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    TEST:
    Oncomine™ Comprehensive Assay Plus

    Company:
    Thermo Fisher Scientific
    Type:
    Laboratory Developed Test
    Related tests:
    Details
    Evidence

    News

    5d
    Comprehensive Evaluation of Copy Number Variation from Gene to Arm-Level Using Targeted Sequencing (AMP 2024)
    OCA Plus supports comprehensive detection of relevant copy number alterations in cancer FFPE samples. Combined with small variant profiling, detection of MSI, TMB, and HRD, OCA Plus facilitates comprehensive analysis of DNA structural changes in cancer that are relevant to precision oncology research.
    Tumor mutational burden • BRCA Biomarker
    |
    TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • HRD (Homologous Recombination Deficiency)
    |
    IDH1 mutation • HRD • IDH1 mutation + Chr del(1p) + Chr del(19q)
    |
    Oncomine™ Comprehensive Assay Plus
    5d
    A Comprehensive Genomic Profiling Solution That Integrates BRCA1/2 Mutational Status and Genomic Instability to Characterize Homologous Recombination Deficiency (AMP 2024)
    We developed a novel method to determine genomic instability for characterizing the consequences of HRD using OCA Plus, which was developed using CGP of cancer FFPE samples to aid research into precision oncology. By combining genomic instability assessment with DNA repair pathway analysis such as mutations in BRCA1/2 and other genes in HRR pathway, OCA Plus will support research into the mechanisms underlying HRD.
    BRCA Biomarker
    |
    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency)
    |
    BRCA2 mutation • BRCA1 mutation • HRD • HRD + BRCA1 mutation
    |
    Oncomine™ Comprehensive Assay Plus
    2ms
    Evaluation of the Oncomine Comprehensive Assay Plus NGS Panel and the OncoScan CNV Assay for Homologous Recombination Deficiency Detection. (PubMed, Mol Diagn Ther)
    The OCA Plus assay and the OncoScan CNV assay show a high but not complete concordance to reference standard homologous recombination deficiency (HRD) detection. The main reason for QC failure or non-concordance in our study was a low tumor fraction estimated in the assay, despite the selection of material by a pathologist with an inclusion criterion of > 30% tumor. QC steps should include careful tumor content evaluation, and results on samples with < 30% tumor should not be reported.
    Journal • PARP Biomarker • BRCA Biomarker • Next-generation sequencing
    |
    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency)
    |
    BRCA2 mutation • BRCA1 mutation • HRD
    |
    OncoScan™ CNV Assay • Oncomine™ Comprehensive Assay Plus
    2ms
    High tumour mutation burden assessed by comprehensive molecular genetic profiling as a targeted therapeutic option for solid tumours (ECP 2024)
    Eight patients received immune checkpoint inhibitor therapy (7 pembrolizumab and 1 atezolizumab). TMB status determined by CGP was found to be an effective method for predicting the response to immune checkpoint inhibitors; both PFS and OS improved markedly for patients who received therapy. In our experience, TMB status, along with microsatellite instability and POLE mutation status, can be used as a predictive biomarker for therapeutic response in a wide range of histologies.
    Tumor mutational burden • PD(L)-1 Biomarker • IO biomarker
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • POLE (DNA Polymerase Epsilon)
    |
    TMB-H • POLE mutation
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Keytruda (pembrolizumab) • Tecentriq (atezolizumab)
    2ms
    Comprehensive molecular genetic profiling: homologous recombination deficiency as a targeted therapeutic option for solid tumours (ECP 2024)
    There was an improvement in OS when patients received PARP inhibitor therapy based on individual scores, although the improvement was more prominent when therapeutic decisions were based on HRD scores. Patients with all histologies, including HGSOC and other histologies, equally benefited from olaparib therapy. We therefore believe that genomically instable non-HGSOC tumours could also benefit from PARP inhibitor therapy, while individual scores could be partly used as a substitute to predict therapeutic response.
    PARP Biomarker
    |
    HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Lynparza (olaparib)
    5ms
    HRD Positivity Rate in Ovarian Cancer Patients (AMP Europe 2024)
    There is new hope for BRCA -negative ovarian cancer patients receiving targeted therapy. Up to 50% of patients could benefit from PARP inhibitor treatment, depending on their HRD status. However, there are important factors to consider when choosing the right test method.
    Clinical • Tumor mutational burden • PARP Biomarker • BRCA Biomarker
    |
    TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • BRCA (Breast cancer early onset)
    |
    AmoyDx® HRD Focus Panel • Oncomine™ Comprehensive Assay Plus
    5ms
    Impact of comprehensive genomic profiling on the diagnosis and clinical management of mesenchymal tumours (ECP 2024)
    In our practice, a significant proportion of patients were prescreened with a smaller NGS panel. Despite this fact, we still found actionable alterations in 23,8% of the patients, which is in line with those reported in the literature (22-61%). Our results demonstrate that CGP can provide useful additional information and can be beneficial in the clinical management of patients with mesenchymal tumours.
