Methods: A retrospective search for tumors harboring RAF1 fusion was performed using our clinical database from 2016 to date. The RNA fusion analysis targets >700 exons of 117 genes for known and novel fusions. Additional genomic alterations, tumor type, and patient demographics were also collected. Results: A total of 8 cases positive for RAF1 fusion were identified from 2526 solid tumors including 6 brain tumors, 1 sarcoma, and 1 hepatoblastoma. Histologic diagnoses of the brain tumors were mostly low grade gliomas with no other driver mutations. Two pilocytic astrocytomas harbored RAF1 fusions without the pathognomonic KIAA1549: BRAF fusions. Although RAF1 fusions have been reported in rhabdomyosarcomas, it is the first time that a RAF1 fusion is associated with hepatoblastoma. 4 of the 8 RAF1 fusions identified are novel (noted with * in the table). The break points in RAF1 were at exon 7, 8, or 10, demonstrating the retention of the kinase domain. Conclusions: We report 8 RAF1 fusion positive solid tumors in children and young adults, mainly in low-grade gliomas. Although rare, the presence of a RAF1 fusion not only facilitates the tumor diagnosis but also provides genomic evidence for potential targeted therapies. References: 1. The AACR Project GENIE Consortium. AACR Project GENIE: powering precision medicine through an international consortium. Cancer Discovery. 2017;7(8):818-831. 2. McEvoy CR et al. Profound MEK inhibitor response in a cutaneous melanoma harboring a GOLGA4-RAF1 fusion. J Clin Invest. 2019; 129:1940-1945. [Table: see text]
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Chen, Monica F., Soo-Ryum Yang, Jessica Tao, Antoine Desilets, Ezra Rosen, Yixuan Gong, Kerry A. Mullaney, et al. "Tumor-agnostic genomic and clinical analysis of solid tumors with BRAF fusions." Journal of Clinical Oncology 41, no. 16_suppl (June 1, 2023): 3146. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3146.
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3146 Background: Approximately 15% of cancers harbor BRAF alterations, of which ~5% are BRAF fusions. BRAF fusions are class II alterations that have worse outcomes than class I V600E alterations. While prior investigational therapies for BRAF fusions had disappointing outcomes, novel therapies are in clinical trials, underscoring the need to better characterize these tumors. Methods: Data from adult and pediatric patients with BRAF fusion+ cancers identified between January 2014 and November 2022 utilizing a center-wide next generation sequencing (NGS) program of >99,000 sequenced samples were analyzed. DNA-based hybrid capture tumor NGS (MSK-IMPACT), ctDNA targeted NGS (MSK-ACCESS), and/or RNA anchored multiplex PCR tumor NGS (MSK-Fusion) were used. Fusions were manually reviewed and considered to have oncogenic potential if they had an in-frame protein fusion involving a non-BRAF partner gene and an intact BRAF kinase domain (exons 11-18). Fusions not previously reported in OncoKB, COSMIC, TCGA, NIH gene, Fusion GDB2, and PubMED were classified as novel. All cases underwent clinical data curation including baseline demographic, tumor characteristics, and treatment histories. Results: 212 patients (0.2%) with BRAF-fusion positive solid tumors were identified. 194 were identified by DNA-based tumor NGS (96 had sufficient tissue for confirmatory RNA-based NGS, all of which were positive). Six were identified by ctDNA NGS and 12 by RNA-based tumor NGS only (5 had insufficient tissue for DNA-based tumor NGS). 83 unique 5’ fusion partners were found, of which 42 were novel. The most frequent tumor types were pilocytic astrocytoma (n=30, 14%), prostate CA (n=28, 13%), melanoma (n=24, 11%), lung CA (n=21, 10%), and colon CA (n=15, 7%). 44% of patients with pilocytic astrocytoma had BRAF fusions, of which 90% were BRAF-KIAA1549. Concomitant alterations (≥10% frequency) included TP53 (24%), TERT (18%), CDKN2A deletions (13%), and CDKN2B deletions (12%). 20% (n=43) were treated with MAPK-pathway directed therapies spanning multiple histologies and lines of therapies. Of the 212 patients, 17 had acquired BRAF fusions after targeted therapy for another oncogene ( EGFR mutation (n=11), BRAF V600E (n=4), FGFR fusion (n=1), NTRK fusion (n=1)). The majority of patients with acquired BRAF fusions had EGFR-mutant lung adenocarcinoma (n=11, 76%); the median time from EGFR targeted therapy initiation to BRAF fusion detection was 25 months (range 16-38 months). Conclusions: A wide variety of adult and pediatric solid tumors harbored de novo BRAF fusions. Complementary RNA sequencing optimized fusion identification in many cases. Multiple novel fusion partners were found. Acquired BRAF fusions were identified after targeted therapy for a variety of distinct oncogenes, the majority of which were EGFR mutations.
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Anderson, Peter Meade, Luisa-Marie Manning, Brian Rubin, Timothy A. Chan, Scott E. Kilpatrick, Rabi Hanna, and Zheng Jin Tu. "Nested set information derived from fusion genes in Ewing sarcoma and other cancers." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e23521-e23521. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e23521.
