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    TEST:
    Oncomine™ Comprehensive Assay v3M

    Company:
    Thermo Fisher Scientific
    Type:
    Laboratory Developed Test
    Related tests:
    17d
    Tumor Molecular Profiling in Early Phase Clinical Trials (clinicaltrials.gov)
    P=N/A, N=40, Recruiting, Oncology Institute of Southern Switzerland | Trial completion date: Dec 2024 --> Dec 2026 | Trial primary completion date: Dec 2024 --> Dec 2026
    Trial completion date • Trial primary completion date
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    Oncomine™ Comprehensive Assay v3M
    2ms
    Reflex somatic testing for the detection of FGFR alterations in urinary tract carcinomas: A dual-institutional experience. (PubMed, Am J Clin Pathol)
    The detection rate for FGFR1-4 alterations in a real-world, dual-institution cohort of urinary tract carcinomas was reported.
    Journal
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    FGFR2 (Fibroblast growth factor receptor 2) • FGFR3 (Fibroblast growth factor receptor 3) • FGFR1 (Fibroblast growth factor receptor 1) • FGFR (Fibroblast Growth Factor Receptor)
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    FGFR2 mutation • FGFR2 fusion • FGFR3 mutation
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    Oncomine™ Comprehensive Assay v3M • Oncomine™ Comprehensive Assay Plus
    6ms
    Molecular Profiling Project (clinicaltrials.gov)
    P=N/A, N=500, Recruiting, National Cancer Centre, Singapore | Trial primary completion date: Dec 2024 --> Dec 2025
    Trial primary completion date
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    Oncomine™ Comprehensive Assay v3M • Oncomine Focus Assay
    7ms
    Dominant Negative PTEN Alterations in Endometrial Carcinoma Are Associated With Retained Immunohistochemical PTEN Expression. (PubMed, Am J Surg Pathol)
    Our results indicate that DN PTEN mutations are common in EC, and are associated with retained IHC staining (intact, reduced, or subclonal loss). These results highlight that IHC and NGS are both required in capturing the full spectrum of PTEN-abnormal EC.
    Journal
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    PTEN (Phosphatase and tensin homolog)
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    PTEN mutation
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    Oncomine™ Comprehensive Assay v3M
    9ms
    A novel likely pathogenic germline variant in CDKN1B in a patient with MEN4 and medullary thyroid cancer. (PubMed, Fam Cancer)
    Evaluation of loss of heterozygosity (LOH) in both MTC and pituitary tissues showed compatibility with copy-neutral LOH, although further evidence is required for definitive confirmation. In conclusion, we report a clinical case of MTC coexisting with MEN4 due to a novel CDKN1B germline heterozygote frameshift variant.
    Journal
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    RET (Ret Proto-Oncogene) • HRAS (Harvey rat sarcoma viral oncogene homolog) • CDKN1B (Cyclin dependent kinase inhibitor 1B)
    |
    Oncomine™ Comprehensive Assay v3M
    11ms
    Pathological variants in HPV-independent vulvar tumours. (PubMed, Sci Rep)
    The PI3K/AKT/mTOR1 pathway was affected in both the groups as well as the cell cycle regulation pathway. Similarly, the DNA repair gene POLE was found mutated in both vulvar cancer groups.
    Journal • BRCA Biomarker
    |
    TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • BRCA2 (Breast cancer 2, early onset) • MYC (V-myc avian myelocytomatosis viral oncogene homolog) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • ARID1A (AT-rich interaction domain 1A) • NOTCH1 (Notch 1) • NF1 (Neurofibromin 1) • PTCH1 (Patched 1) • CDK4 (Cyclin-dependent kinase 4) • MSH2 (MutS Homolog 2) • NOTCH2 (Notch 2) • CREBBP (CREB binding protein) • CDK2 (Cyclin-dependent kinase 2) • PSMD1 (Proteasome 26S Subunit Non-ATPase 1) • TBL1XR1 (TBL1X Receptor 1)
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    TP53 mutation • AKT1 amplification
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    Oncomine™ Comprehensive Assay v3M
    12ms
    Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for Detecting ERBB2 and Other Gene Amplifications in Solid Tumors. (PubMed, Cancers (Basel))
    This study highlights the strengths and limitations of amplicon-based NGS assays in detecting amplifications using real-world data.