    Clinical • Tumor mutational burden • PARP Biomarker • IO biomarker
    |
    TMB (Tumor Mutational Burden) • HRD (Homologous Recombination Deficiency) • MDM2 (E3 ubiquitin protein ligase) • MYOD1 (Myogenic Differentiation 1)
    |
    TMB-H • HRD • CDK4 amplification • MDM2 amplification + CDK4 amplification • CDK4 mutation • High HRD score
    |
    Oncomine™ Comprehensive Assay Plus
    5ms
    Retrospective assessment of the usefulness of comprehensive genomic analysis for identifying targetable therapeutic options for solid tumours (ECP 2024)
    Our study aimed to assess the usefulness of an extended panel from the perspective of targetable mutations in solid tumours. We detected targetable mutations in 8.2% of the patients. However, all the mutations detected in our study are included and therefore detectable by smaller 50 or 160 gene panels, such as Oncomine Focus or Comprehensive Assay v3.
    Retrospective data • Genomic analysis • Omic analysis
    |
    Oncomine Focus Assay • Oncomine™ Comprehensive Assay Plus
    5ms
    FGFR alterations in a contemporary real-world cohort of advanced or metastatic urothelial carcinoma (ECP 2024)
    Based on reflex molecular analysis performed on consecutive advanced/metastatic BCs, we found FGFR alterations to be present in approximately 17% of UCs, with FGFR3 being more frequently altered than FGFR1 and FGFR2 genes. These patients could gain clinical benefits from receiving a FGFR inhibitor such as erdafitinib which is an approved drug to treat FGFR-altered BCs lacking response to chemotherapy. Future studies will include a larger cohort to assess the correlation of FGFR alterations with histologic subtypes of invasive UC.
    Real-world evidence • Clinical • Real-world • Metastases
    |
    FGFR2 (Fibroblast growth factor receptor 2) • FGFR3 (Fibroblast growth factor receptor 3) • FGFR1 (Fibroblast growth factor receptor 1) • FGFR (Fibroblast Growth Factor Receptor)
    |
    FGFR1 amplification • FGFR2 mutation • FGFR2 fusion • FGFR3 mutation • FGFR mutation • FGFR3 fusion
    |
    Oncomine™ Comprehensive Assay v3M • Oncomine™ Comprehensive Assay Plus
    |
    Balversa (erdafitinib)
    5ms
    Comprehensive genomic profiling and immunohistochemical analysis of prepubertal-type testicular neuroendocrine tumours in post pubertal patients reveal a possible relationship with small intestinal neuroendocrine tumours (ECP 2024)
    Immunohistochemistry showed varying degrees of positivity for intestinal markers in our patients. In one patient, we identified a deletion involving chromosome 18q in a region previously described as characteristic of small intestinal neuroendocrine tumours. These findings indicate intestinal differentiation and a possible relationship between these tumours and small intestinal neuroendocrine tumours.
    Clinical
    |
    SMAD4 (SMAD family member 4) • NKX2-1 (NK2 Homeobox 1) • POU5F1 (POU Class 5 Homeobox 1) • CDX2 (Caudal Type Homeobox 2) • SYP (Synaptophysin) • SMAD2 (SMAD Family Member 2)
    |
    SPEN mutation
    |
    Oncomine™ Comprehensive Assay Plus
    6ms
    Harmonization of homologous recombination deficiency testing in ovarian cancer: Results from the MITO16A/MaNGO-OV2 trial. (PubMed, Eur J Cancer)
    Our data suggest the feasibility of commercial testing for assessing HRD status, with a good concordance with the reference method and association with clinical outcome.
    Journal • BRCA Biomarker
    |
    HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)
    |
    Myriad myChoice® CDx • TruSight Oncology 500 Assay • Oncomine™ Comprehensive Assay Plus • SOPHiA DDM HRD Solution • TruSight Oncology 500 HRD Assay
    6ms
    Prognostic genomic signatures in RAS/BRAF mutant (mut) metastatic colorectal cancer (mCRC) patients (pts) from the phase II study of NIVolumab (niv) plus FOLFOXIRI/Bevacizumab (bev) in first-line therapy of Advanced COloRectal cancer (NIVACOR- GOIRC-03-2018) (ESMO-GI 2024)
    These preliminary data suggest that CGP may identify prognostic genomic alterations in BRAF/RAS mut MSS mCRC pts receiving immune checkpoint inhibitors.