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e23521 Background: Ewing family tumors including Ewing sarcoma (ES) and desmoplastic small round cell tumor (DSRCT) are characterized by EWSR1 and ETS fusion partners including EWS-FLI1, EWS-ERG, EWS-WT1, and others. Since 2019 our Next Generation Sequencing (NGS) sarcoma panel (N = 338) identified both fusion partners and exons containing the EWS breakpoint in ES and DSRCT. Hence, it should be possible to learn more about the exact breakpoints of EWS fusion genes. The molecular diversity and functionality of these fusion transcripts, especially the exact sequence, which could be identical, similar, or unique, may have significant biological implications for diagnostics and treatment options. We have used in-frame analysis of EWS gene fusion breakpoints to identify corresponding polypeptides spanning the breakpoints of the most common EWS gene fusions to provide useful insights about ES and DSRCT. Methods: Pathology reports and EWS gene fusions were analyzed using the Cleveland Clinic NGS panel which is based on anchored multiplex polymerase chain reaction (PCR) enriched for 34 gene targets. The amplicons were subjected to massively parallel sequencing with 151x2 cycle pair-end reads. An informatics pipeline was used for read alignment (GRCh37 as reference genome), fusion identification, and annotation. The DNA sequence across fusion junction and translational amino acid sequences were extracted for comparison in a preliminary teaching set (37/338 EWS fusions). Results: EWS-FLI1 fusions at exon 7-7 (chr22:29683123-chr11:128675261) and exon 7-6 (chr22:29683123-chr11:128651853) were the most common fusion genes in ES (N = 24/32;75%). Other ES gene fusions included exons 10-6, 7-10, 9-8, 7-2 EWS-FEV, 7-8 EWS-ERG, 7-9 EWS-ERG, and 10-9 EWS-ERG. EWS-WT1 gene fusions (chr22:29683123-chr11:32414301) in DSRCT exon 7-7 occurred in 4 of 5 cases (80%). In frame analysis of the common gene fusions in 75% of ES and DSRCT (total n = 37) yielded identical corresponding polypeptides that span the breakpoint (table). Conclusions: Analysis of ES and DSRCT fusion genes provides evidence that cancer-specific fusion genes are associated with common identical breakpoints and corresponding in-frame polypeptides. Our results show that the identification of in-frame polypeptides from the fusion gene sequencing can identify potential nested sets of cancer-specific mRNAs and polypeptides. This information may become relevant for diagnostic and therapeutic targets future vaccines and diagnostics against ES and DSRCT as well as other cancers characterized by fusion genes or frameshift mutations. [Table: see text]
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Michuda, Jackson, Ben Ho Park, Amy Lauren Cummings, Siddhartha Devarakonda, Bert O'Neil, Sumaiya Islam, Jerod Parsons, et al. "Use of clinical RNA-sequencing in the detection of actionable fusions compared to DNA-sequencing alone." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 3077. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.3077.
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3077 Background: While targeted DNA-seq can detect clinically actionable fusions in tumor tissue samples, technical and analytical challenges may give rise to false negatives. RNA-based, whole-exome sequencing provides a complementary method for fusion detection, and may improve the identification of actionable variants. In this study, we quantify this benefit using a large, real-world clinical dataset to assess actionable fusions detected from RNA in conjunction with DNA profiling. Methods: Using the Tempus Research Database, we retrospectively analyzed a de-identified dataset of ̃80K samples (77.4K patients) profiled with the Tempus xT assay (both DNA-seq with fusion detection in 21 genes and whole exome capture RNA-seq). Only patients that had successful RNA- and DNA-seq were included. Fusions were detected using the Tempus bioinformatic and clinical workflow. Candidate fusions were filtered based on read support thresholds, fusion annotation ( i.e., breakpoints, reading frame, conserved domains), and manual review. OncoKB was used to select fusion alterations in levels 1 and 2 and to identify those indication-matched to targeted therapies. Results: We identified 2118 level 1 and 2 fusion events across 1945 patients across 20 different cancer types. Most fusions were observed in non-small cell lung cancer (NSCLC) (25%) and biliary cancer (9%) samples. Of the 2118 fusion events, 29.1% (616) were detected only through RNA-seq while 4.8% (101) of the events were identifiable only through DNA-seq. Notably, 69.4% of fusions in low-grade glioma and 58.2% in sarcomas were detected only by RNA-seq. When evaluating specific gene fusion events, RNA-seq consistently improved the detection of fusions compared to DNA-seq alone (Table) across all cancer types. A total of 1106 fusions were classified as targetable by OncoKB indication-matched therapies with 19% (214) of these identifiable through RNA-seq alone, 5% (54) by DNA-seq alone, and 76% (838) identifiable through RNA- and DNA-seq. Overall, fusions identified through RNA-seq alone led to a 24% increase in the number of patients who were eligible to receive matched therapies (214 / 892). This included imatinib for patients with CML/BLCL (69.8%), crizotinib for NSCLC (40.3%) and entrectinib for NTRK and ROS1 fusions (32.5%). Conclusions: The addition of RNA-seq to DNA-seq significantly increased the detection of fusion events and ability to match patients to targeted therapies. Results support consideration of combined RNA-DNA-seq for standard-of-care fusion calling. [Table: see text]
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Michuda, Jackson, Ben Ho Park, Amy Lauren Cummings, Siddhartha Devarakonda, Bert O'Neil, Sumaiya Islam, Jerod Parsons, et al. "Use of clinical RNA-sequencing in the detection of actionable fusions compared to DNA-sequencing alone." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 3077. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.3077.