    Journal • Next-generation sequencing
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    HER-2 (Human epidermal growth factor receptor 2)
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    HER-2 amplification
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    Oncomine™ Comprehensive Assay v3M • Oncomine Focus Assay • Oncomine™ Comprehensive Assay Plus
    1year
    The Use of Internal Controls in Next-Generation Sequencing to Improve BRCA1 and BRCA2 Gene Copy Loss Detection (AMP 2024)
    SNAQ-SEQ copy loss detection was based on estimating the exon abundance of ATM, BRCA1, BRCA2, and PALB2 genes, converting abundance into copies per cell and then detecting genes with significantly lower copy number. The CNV detection comparison between OCAv3 with and without SNAQ indicated that analysis with SNAQ was more robust, giving a result for every gene in every sample. Further, there were copy losses detected by OCAv3 that were not supported by SNAQ analysis.
    BRCA Biomarker • Next-generation sequencing
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    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • PALB2 (Partner and localizer of BRCA2)
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    Oncomine™ Comprehensive Assay v3M
    1year
    Segmental CNV Detection with Oncomine Comprehensive Assay v3: Combined SNV and CNV Detection for Improved Glioma Diagnostics (AMP 2024)
    Segmental CNV detection is feasible with the OCAv3 platform. Identified thresholds resulted in 100% sensitivity and specificity, although 20% to 30% of CDKN2A and +7/-10 cases require FISH reflex. If validated, this solution affords an efficient strategy in terms of hands-on-time, cost, and tissue use for combined SNV and CNV detection, particularly in a resource-constrained setting.
    EGFR (Epidermal growth factor receptor) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A)
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    EGFR amplification • CDKN2A deletion
    |
    Oncomine™ Comprehensive Assay v3M
    1year
    Validation and Clinical Utility of the Oncomine Comprehensive Assay v3 (OCAv3) for Comprehensive Genomic Profiling of Solid Tumors Using the GeneXus System (AMP 2024)
    The OCAv3 assay on the GeneXus System provides a rapid and reliable method for CGP of solid tumors from FFPE samples, enabling the identification of clinically actionable mutations for personalized oncology. Whereas limitations exist in homopolymer regions and coverage variability through all targets, the assay's turnaround time, low input material requirement, and overall performance when using optimal cut-offs support its adoption in clinical practice.
    Clinical
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    MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    MET exon 14 mutation
    |
    Oncomine™ Comprehensive Assay v3M
    1year
    Clinical Utility of Novel Fusion Detection by Amplicon-Based Next-Generation Sequencing versus Whole-Transcriptome Sequencing in Practice (AMP 2024)
    In this real-world clinical dataset, WTS performed significantly worse than amplicon-based sequencing for detection of clinically meaningful fusions, predominantly due to a high QNS rate. It did not significantly increase the detection rate of novel fusions. Although amplicon-based methods may have limitations due to the inability to detect novel fusions, this can be overcome with design for additional targets, and is balanced by a superior ability to test a wide range of clinical samples without failure.
    Clinical • Next-generation sequencing
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    ALK (Anaplastic lymphoma kinase) • FGFR3 (Fibroblast growth factor receptor 3) • NRG1 (Neuregulin 1) • KIF5B (Kinesin Family Member 5B) • TACC3 (Transforming acidic coiled-coil containing protein 3) • CCDC6 (Coiled-Coil Domain Containing 6) • VTCN1 (V-Set Domain Containing T Cell Activation Inhibitor 1) • YAP1 (Yes associated protein 1) • STAT6 (Signal transducer and activator of transcription 6) • MAML2 (Mastermind Like Transcriptional Coactivator 2) • NAB2 (NGFI-A Binding Protein 2)
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    FGFR3 fusion
    |
    Oncomine™ Comprehensive Assay v3M
    1year
    Prevalence of BRCA1, BRCA2, and PALB2 genomic alterations among 924 Taiwanese breast cancer assays with tumor-only targeted sequencing: extended data analysis from the VGH-TAYLOR study (SABCS 2024)
    This study reported a cohort of Taiwanese breast cancers harboring mutations in BRCA1, BRCA2, and PALB2 through tumor-only sequencing, which underscores the impact of these genes on breast cancer risk and potential therapeutic opportunities. Tumor-only sequencing has enabled a greater number of patients to uncover their genomic alterations, offering additional insights for management strategies. These include recommendations for germline testing and the prospective utilization of PARP inhibitors to augment treatment efficacy.
    PARP Biomarker • BRCA Biomarker
    |
    HER-2 (Human epidermal growth factor receptor 2) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • PALB2 (Partner and localizer of BRCA2) • BRCA (Breast cancer early onset) • RAD51 (RAD51 Homolog A)
    |
    BRCA2 mutation • BRCA1 mutation • PALB2 mutation • BRCA mutation • RAD51 mutation
    |
    Oncomine™ Comprehensive Assay v3M