    P2 data • Clinical • Tumor mutational burden • PD(L)-1 Biomarker • IO biomarker • Metastases
    |
    BRAF (B-raf proto-oncogene) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • IFNG (Interferon, gamma)
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Opdivo (nivolumab) • Avastin (bevacizumab) • 5-fluorouracil • oxaliplatin • irinotecan • leucovorin calcium
    6ms
    Positive hyperselection of sensitizing genomic alterations (GAs) in RAS/BRAF wild-type (wt) metastatic colorectal cancer (mCRC) patients (pts) from the phase III study of first-line FOLFIRI/cetuximab versus FOLFIRI/cetuximab followed by cetuximab (Cet) alone (ERMES) (ESMO-GI 2024)
    These preliminary data suggest that CGP of RAS/BRAF wt mCRC pts receiving first-line anti-EGFR based therapy may allow hyperselection of patients with better prognosis.
    P3 data • Clinical • Metastases
    |
    BRAF (B-raf proto-oncogene) • RAS (Rat Sarcoma Virus) • SMAD2 (SMAD Family Member 2)
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Erbitux (cetuximab) • 5-fluorouracil • irinotecan • leucovorin calcium
    7ms
    Longitudinal outcomes of obeticholic acid therapy in ursodiol-nonresponsive primary biliary cholangitis: Stratifying the impact of add-on fibrates in real-world practice. (PubMed, Aliment Pharmacol Ther)
    Triple therapy was superior in achieving therapeutic goals in UDCA-nonresponsive PBC. Decompensation was linked to pre-existing portal hypertension.
    Journal • Real-world evidence • Real-world
    |
    Oncomine™ Comprehensive Assay Plus
    7ms
    Effect of plasma-based molecular testing in patients with newly diagnosed advanced NSCLC on initiation of targeted agents in patients with targetable genomic alterations: A real world experience from the Middle East. (ASCO 2024)
    Though our TAT for ct-DNA and tissue based NGS testing was similar, ct-DNA based NGS testing enables earlier initiation of targeted treatment for newly diagnosed advanced NSCLC patients with targetable mutations. In the real world, this increases access to targeted agents and may translate to a subsequent improvement in survival outcomes.
    Real-world evidence • Clinical • IO biomarker • Real-world • Metastases
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    Oncomine™ Comprehensive Assay Plus
    7ms
    Molecular profiling using next generation sequencing with high-purity enrichment of circulating tumor cells. (ASCO 2024)
    Molecular analysis of CTCs is a challenge since CTCs are very rare in the blood and there are technical limitations in isolating CTCs with sufficient purity for NGS analysis. In this study, we developed the process for NGS analysis on very small number of high-purity CTCs using CytoGen's Smart Biopsyâ„¢ System. Taken together with the results from our ongoing clinical trials, this process could provide information for the diagnosis and appropriate treatment of breast cancer and NSCLC patients.
    Circulating tumor cells • Next-generation sequencing • Tumor cell
    |
    KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • NF2 (Neurofibromin 2) • NOTCH3 (Notch Receptor 3) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C)
    |
    Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine™ Comprehensive Assay Plus
    7ms
    Prognostic genomic signatures in patients with RAS and BRAF wild-type (wt) metastatic colorectal cancer (mCRC) from the phase III study of first-line FOLFIRI/cetuximab versus FOLFIRI/cetuximab followed by cetuximab (Cet) alone (ERMES study). (ASCO 2024)
    These preliminary data suggest that CGP of mCRC patients can identify prognostic genomic signatures, which might allow a better stratification of patients and the identification of subgroups that might benefit a treatment de-escalation strategy.
    P3 data • Clinical • Metastases
    |
    HER-2 (Human epidermal growth factor receptor 2) • BRAF (B-raf proto-oncogene) • FGFR4 (Fibroblast growth factor receptor 4) • RAS (Rat Sarcoma Virus) • IL13 (Interleukin 13) • IL4 (Interleukin 4) • SMAD2 (SMAD Family Member 2)
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Erbitux (cetuximab) • 5-fluorouracil • irinotecan • leucovorin calcium
    8ms
    Prediction of homologous recombination deficiency from Oncomine Comprehensive Assay Plus correlating with SOPHiA DDM HRD Solution. (PubMed)
    The Oncomine Comprehensive Assay Plus provides a reliable biomarker for homologous recombination deficiency.
    Journal • PARP Biomarker
    |
    Oncomine™ Comprehensive Assay Plus • SOPHiA DDM HRD Solution
    9ms
    Molecular profiling using next generation sequencing with high purity enrichment of circulating tumor cells (AACR 2024)
    Molecular analysis of CTCs is a challenge since CTCs are very rare in the blood and there are technical limitations in isolating CTCs with sufficient purity. In this study, we developed the process for NGS analysis on very low number of CTCs with high purity, isolated using CytoGen's Smart Biopsyâ„¢ system. Overall, these process could provide information for diagnosis and appropriate treatment of metastatic breast cancer along with the results of our ongoing clinical trials.