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3077 Background: While targeted DNA-seq can detect clinically actionable fusions in tumor tissue samples, technical and analytical challenges may give rise to false negatives. RNA-based, whole-exome sequencing provides a complementary method for fusion detection, and may improve the identification of actionable variants. In this study, we quantify this benefit using a large, real-world clinical dataset to assess actionable fusions detected from RNA in conjunction with DNA profiling. Methods: Using the Tempus Research Database, we retrospectively analyzed a de-identified dataset of ̃80K samples (77.4K patients) profiled with the Tempus xT assay (both DNA-seq with fusion detection in 21 genes and whole exome capture RNA-seq). Only patients that had successful RNA- and DNA-seq were included. Fusions were detected using the Tempus bioinformatic and clinical workflow. Candidate fusions were filtered based on read support thresholds, fusion annotation ( i.e., breakpoints, reading frame, conserved domains), and manual review. OncoKB was used to select fusion alterations in levels 1 and 2 and to identify those indication-matched to targeted therapies. Results: We identified 2118 level 1 and 2 fusion events across 1945 patients across 20 different cancer types. Most fusions were observed in non-small cell lung cancer (NSCLC) (25%) and biliary cancer (9%) samples. Of the 2118 fusion events, 29.1% (616) were detected only through RNA-seq while 4.8% (101) of the events were identifiable only through DNA-seq. Notably, 69.4% of fusions in low-grade glioma and 58.2% in sarcomas were detected only by RNA-seq. When evaluating specific gene fusion events, RNA-seq consistently improved the detection of fusions compared to DNA-seq alone (Table) across all cancer types. A total of 1106 fusions were classified as targetable by OncoKB indication-matched therapies with 19% (214) of these identifiable through RNA-seq alone, 5% (54) by DNA-seq alone, and 76% (838) identifiable through RNA- and DNA-seq. Overall, fusions identified through RNA-seq alone led to a 24% increase in the number of patients who were eligible to receive matched therapies (214 / 892). This included imatinib for patients with CML/BLCL (69.8%), crizotinib for NSCLC (40.3%) and entrectinib for NTRK and ROS1 fusions (32.5%). Conclusions: The addition of RNA-seq to DNA-seq significantly increased the detection of fusion events and ability to match patients to targeted therapies. Results support consideration of combined RNA-DNA-seq for standard-of-care fusion calling. [Table: see text]
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Yang, Sheng, Fuyu Gong, Guoqiang Wang, and Xiaohui He. "Anaplastic lymphoma kinase (ALK) partners identified by next-generation sequencing in Chinese patients with solid tumors." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): 3555. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.3555.
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3555 Background: Anaplastic lymphoma kinase (ALK) rearrangement is a validated therapeutic driver gene in non-small cell lung cancer (NSCLC). More than 30 different fusion partner genes of ALK in NSCLC have been reportedand most of these ALK fusions respond well to ALK inhibitors crizotinib. With the development of next-generation sequencing (NGS), more novel partners for ALK rearrangement have been identified. Here, we aimed to report the landscape of ALK rearrangement in Chinese patients with solid tumors. Methods: Tissue or blood samples were subjected to NGS in a College of American Pathologists-certified and Clinical Laboratory Improvement Amendments-accredited lab for ALK arrangement. Results: In total, we profiled more than 40,000 patients, among which 72 cases with 52 ALK fusion partner, harboring 17 reported partners and 35 novel partners. The average ALK rearrangement patients' age was 53 years (range, 17-76 years). Among all the ALK fusion cases (n = 72), lung cancer were the largest proportion with 77.8% (n = 56), colorectal cancer accounted for, 5.5% (n = 4), liver cancer accounted for 4.2% (n = 3), biliary cancer, melanoma, carcinosarcoma and inflammatory myofibroblastic tumor accounted for 2.8% (n = 2) respectively, and only one case (n = 1) was malignant peritoneal mesothelioma. The most common ALK fusion partners were KIF5B (n = 6), DCTN1 (n = 5) and STRN (n = 5). In 38 cases, 35 novel ALK fusion partners were discovered. The novel CLIP4-ALK, EHBP1-ALK, PLB1-ALK occurred twice in 6 patients, which were two lung cancer patients with CLIP4-ALK fusion, two lung cancer patients with PLB1-ALK fusion, one hepatic cellular cancer patients with EHBP1-ALK, and one melanoma patients with EHBP1-ALK. There were two special lung cancer cases with two ALK fusions. One case detected the novel LRIG1-ALK fusion and novel PLB1-ALK fusion, the other case detected novel GLI3-ALK fusion and reported HIP1-ALK fusion. Conclusions: Novel ALK fusions are detected in patients with not only NSCLC but also other solid tumors. NGS fusion assay is an optional method for screening novel fusions.
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Ladanyi, Marc, Sinchita Roy-Chowdhuri, Lauren Ritterhouse, Felix Sahm, Ricarda Norenberg, Kui Shen, Chi Chen, et al. "Abstract CT545: Variability in NTRK gene fusions does not appear to impact response to larotrectinib." Cancer Research 82, no. 12_Supplement (June 15, 2022): CT545. http://dx.doi.org/10.1158/1538-7445.am2022-ct545.
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Abstract Introduction: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. Gene fusions arise from inter- and intrachromosomal rearrangements involving the 3’ region of the NTRK gene and the 5’ end of a fusion partner gene, leading to the expression of a constitutively active tropomyosin receptor kinase (TRK) fusion protein. Larotrectinib is a highly selective and central nervous system (CNS)-active TRK inhibitor approved for the treatment of adult and pediatric patients with TRK fusion cancer. Larotrectinib has previously demonstrated an objective response rate (ORR) of 75% in 206 patients with non-primary CNS solid tumors (Hong et al, ASCO 2021). Here, we report on the TRK fusion exon junction organization in patients with TRK fusion cancer receiving larotrectinib. Methods: Patients with non-primary CNS TRK fusion cancer treated with larotrectinib were identified from three clinical trials (NCT02122913, NCT02576431, and NCT02637687). NTRK gene fusion data were determined by local molecular testing. The testing method, NTRK gene fusions, and exon structure were extracted from the molecular pathology reports from 212 patients. The data cut-off was July 20, 2020. Results: TRK fusion exon junction data were available for 80 patients from 14 different tumor types. Median age was 47 years (range 0.5-84 years). The ORR for these patients was 82.5% (95% confidence interval [CI] 72.4-90.1). Patients had gene fusions involving NTRK1 (40%), NTRK2 (4%), or NTRK3 (56%), a pattern similar to that seen in the larger dataset. We detected 20 different NTRK gene fusions; the most common were ETV6-NTRK3, TPM3-NTRK1, and LMNA-NTRK1 detected in 39 (49%), ten (13%), and seven (9%) patients, respectively. There were 12, three, and five different fusion partners associated with NTRK1, NTRK2, and NTRK3, respectively. The majority (12/20; 60%) of fusions were intrachromosomal rearrangement events: 8/12 (67%) related to NTRK1, 2/3 (67%) related to NTRK2, and 2/5 (40%) related to NTRK3. There were 35 different 5’/3’ gene breakpoint combinations: 3’ fusion points were located at NTRK1 exon 8 (n = 2), NTRK1 exon 9 (n = 5), NTRK1 exon 10 (n = 15), NTRK1 exon 11 (n = 6), NTRK1 exon 12 (n = 3), NTRK1 exon 13 (n = 1), NTRK2 exon 15 (n = 2), NTRK2 exon 16 (n = 1), NTRK3 exon 14 (n = 21), and NTRK3 exon 15 (n = 24). For ETV6-NTRK3 fusions, the NTRK3 fusion point was at exon 14 in ten of 11 thyroid carcinomas, but in only three of 13 salivary gland tumors. Conclusions: Among 80 patients with TRK fusion cancer, we detected 20 different NTRK gene fusions, of which 55% occurred in only one patient each. There were 36 different fusion variants. Despite the variability of the fusion structure, larotrectinib was equally efficacious. The large number of potential different fusion partners and involvement of various breakpoints highlight the need for validated and appropriate testing methodologies that are agnostic of 5’ partners and breakpoints. Citation Format: Marc Ladanyi, Sinchita Roy-Chowdhuri, Lauren Ritterhouse, Felix Sahm, Ricarda Norenberg, Kui Shen, Chi Chen, Marc Fellous, Nicoletta Brega, Cornelis M. van Tilburg, Jessica J. Lin, Marcia S. Brose, Ulrik N. Lassen, Ray McDermott, Theodore W. Laetsch, David S. Hong, Alexander Drilon, Erin R. Rudzinski. Variability in NTRK gene fusions does not appear to impact response to larotrectinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT545.
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Williams, Gareth Haydn, Robert Paul Thatcher, Borja Nevado Polo, Tiffany Eira Haddow, Keeda-Marie Hardisty, and Marco Loddo. "Druggable fusion gene landscape in solid tumors." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): e13517-e13517. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13517.
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e13517 Background: Kinases activated by gene fusions represent an important class of oncogenes in solid tumors highlighted by the unique site agnostic FDA approval of larotrectinib for NTRK gene rearrangements. However, the frequency and types of druggable fusions in solid tumors are not well characterized from the clinical perspective. Methods: Oncofocus is a clinically validated precision oncology platform that includes analysis of 399 druggable driver-partner oncogenic fusion genes linked to 140 unique targeted therapy protocols. A retrospective analysis of Oncofocus trending data in a real-life cohort of 1111 patients has been used to determine the actionable fusion gene landscape in solid tumors. Results: Eighty nine actionable fusion genes were identified in 1111 samples of solid tumors linked to 73 targeted therapy protocols. Seven of the samples harbored multiple fusion genes. Eighty two of the 1111 samples tested had at least one actionable fusion gene representing a frequency of 7.38%. The highest frequency of actionable fusions were observed in glioblastoma (23%), head and neck (12%), kidney (11%) and prostate (10%) cancers. Four of the seven samples with multiple actionable fusions were found in glioblastoma. Pancreatic, lung and endometrial cancers and cancer of unknown primary (CUPs) had an actionable fusion gene frequency ranging from 7-9%. TBL1XR1-PIK3CA, MET-MET, WHSC1L1-FGFR1 and EGFR VIII fusions were identified as the most common druggable fusions. All actionable fusion genes were found to interact with one or more of the following pathways RAS/RAF/MEK/ERK, PI3K/AKT/MTOR, PLCy/PKC and JAK/STAT. Although a targeted agent for TRK fusions now has FDA approval, this rearrangement appears to be a rare event. In contrast, inhibitors targeting the TBL1XR1-PIK3CA, MET-MET, WHSC1L1-FGFR1 fusions and linked downstream signalling pathways appear to offer much broader clinical utility. Conclusions: Druggable fusions were identified at an unexpectedly high frequency and should therefore be included as part of routine comprehensive precision oncology testing. Notably, many of the actionable fusions are not tumor type specific reinforcing the “site agnostic” approach to profiling and supporting the concept of “molecular basket” clinical trials. Precision oncology trending data also provides actionable mutational landscapes which can be used to refine precision oncology testing, patient selection for targeted therapy protocols and enhancement of clinical trial design.