    Circulating tumor cells • Next-generation sequencing • Tumor cell
    |
    KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • NF2 (Neurofibromin 2) • NOTCH3 (Notch Receptor 3) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C)
    |
    TP53 mutation • KRAS mutation • BRAF mutation • NF2 mutation • NOTCH3 mutation
    |
    Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine™ Comprehensive Assay Plus
    9ms
    EGFR Sensitive Non-Small Cell Lung Cancer with and without EGFR Amplification Show Similar Sensitivity to First Line Osimertinib. Acquired EGFR Amplification is Rare but Presents a Potential Therapeutic Pitfall without Close Analysis of Next Generation Sequencing Results (USCAP 2024)
    These results demonstrate that EGFR amplification in a first-line setting retains sensitivity to the standard of care, osimertinib. Caution should be exhibited when assessing new EGFR amplification for therapeutic decisions, especially when the original biopsy was of poor quality. False negative findings of gene amplification due to low tumor cellularity are known phenomenon in NGS testing.
    Clinical • Next-generation sequencing
    |
    EGFR (Epidermal growth factor receptor)
    |
    EGFR mutation • EGFR amplification • EGFR wild-type
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Tagrisso (osimertinib)
    9ms
    Homologous Recombinant Deficiency Does Not Share Morphologic Surrogates of BRCA-mutated High-Grade Serous Carcinoma (USCAP 2024)
    BRCA mutation is one cause of HRD and appears that SET morphology associated with HGSC is unique to BRCA-mutation and not under the umbrella of other causes and effects of HRD. HRD in HGSC may produce its own molecular surrogate that is yet to be discovered. Definitive determination of which platform is superior for clinical validation of HRD assessment as a surrogate to Myriad MyChoiceDX gold standard requires matched analysis against Myriad and patient's progression free survival.
    BRCA Biomarker
    |
    HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)
    |
    HRD • BRCA wild-type • BRCA mutation
    |
    Myriad myChoice® CDx • Oncomine™ Comprehensive Assay Plus
    9ms
    Harmonization of tumor mutation burden testing with comprehensive genomic profiling assays: an IQN Path initiative. (PubMed, J Immunother Cancer)
    This study estimated TMB cut-off values for commercially available CGP panels. The results showed a good performance of all panels on clinical samples and the calculated cut-offs support better accuracy measures for TSO500. The validated cut-off values can drive clinical interpretation of TMB testing in clinical research and clinical practice.
    Journal • Tumor mutational burden • IO biomarker
    |
    TMB (Tumor Mutational Burden)
    |
    FoundationOne® CDx • TruSight Oncology 500 Assay • Oncomine™ Comprehensive Assay Plus
    10ms
    Unveiling The Clinical Impact Of Tumor-Based Next-Generation Sequencing In Ovarian Cancer: Insights From Real-World Data (ESGO 2024)
    Conclusion Tumor-based NGS frequently provides clinically significant information. It holds the potential to reveal specific therapeutic targets and contribute to clinical decision-making
    Real-world evidence • Clinical • Next-generation sequencing • Real-world
    |
    FoundationOne® CDx • Oncomine™ Comprehensive Assay v3M • Oncomine™ Comprehensive Assay Plus
    12ms
    Genomic alteration in sporadic adolescent and young adult-onset colorectal adenocarcinoma. (ASCO-GI 2024)
    This study is the comprehensive report hotspot mutations using NGS in sporadic AYA-onset sporadic CRC patients. The most commonly identified gene mutation frequencies among AYA-onset were similar to those reported in adult-onset, except for FBXW7, PIK3CA, NOTCH1, FGFR3, ERBB2, and PTEN mutations that had a slightly higher frequency. Further studies on larger sample set for genetic and epigenetic landscape are required.
    Clinical
    |
    HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • NRAS (Neuroblastoma RAS viral oncogene homolog) • PTEN (Phosphatase and tensin homolog) • FGFR3 (Fibroblast growth factor receptor 3) • NOTCH1 (Notch 1) • SMAD4 (SMAD family member 4) • FBXW7 (F-Box And WD Repeat Domain Containing 7)
    |
    TP53 mutation • KRAS mutation • BRAF mutation • NRAS mutation • PIK3CA mutation • HER-2 mutation • PTEN mutation • SMAD4 mutation
    |
    Oncomine™ Comprehensive Assay Plus
    1year
    Comprehensive Genomic Profiling of Early Hormone Receptor Positive Breast Cancer Reveals Diverse Genomic Alterations (AMP 2023)
    In a retrospective analysis, we used comprehensive genomic profiling in the well-studied early-stage HR+ BC Tamoxifen and Exemestane Adjuvant Multinational (TEAM) trial cohort to characterize genomic alterations that contribute to oncogenesis and may drive recurrence. The genomic landscape of early HR+ BC is diverse and contains many actionable alterations. In addition to activating mutations in well-known BC associated oncogenes, the landscape included high-level CN gain in several RTK genes. The relatively high level of aneuploidy in early-stage HR+ BC was unanticipated and associated with poor risk.