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Wang, Jidong, Yushuai Han, Weiran Wang, and Tonghui Ma. "Abstract 5746: Analysis of molecular characteristics of gliomas harboring gene fusions." Cancer Research 82, no. 12_Supplement (June 15, 2022): 5746. http://dx.doi.org/10.1158/1538-7445.am2022-5746.
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Abstract Background: Genotyping plays an important role in tumor diagnosis and prognosis. The 2016 central nervous system (CNS) WHO added molecular parameters to classify CNS tumors on the basis of routine histological features, but the characteristics of gene fusion variations have not been clarified in CNS tumors. Methods: In order to identify the characteristics of gene fusions in Chinese patients with CNS malignant tumors, we retrospectively analyzed the next-generation sequencing data of 234 patients (pts) with gene fusions. Results: According to WHO classification of CNS tumor, 121 pts (51.7%) were low-grade gliomas (LGG, grade I, II), and 113 pts (48.3%) were high-grade gliomas (HGG, grade III, IV). The age of pts with LGG (14.1 ± 16.1) was significantly lower than HGG pts (50.2 ± 17.4) (P<0.0001). There was no significant gender difference between them (P = 0.161). In the fusion map of pts with LGG, gene fusions of KIAA1549-BRAF (n=82, 67.7%) and FGFR3-TACC3 (n=7, 5.8%) occurred frequently. Meanwhile, there were 5.7% pts carrying BRAF fusions with other partners, and some other sporadic fusions. Among HGG cases, the most frequent gene fusion was FGFR3-TACC3 (n=36, 31.9%), followed by fusions in EGFR (n=22, 19.5%), MET (n=16, 14.2%), BRAF (n=8, 7.1%), ROS1 (n=5, 4.4%), and other sporadic genes. It can be seen that gene fusion characteristics varied from gliomas with different malignant degrees. KIAA1549-BRAF fusion tended to occur in LGG (67.7% vs. 2.7%, P < 0.0001) than HGG, and FGFR3-TACC3 tended to occur in HGG ( 31.9% vs. 5.8%, P< 0.0001) than LGG. In addition, FGFR3-TACC3 fusion pts were exclusive with IDH1/2 mutations, but tended to be co-mutate with TERT promoter variants (P<0.0001). IDH-mutation-positive glioma usually exhibit a better clinical result, while TERT promoter-mutated glioma predicts a poor outcome. We also found that 75% (12/16) of MET fusion-positive gliomas pts had TP53 co-coexisting and 56.3% (9/16) of MET fusion-positive gliomas pts co-occurred with MET amplification, while only 0.9% (1/105) of pts harboring other fusions were MET amplification positive. Meanwhile, 95.0% (21/22) of EGFR fusion-positive pts co-occurred with EGFR amplification. Conclusion: By comprehensively analyzing the gene fusion map of Chinese patients with gliomas, we found the gene fusion characteristics of LGG differed from that of HGG. These fusion features may be important molecular information for judging the grade of malignancy and prognosis of patients. Citation Format: Jidong Wang, Yushuai Han, Weiran Wang, Tonghui Ma. Analysis of molecular characteristics of gliomas harboring gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5746.
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Rabushko, Elizaveta, Maxim Sorokin, Maria Suntsova, Alexander P. Seryakov, Denis V. Kuzmin, Elena Poddubskaya, and Anton A. Buzdin. "Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data." Biomedicines 10, no. 8 (August 2, 2022): 1866. http://dx.doi.org/10.3390/biomedicines10081866.
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Drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins demonstrate impressive anti-cancer activities. The fusion presence in the cancer is the respective drug prescription biomarker, but their identification is challenging as both the breakpoint and the exact fusion partners are unknown. RNAseq offers the advantage of finding both fusion parts by screening sequencing reads. Paraffin (FFPE) tissue blocks are the most common way of storing cancer biomaterials in biobanks. However, finding RTK fusions in FFPE samples is challenging as RNA fragments are short and their artifact ligation may appear in sequencing libraries. Here, we annotated RNAseq reads of 764 experimental FFPE solid cancer samples, 96 leukemia samples, and 2 cell lines, and identified 36 putative clinically relevant RTK fusions with junctions corresponding to exon borders of the fusion partners. Where possible, putative fusions were validated by RT-PCR (confirmed for 10/25 fusions tested). For the confirmed 3′RTK fusions, we observed the following distinguishing features. Both moieties were in-frame, and the tyrosine kinase domain was preserved. RTK exon coverage by RNAseq reads upstream of the junction site were lower than downstream. Finally, most of the true fusions were present by more than one RNAseq read. This provides the basis for automatic annotation of 3′RTK fusions using FFPE RNAseq profiles.
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Xu, Yurong, Yingxue Qi, Ningning Luo, Qin Zhang, Yaqing Wu, and Chuang Qi. "Comparison of fusions detection by next generation sequencing between malignant pleural effusion and tumor tissue in lung cancer." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): e21059-e21059. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e21059.