    Tumor mutational burden
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • FGFR2 (Fibroblast growth factor receptor 2) • FGFR1 (Fibroblast growth factor receptor 1) • CDH1 (Cadherin 1) • POLD1 (DNA Polymerase Delta 1) • MAP3K1 (Mitogen-Activated Protein Kinase Kinase Kinase 1) • GATA3 (GATA binding protein 3)
    |
    TP53 mutation • TMB-H • HR positive • HER-2 negative • PIK3CA mutation • POLD1 mutation
    |
    Oncomine™ Comprehensive Assay Plus
    |
    tamoxifen • exemestane
    1year
    Molecular Profiling and Human Papillomavirus Identification of Digital Papillary Adenocarcinoma (ASDP 2023)
    POLE mutations frequently occurred in DPA and their clinical significance and association with low-risk HPV in DPA warrants further investigation. Poster type: Poster Defense
    TP53 (Tumor protein P53) • NF1 (Neurofibromin 1) • POLE (DNA Polymerase Epsilon)
    |
    POLE mutation
    |
    Oncomine™ Comprehensive Assay Plus
    1year
    Biomarker Assessment Through Comprehensive Genomic Profiling (AMP 2023)
    In this workshop, hear how one research laboratory is leveraging the Oncomine Comprehensive Assay Plus (OCA+) to perform CGP in-house. Additionally, see results from a multi-site study evaluating performance of OCA+ across several parameters.
    Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    Oncomine™ Comprehensive Assay Plus
    1year
    Next generation sequencing of breast cancer in the neoadjuvant setting. (PubMed, Pathobiology)
    This study showcases the significance of employing comprehensive genomic testing in breast cancer cases, primarily due to the scarcity of specific target assays. The detection of somatic mutations, coupled with the availability of targeted therapies, holds promise as a potential therapeutic avenue to enhance tumor response rates during NAT, or as a complementary treatment following surgery. Moreover, evaluating the TMB in non-pCR samples could serve as a valuable criterion for selecting patients suitable for immunotherapy. Further exploration through clinical trials is imperative to investigate these prospects.
    Journal • Tumor mutational burden • BRCA Biomarker • IO biomarker • Next-generation sequencing
    |
    HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • MET (MET proto-oncogene, receptor tyrosine kinase) • BRCA1 (Breast cancer 1, early onset) • BRCA (Breast cancer early onset)
    |
    TP53 mutation • BRCA mutation
    |
    Oncomine™ Comprehensive Assay Plus
    over1year
    Identification of 'secondary' germline cancer predisposition variants from somatic tumour testing: Should we evolve towards universal screening? (ESMO 2023)
    Detected germline mutations included high penetrance cancer predisposing genes as BRCA1. This detection rate reflects the clinical utility, for patients and their families, of using the somatic genomic analysis as a source of information about a potential hereditary cancer predisposition syndrome.
    BRCA Biomarker
    |
    BRCA1 (Breast cancer 1, early onset) • PMS2 (PMS1 protein homolog 2) • MUTYH (MutY homolog)
    |
    BRCA1 mutation
    |
    Oncomine™ Comprehensive Assay Plus
    over1year
    Multicentric evaluation of amplicon-based next-generation sequencing solution for local comprehensive molecular tumor profiling (ESMO 2023)
    The high concordance rate with orthogonal methods highlights the assay's potential in guiding clinical decision-making for personalized cancer care. OCA+ may provide comprehensive genomic information for cancer management and may be a valuable tool for further implementing precision medicine in oncology.
    Clinical • Tumor mutational burden • Next-generation sequencing
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)
    |
    Oncomine™ Comprehensive Assay Plus
    over1year
    Diagnosis of Metastatic SHH-Activated Medulloblastoma in Adult via Bone Biopsy and Next- Generation Sequencing (AMP Europe 2023)
    "NGS can play a pivotal role in providing a definitive diagnosis and guide therapeutic efforts in central nervous system tumors."
    Clinical
    |
    TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • MYCN (MYCN Proto-Oncogene BHLH Transcription Factor) • PTCH1 (Patched 1) • KDM6A (Lysine Demethylase 6A)
    |
    TP53 mutation • TP53 wild-type • PIK3CA E545K • PTCH1 mutation • PIK3CA E545
    |
    Oncomine™ Comprehensive Assay Plus
    |
    temozolomide • Erivedge (vismodegib)
    over1year
    Next-Generation Sequencing-Guided Therapy for BRAF V600E Mutant Glioblastoma Results in Stable Disease (AMP Europe 2023)
    "The patient underwent a standard post-operative treatment with radiation and 12 cycles of temozolomide...Given the presence of BRAF V600E mutation, the patient was started on dabrafenib 150mg BID and trametinib 2mg (10/07/2022). NGS can provide useful data for successful targeted therapy of patients with GBM."