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e21059 Background: Anaplastic lymphoma kinase ( ALK), c-ros oncogene 1 receptor tyrosine kinase ( ROS1), ret proto-oncogene ( RET) and neurotrophic receptor kinase ( NTRK) are important driver genes in lung cancer. Each of these four genes fusions as therapeutic targets have been recommended by the national comprehensive cancer network (NCCN) guidelines for non-small cell lung cancer (NSCLC). Malignant pleural effusion (MPE) is observed in multy types of malignancies, especially in lung cancer. Studies have indicated that next generation sequencing (NGS) detection of somatic mutations by MPE is reliable. Nevertheless, the distribution and comparison of fusions in lung cancer between malignant pleural effusion and tumor tissue specimen have not been well characterized yet. Methods: In this study, 9-gene, 69-gene and 539-gene panel NGS profiling were performed by MPE and tumor tissue in 640 and 10013 patients with lung cancer respectively. The variation analysis between patients with or without gene fusion in different sample groups were calculated by fisher exact test via SPSS v26.0. Results: In lung cancer patients using MPE detection, 59 of 640 (9.22%) were found harboring at least one of the four gene fusions, and the ratio of ALK, ROS1, RET and NTRK fusion was 6.25% (40/640), 1.41% (9/640), 0.63% (4/640) and 0.47% (3/640) respectively. Meanwhile, we found gene fusions in 6.25% (626/10013) lung cancer patients using tumor tissue detection, including 3.66% (366/10013) ALK fusion, 1.07% (107/10013) ROS1 fusion, 1.09% (108/10013) RET fusion and 0.22% (626/10013) NTRK fusion. Significant differences of gene fusion frequency between different sample groups were found via fisher exact test ( p = 0.005), especially ALK fusion ( p = 0.001). Conclusions: The frequency of fusion in MPE was significantly higher than in tumor tissue, especially ALK fusion. However, as a retrospective study, the conclusions and the specific mechanisms are needed to be verified.
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Roy, Shikha, and Dinesh Gupta. "DriverFuse: An R package for analysis of next-generation sequencing datasets to identify cancer driver fusion genes." PLOS ONE 17, no. 2 (February 3, 2022): e0262686. http://dx.doi.org/10.1371/journal.pone.0262686.
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We developed the DriverFuse package to integrate orthogonal data types such as Structural Variants (SV) and Copy Number Variations (CNV) to characterize fusion genes in cancer datasets. A fusion gene is reported as a driver or passenger fusion gene, based on mapping SV and CNV profiles. DriverFuse generates a fusion plot of fusion genes with their mapping SV, CNV profile, domain architecture and classification of its role in cancer. The analysis facilitates discrimination of driver fusions from passenger fusions. To demonstrate the utility of DriverFuse, we analyzed two datasets, one each for CCLE (Cancer Cell Line Encyclopedia) for lung cancer and HCC1395BL for breast cancer. The analysis validates the driver fusion genes that are already reported for the datasets. Thus, DriverFuse is a valuable tool for studying the driver fusion genes in cancers, enabling the identification of recurrent complex rearrangements that provide intuitive insights into disease driver events.
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Husain, Hatim, Chaugiang Duong, Steven Rivera, Nathan Montgomery, Roisin Puentes, Derek Lyle, and Fernando J. Lopez-Diaz. "A study of the gaps and opportunities with fusion detection beyond NTRKs on 422 patients from the community." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): e15186-e15186. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.e15186.
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e15186 Background: Gene fusions have important implications for therapeutic selection and patient quality of care and many fusions are targeted effectively in a tumor type agnostic manner. While most assays detect hundreds of fusions at once, typically the results are masked and analyzed according to medical requisition. Unfortunately, patients in the community setting most often are only tested for NTRK fusions, which have a prevalence of ~ 1%, and often following a positive IHC screen result. Here we compared side by side the clinical actionability gap in the community when using panTRK IHC testing and NGS fusion panels for NTRKs or for additional fusions, with both NGS panels selected presenting identical assay performance characteristics and medicare coverage. Methods: Clinical samples (n = 8307) from 33 tumor types were tested for RNA fusions using a hybridization capture RNA-seq based fusionome assay for solid tumors in our clinical laboratory, targeting RNA breakpoints at 1104 genes. Deidentified results were analyzed for either the 19 actionable fusion genes (ALK, BRAF, FGFR1-4, MET, NOTCH1/2, NRG1, NTRK1-3, PDGFB, PDGFRA/B, RAF1, RET and ROS1) reportable under Solid Tumor NGS fusion Panel, or only for NTRK fusions. Pan-TRK IHC results on fusion positive patients were analyzed. All the Deidentified patient data presented, was analyzed according to an IRB-approved protocol. Results: Targeted therapy -associated fusions were present in 422 (5.1%) patients, where 53% of patients were female with a median age of 68 years old, and 47% were male with a median age of 70 years old. However, when filtering only for NTRK fusions, just 104 (1.25%) patients had an actionable fusion (38 NTRK1, 10 NTRK2, 56 NTRK3). The additional 318 (3.8%) patients had other therapy candidate fusions: ALK (0.6%), BRAF 0.3%, FGFRs 0.9%, MET 0.4%, NOTCH2 0.2%, NRG1 0.2%, PDGFRA 0.1%, RAF1 0.2%, RET 0.5%, ROS1 0.2%, excluding NTRK positive cases. There were only 2 (0.02%) cases that were positive for both an NTRK fusion and an additional Targeted Panel fusion gene. Interestingly, we found that IHC testing was able to identify 75% of NTRK1 and 55% NTRK2 positive samples but only 20% of NTRK3 fusion positive patients. Moreover only 54% of the panTRK IHC positive patients expressed and NTRK fusion while 46% expressed one of the other 16 druggable fusions, with FGFRs on 20%, and ALK and ROS1 with 4% each. Conclusions: The data demonstrates that up to 4 -fold more patients can have a fusion matched therapy when testing for these 19 druggable fusions at once as compared to testing only for NTRK fusions or following IHC testing. Moreover, IHC testing as a screening method as very poor sensitivity for NTRK fusions, specially for NTRK3. Changes on the molecular testing paradigm in the community setting is needed to provide more patients with a therapeutic opportunity, when assay performance and financial considerations are equal to increase cancer care access.