    Clinical
    |
    PD-L1 (Programmed death ligand 1) • BRAF (B-raf proto-oncogene) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • TERT (Telomerase Reverse Transcriptase) • SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1)
    |
    PD-L1 expression • BRAF V600E • BRAF V600 • TERT mutation • IDH wild-type • TERT promoter mutation
    |
    Oncomine™ Comprehensive Assay Plus
    |
    Mekinist (trametinib) • Tafinlar (dabrafenib) • temozolomide
    over1year
    Molecular Characteristics of a C11orf95-RELA Fusion Gliosarcoma: A Case Report (AMP Europe 2023)
    In this report we present an extremely rare case of C11orf95-RELA fusion supratentorial ependymoma that underwent a complete sarcomatous transformation. The presence of C11orf95-RELA fusion in this case highlights the importance of considering the diagnosis of ependymoma in sarcomatous brain tumors and of performing unbiased molecular studies in these cases. Importantly, this report sheds light on key biological and evolutionary aspects of this rare tumor, such as an aberrant overactivation of the RAS/RAF/MAPK signaling pathway.
    Clinical
    |
    TP53 (Tumor protein P53) • HRAS (Harvey rat sarcoma viral oncogene homolog) • NF1 (Neurofibromin 1) • BCOR (BCL6 Corepressor) • STAG2 (Stromal Antigen 2) • GFAP (Glial Fibrillary Acidic Protein) • RELA (RELA Proto-Oncogene) • ZFTA (Zinc Finger Translocation Associated)
    |
    TP53 mutation • NF1 mutation • HRAS mutation • STAG2 mutation • IDH wild-type
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    Oncomine™ Comprehensive Assay Plus
    over1year
    Exploring the use of Genomic Instability Metric (GIM) to determine Homologous Recombination Deficiency (HRD) in cancer (EACR 2023)
    Acknowledgements: NSF, MES: D01-395/18.12.2020, D01-278-14.12. 2022, D01-302/17.12.2021, D01 165/28.07.2022; KP-06-OPR03/1719.12.2018/NSF
    Tumor mutational burden • PARP Biomarker • MSi-H Biomarker • BRCA Biomarker
    |
    TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)
    |
    BRCA2 mutation • BRCA1 mutation • TMB-H • MSI-H/dMMR • HRD • TMB-L • HRD + BRCA1 mutation
    |
    Oncomine™ Comprehensive Assay Plus
    over1year
    The determination of Homologous Recombination Deficiency by comprehensive genomic profiling panel associates with clinical outcome in Ovarian Cancer patients. (EACR 2023)
    HRD status determined with both assays was associated to Progression-Free Survival (PFS) after first line bevacizumab and platinum-based therapy and Overall Survival (OS) in univariate and multivariate analysis.Results and DiscussionsHRD status obtained by OCA was compared with the reference Myriad assay in 86/97 samples for which both test results were available...In univariate analysis for OS, OCA was prognostic (HR=0.44, p=0.016) but not Myriad (HR 0.71, P=0,3). Multivariate analysis for OS was not performed due to low number of events.ConclusionThese data suggest the feasibility of OCA testing for assessing HRD status, with a good concordance with the gold standard assay and association with clinical outcome.
    Clinical data • Clinical • PARP Biomarker • BRCA Biomarker
    |
    HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)
    |
    HRD • BRCA mutation
    |
    Myriad myChoice® CDx • Oncomine™ Comprehensive Assay Plus
    |
    Avastin (bevacizumab)
    over1year
    Multicentric prospective study assessing clinical benefit of targeted treatment for patients with biliary tract cancers (ESMO-GI 2023)
    Targeted therapy was actually started for 95 pts (16%), with 15 (16%) pts treated with ivosidenib for IDH1 mutations, 63 (66%) with FGFR2 inhibitors for FGFR2 alterations, 3 (3%) with immune checkpoint inhibitors (ICIs) for MSI-H, 9 (10%) with BRAF+MEK inhibitors for BRAFV600E mutations and 4 (4%) with HER2 inhibitors for HER2 amplification... NGS is feasible in daily clinical practice and it should be performed, as recommended, for all pts affected by advanced BTC, since biomarker-directed treatment for BTCs has clinically meaningful benefit in pretreated patients.
    Clinical • MSi-H Biomarker • IO biomarker
    |
    MSI (Microsatellite instability) • FGFR2 (Fibroblast growth factor receptor 2) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1)
    |
    BRAF V600E • MSI-H/dMMR • HER-2 amplification • BRAF V600 • IDH1 mutation • FGFR2 mutation
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    FoundationOne® CDx • Archer® FusionPlex® Oncology Research Kit • Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine™ Comprehensive Assay Plus
    |
    Tibsovo (ivosidenib)
    over1year
    Fully automated comprehensive genomic profiling for detection of cancer variants, gene fusions, and complex oncology endpoints (AACR 2023)
    The Genexus System combines minimal touch points and a rapid turnaround time to enable comprehensive genomic profiling for research assays such as OCA Plus for detection of rare variants and low-level fusion transcripts. Further, by providing accurate characterization of key oncology research endpoints, the Genexus System can accelerate research in oncology. For research use only.