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Stengel, Anna, Rabia Shahswar, Torsten Haferlach, Wencke Walter, Stephan Hutter, Manja Meggendorfer, Wolfgang Kern, and Claudia Haferlach. "Whole transcriptome sequencing detects a large number of novel fusion transcripts in patients with AML and MDS." Blood Advances 4, no. 21 (November 4, 2020): 5393–401. http://dx.doi.org/10.1182/bloodadvances.2020003007.
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Abstract Fusion transcripts are frequent genetic abnormalities in myeloid malignancies and are often the basis for risk stratification, minimal residual disease (MRD) monitoring, and targeted therapy. We comprehensively analyzed the fusion transcript landscape in 572 acute myeloid leukemia (AML) and 630 myelodysplastic syndrome (MDS) patients by whole transcriptome sequencing (WTS). Totally, 274 fusion events (131 unique fusions) were identified in 210/572 AML patients (37%). In 16/630 MDS patients, 16 fusion events (15 unique fusions) were detected (3%). In AML, 141 cases comprised entity-defining rearrangements (51% of all detected fusions) and 21 (8%) additional well-known fusions, all detected by WTS (control group). In MDS, only 1 fusion was described previously (NRIP1-MECOM, n = 2). Interestingly, a high number of so-far unreported fusions were found (41% [112/274] in AML, 88% [14/16] in MDS), all validated by cytogenetic and/or whole genome sequencing data. With 1 exception (CTDSP1-CFLAR, n = 2), all novel fusions were observed in 1 patient each. In AML, cases with novel fusions showed concomitantly a high frequency of TP53 mutations (67%) and of a complex karyotype (71%), which was also observed in MDS, but less pronounced (TP53, 26%; complex karyotype, 21%). A functional annotation of genes involved in novel fusions revealed many functional relevant genes (eg, transcription factors; n = 28 in AML, n = 2 in MDS) or enzymes (n = 42 in AML, n = 9 in MDS). Taken together, new genomic alterations leading to fusion transcripts were much more common in AML than in MDS. Any novel fusions might be of use for developing markers (eg, for MRD monitoring), particularly in cases without an entity-defining abnormality.
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Duong, Chaugiang, Steven Lau-Rivera, Rory Jackson, Pathum Kanagasunderam, Roya Hariri, Nathan Montgomery, Derek Lyle, and Fernando Lopez Diaz. "Abstract 1312: A study of the clinical utility of NTRKs only vs. comprehensive gene fusion panel testing from a single assay platform." Cancer Research 84, no. 6_Supplement (March 22, 2024): 1312. http://dx.doi.org/10.1158/1538-7445.am2024-1312.
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Abstract Background: Gene fusions have important implications for therapeutic selection and patient quality of care, and though they have a low prevalence individually, many fusions are targeted effectively, agnostic of any tumor type. Unfortunately, patients in the community oncology setting are most often only tested for NTRK fusions, which have a prevalence of around 1%. Here, we compared side by side the actual clinical actionability differences using real-world testing data between broad vs. NTRK fusion only panels offered by our clinical laboratory, both with identical assay performance characteristics, reimbursement, and cost levels. Methods: Clinical samples(n=8307) from 33 tumor types were tested for known and novel RNA fusions using our hybridization capture RNA-seq based Solid Tumor Fusion Panels in our clinical laboratory, which targets RNA breakpoints at 1104 genes. Deidentified results were analyzed before or after filtering for fusions based on either a Targeted Solid Tumor NGS fusion Panel (16 drug targetable genes) or only NTRKs fusions. Deidentified patient data presented was analyzed according to an IRB-approved protocol. Results: The prevalence of fusions in the cohort was 30.5% involving any of the 1104 targeted genes by the assay (27% in frame, 20% out of frame, and 41% others). Druggable fusions were present in 5.1% (422) of patients, where 53% were female with a median age of 68 years old, and 47% were male with a median age of 70. However, when filtering only for NTRK fusions, only 104 patients had an NTRK fusion (38 NTRK1, 10 NTRK2, 56 NTRK3), while an additional 318 patients had detected fusions from the Targeted Panel. These druggable fusions had the following prevalences; ALK 0.6 %, BRAF 0.3%, FGFR1 0.2%, FGFR2 0.3%, FGFR3 0.4%, FGFR4 0.0% n=4, MET 0.4%, NOTCH1 0.0% n=1, NOTCH2 0.2%, NRG1 0.2%, PDGFB 0.0% n=3, PDGFRA 0.1%, PDGFRB 0% n=0, RAF1 0.2%, RET 0.5%, ROS1 0.2%, excluding NTRK positive cases. The incidence of NTRK 1/2/3 fusions was 1.25%, while 3.8% of patients have other fusions included on the Targeted Panel in the absence of an NTRK fusion. Two (2, 0.02%) patients had both an NTRK fusion and an additional fusion covered on one of the other 16 genes in the Targeted NGS fusion panel. Conclusion: Actionable fusions showed a combined prevalence in the clinical setting of 5.1%. This study demonstrates that when fusion testing is performed, four times more patients can benefit from a therapeutic option than when testing for these 16 genes compared to the widespread panel of the current clinicians’ favorite choice of only NTRK fusions. More data and education are needed to change the testing paradigm of treating physicians to test broader sets of fusions when assay performance and financial considerations are equal to increase cancer care access. Citation Format: Chaugiang Duong, Steven Lau-Rivera, Rory Jackson, Pathum Kanagasunderam, Roya Hariri, Nathan Montgomery, Derek Lyle, Fernando Lopez Diaz. A study of the clinical utility of NTRKs only vs. comprehensive gene fusion panel testing from a single assay platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1312.
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Bossi, Paolo, Marco Siano, Cristiana Bergamini, Maria Cossu Rocca, Andrea P. Sponghini, Marco Giannoccaro, Luca Tonella, et al. "Are Fusion Transcripts in Relapsed/Metastatic Head and Neck Cancer Patients Predictive of Response to Anti-EGFR Therapies?" Disease Markers 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/6870614.
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Prediction of benefit from combined chemotherapy and the antiepidermal growth factor receptor cetuximab is a not yet solved question in head and neck squamous cell carcinoma (HNSCC). In a selected series of 14 long progression-free survival (PFS) and 26 short PFS patients by whole gene and microRNA expression analysis, we developed a model potentially predictive of cetuximab sensitivity. To better decipher the “omics” profile of our patients, we detected transcript fusions by RNA-seq through a Pan-Cancer panel targeting 1385 cancer genes. Twenty-seven different fusion transcripts, involving mRNA and long noncoding RNA (lncRNA), were identified. The majority of fusions (81%) were intrachromosomal, and 24 patients (60%) harbor at least one of them. The presence/absence of fusions and the presence of more than one fusion were not related to outcome, while the lncRNA-containing fusions resulted enriched in long PFS patients (P=0.0027). The CD274-PDCD1LG2 fusion was present in 7/14 short PFS patients harboring fusions and was absent in long PFS patients (P=0.0188). Among the short PFS patients, those harboring this fusion had the worst outcome (P=0.0172) and increased K-RAS activation (P=0.00147). The associations between HNSCC patient’s outcome following cetuximab treatment and lncRNA-containing fusions or the CD274-PDCD1LG2 fusion deserve validation in prospective clinical trials.
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Mahan, KT, GV Yu, SR Kalish, and SV Corey. "Podiatry Institute ankle fusion technique." Journal of the American Podiatric Medical Association 87, no. 3 (March 1, 1997): 101–16. http://dx.doi.org/10.7547/87507315-87-3-101.
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The authors review the ankle and pantalar fusion literature. The authors performed a retrospective review on 42 ankle and pantalar fusions, emphasizing the role of internal fixation. The Podiatry Institute technique for internal fixation of ankle fusions is described and experience with the technique is reviewed. Complications included delayed union and nonunion at the fusion site or the repaired fibular osteotomy site and tibial fractures at screw stress riser sites. Modifications to reduce these complications are discussed. Experience with internal fixation in ankle and pantalar fusions, both in this study and in current literature, has been positive.
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Chen, Huayou, Zhi Chen, Bangguo Wu, Jawad Ullah, Tianxi Zhang, Jinru Jia, Hongcheng Wang, and Tianwei Tan. "Influences of Various Peptide Linkers on the Thermotoga maritima MSB8 Nitrilase Displayed on the Spore Surface of Bacillus subtilis." Journal of Molecular Microbiology and Biotechnology 27, no. 1 (2017): 64–71. http://dx.doi.org/10.1159/000454813.
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In the present study, fusion genes composed of <i>Thermotoga maritima</i> MSB8 nitrilase and <i>Bacillus subtilis</i> 168 outer coat protein CotG were constructed with various peptide linkers and displayed on <i>B. subtilis</i> DB 403 spores. The successful display of CotG-nit fusion proteins on the spore surface of <i>B. subtilis</i> was verified by Western blot analysis and activity measurement. It was demonstrated that the fusion with linker GGGGSEAAAKGGGGS presented the highest thermal and pH stability, which is 2.67- and 1.9-fold of the fusion without linker. In addition, fusion with flexible linker (GGGGS)<sub>3</sub> demonstrated better thermal and pH stability than fusions with linkers GGGGS and (GGGGS)<sub>2</sub>. Fusion with rigid linker (EAAAK) demonstrated better thermal stability than fusions with linkers (EAAAK)<sub>2</sub> and (EAAAK)<sub>3</sub>. Fusions with linker (EAAAK)<sub>2</sub> demonstrated better pH stability than fusions with linkers (EAAAK) and (EAAAK)<sub>3</sub>. In the presence of 1 m<smlcap>M</smlcap> dithiothreitol, 1% (v/v) sodium dodecyl sulfate, and 20% (v/v) ethanol, the optimal linkers of the fusions were MGSSSN, GGGGSEAAAKGGGGS, and (GGGGS)<sub>3</sub>, respectively. In summary, our results showed that optimizing the peptide linkers with different type, length, and amino acid composition of the fusion proteins would be an efficient way to maintain the stability of fusion proteins and thus improve the nitrilase display efficiency, which could provide an effective method for rational design peptide linkers of displayed nitrilase on <i>B. subtilis</i>.