    Tumor mutational burden
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    HER-2 (Human epidermal growth factor receptor 2) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • HRD (Homologous Recombination Deficiency)
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    HER-2 amplification
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    Oncomine™ Comprehensive Assay Plus
    almost2years
    Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment. (PubMed, J Pers Med)
    A total of 100% of the variants in the diagnostic samples and 80% of the variants in the AcroMetrix™ assessment sample were detected by both panels, and the panels reported highly similar variant allele frequency. A proportion of 14/19 (74%) samples were classified in the same TMB category; (4) Comparable results were obtained using OCAP and TSO500, suggesting that both panels could be applied to screen patients for enrolment in personalized cancer treatment trials.
    Journal • Tumor mutational burden
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    TMB (Tumor Mutational Burden)
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    TruSight Oncology 500 Assay • Oncomine™ Comprehensive Assay Plus
    almost2years
    Next-Generation Sequencing (NGS) of Multivergent Morphologies in Colorectal Carcinomas (CRCs) Identifies Unique Targetable Alterations (USCAP 2023)
    Multivergent morphology is rare in CRC but is highly predictive of the presence of targetable molecular alterations. In such cases, NGS of multiple areas with different morphology may identify potential therapeutic targets that would otherwise be missed. While most cases have recognizable driver alterations, the less common targetable alterations frequently identified in these cases could open up additional trial options for salvage therapy.
    Tumor mutational burden • MSi-H Biomarker • BRCA Biomarker • IO biomarker • Next-generation sequencing
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    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • FGFR2 (Fibroblast growth factor receptor 2) • PTEN (Phosphatase and tensin homolog) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • DNMT3A (DNA methyltransferase 1) • ARID1A (AT-rich interaction domain 1A) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha) • NF1 (Neurofibromin 1) • JAK2 (Janus kinase 2) • POLE (DNA Polymerase Epsilon) • GNAQ (G Protein Subunit Alpha Q) • RUNX1 (RUNX Family Transcription Factor 1) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • PALB2 (Partner and localizer of BRCA2) • KMT2A (Lysine Methyltransferase 2A) • BCL6 (B-cell CLL/lymphoma 6) • TET2 (Tet Methylcytosine Dioxygenase 2) • TOP2A (DNA topoisomerase 2-alpha) • ETV6 (ETS Variant Transcription Factor 6) • MLH1 (MutL homolog 1) • KMT2D (Lysine Methyltransferase 2D) • PTCH1 (Patched 1) • SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily A, member 4) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • RNF43 (Ring Finger Protein 43) • CDK12 (Cyclin dependent kinase 12) • SMAD4 (SMAD family member 4) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • KMT2C (Lysine Methyltransferase 2C) • PMS2 (PMS1 protein homolog 2) • WT1 (WT1 Transcription Factor) • ATRX (ATRX Chromatin Remodeler) • B2M (Beta-2-microglobulin) • CDH1 (Cadherin 1) • CHEK2 (Checkpoint kinase 2) • CREBBP (CREB binding protein) • SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1) • BCOR (BCL6 Corepressor) • FAT1 (FAT atypical cadherin 1) • PIK3R1 (Phosphoinositide-3-Kinase Regulatory Subunit 1) • RBM10 (RNA Binding Motif Protein 10) • RAD51C (RAD51 paralog C) • RAD50 (RAD50 Double Strand Break Repair Protein) • GLI1 (GLI Family Zinc Finger 1) • PIK3CB (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) • STAG2 (Stromal Antigen 2) • CUL4A (Cullin 4A) • EP300 (E1A binding protein p300) • IL7R (Interleukin 7 Receptor) • RAD51D (RAD51 paralog D) • RICTOR (RPTOR Independent Companion Of MTOR Complex 2) • SETBP1 (SET Binding Protein 1) • ARID2 (AT-Rich Interaction Domain 2) • MSH3 (MutS Homolog 3) • NOTCH4 (Notch 4) • GNAS (GNAS Complex Locus) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • NCOR1 (Nuclear Receptor Corepressor 1) • PIM1 (Pim-1 Proto-Oncogene) • CASP8 (Caspase 8) • PPM1D (Protein Phosphatase Mg2+/Mn2+ Dependent 1D) • PPP2R2A (Protein Phosphatase 2, Regulatory Subunit B, Alpha) • DICER1 (Dicer 1 Ribonuclease III) • FANCM (FA Complementation Group M) • KMT2B (Lysine Methyltransferase 2B) • POT1 (Protection of telomeres 1) • PRDM1 (PR/SET Domain 1) • AMER1 (APC Membrane Recruitment Protein 1) • CHD4 (Chromodomain Helicase DNA Binding Protein 4) • CSMD3 (CUB And Sushi Multiple Domains 3) • FANCD2 (FA Complementation Group D2) • LATS1 (Large Tumor Suppressor Kinase 1) • TAP1 (Transporter 1) • ACVR2A (Activin A Receptor Type 2A) • CUL4B (Cullin 4B) • DSC1 (Desmocollin 1) • MAP2K4 (Mitogen-Activated Protein Kinase Kinase 4) • RASA1 (RAS P21 Protein Activator 1) • SLX4 (SLX4 Structure-Specific Endonuclease Subunit) • USP9X (Ubiquitin Specific Peptidase 9 X-Linked)
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    TMB-H • MSI-H/dMMR • POLE mutation • RNF43 mutation • PMS2 mutation
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    Oncomine™ Comprehensive Assay Plus
    almost2years
    Characterization of Homologous Recombination Deficiency-Associated Pancreatic Ductal Adenocarcinoma Using Oncomine Comprehensive Assay Plus NGS-Based Cancer Panel (USCAP 2023)
    In contrast to 14.5-16.5% through NGS panels and 24-44% through WES or WGS reported in the literatures, our HRD assessment using Oncomine Plus NGS-based cancer panel revealed a high prevalence of 33% in our PDAC cohort, suggesting NGS-based panel method could be a potential powerful tool for HRD estimate. Interestingly, our HRD-associated PDAC cohort showed a different distribution of concurrent variants compared to TCGA PDAC, which might be suggestive of the biologic differences between HRD-associated PDAC cohort and non-HRD-associated PDAC cohort.
    Tumor mutational burden • PARP Biomarker • MSi-H Biomarker • BRCA Biomarker • Next-generation sequencing
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    KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • ATM (ATM serine/threonine kinase) • HRD (Homologous Recombination Deficiency) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • ARID1A (AT-rich interaction domain 1A) • PALB2 (Partner and localizer of BRCA2) • RNF43 (Ring Finger Protein 43) • CDK12 (Cyclin dependent kinase 12) • SMAD4 (SMAD family member 4) • CHEK2 (Checkpoint kinase 2) • RAD51 (RAD51 Homolog A) • FANCA (FA Complementation Group A) • RAD51B (RAD51 Paralog B) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD50 (RAD50 Double Strand Break Repair Protein) • RAD51D (RAD51 paralog D) • CHEK1 (Checkpoint kinase 1) • BARD1 (BRCA1 Associated RING Domain 1) • MRE11A (MRE11 homolog, double strand break repair nuclease) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • RAD54L (DNA Repair And Recombination Protein RAD54) • FANCF (FA complementation group F) • FANCL (FA Complementation Group L) • HDAC2 (Histone deacetylase 2) • FANCD2 (FA Complementation Group D2) • FANCE (FA Complementation Group E) • FANCC (FA Complementation Group C)
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    KRAS mutation • TMB-H • MSI-H/dMMR • HRD • KRAS Q61H
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    Oncomine™ Comprehensive Assay Plus
    almost2years
    Molecular Landscape of Hepatocellular Carcinoma (HCC) and the Recurrence Risk Assessment Score (RRAS): Correlating Molecular Signatures to RRAS (USCAP 2023)
    HCCs with RRAS of 4 were more likely to harbor TP53 alterations and those with scores of <4 were more likely to have CTNNB1 alterations, though neither alteration seems to correlate with recurrence. Conversely, higher accumulation of genetic and chromosomal gains and losses were associated with recurrence and not RRAS. In the setting of a cohort with demonstrated concordance between RRAS of 4 and recurrence, the lack of significant association with molecular findings suggests that RRAS may be a prognostic factor independent of molecular typing.
    TP53 (Tumor protein P53) • TERT (Telomerase Reverse Transcriptase) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)
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    TERT mutation • TERT promoter mutation
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    Oncomine™ Comprehensive Assay Plus
    almost2years
    Somatic Genomic Alteration Prevalence and Association with Tumor Grade Reclassification in Prostate Cancer Patients Undergoing Active Surveillance (USCAP 2023)
    We provide a first assessment of somatic genomic alterations in PCa in a large multi-institutional cohort of patients on active surveillance. Potentially owing to the low prevalence of pathogenic genomic alterations (7.9%), no association between pathogenic genomic alterations and grade reclassification was identified.
    Clinical • BRCA Biomarker
    |
    TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • PTEN (Phosphatase and tensin homolog) • FGFR1 (Fibroblast growth factor receptor 1) • ATM (ATM serine/threonine kinase) • CHEK2 (Checkpoint kinase 2) • SPOP (Speckle Type BTB/POZ Protein) • APEX1 (Apurinic/Apyrimidinic Endodeoxyribonuclease 1)
    |
    BRCA2 mutation • BRCA1 mutation • ATM mutation • FGFR1 amplification
    |
    Oncomine™ Comprehensive Assay Plus