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    TEST:
    OncoScan™ CNV Assay

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

    News

    1m
    Diagnostic and Clinical Utility of OncoScan Microarray and NGS-Based Sequencing in Pediatric Solid Tumors: Children's Mercy Hospital Experience (AMP 2024)
    OS+ is a reliable test to identify clinically relevant genomic alterations, cnLOH, and several hotspot mutations in pediatric FFPE solid tumor specimens. WGS/WES significantly increases the yield of actionable somatic mutations and cancer-predisposing germline variants. The cost, turnaround time, and tumor percentage in the specimen make OS+ followed by WES principal tests for pediatric solid tumor analysis at our institution.
    Clinical • Next-generation sequencing
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    EGFR (Epidermal growth factor receptor) • 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) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NF1 (Neurofibromin 1) • MLH1 (MutL homolog 1) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1) • H3-3A (H3.3 Histone A)
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    TP53 mutation • BRAF V600E • KRAS mutation • EGFR mutation • PIK3CA mutation • BRAF V600 • PTEN mutation • BRAF fusion
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    OncoScan™ CNV Assay
    1m
    Novel Nanopore-Based Copy Number Analysis for Ultrafast Renal Tumor Classification (AMP 2024)
    In this study, we applied the iSCORED pipeline for ultrafast, genome-wide CNV information of renal tumors with results showing complete concordance with established CNV analysis methods. This method could facilitate pathological diagnosis and potentially inform targeted treatment in less than 2 hours. Future directions include expanding analyzed tumor types and integrating methylation classification into the pipeline.
    OncoScan™ CNV Assay • TruSight Tumor 170 Assay
    3ms
    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
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    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency)
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    BRCA2 mutation • BRCA1 mutation • HRD
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    OncoScan™ CNV Assay • Oncomine™ Comprehensive Assay Plus
    5ms
    Genomic Insights into High-Grade Infarct-Associated Bone Sarcomas. (PubMed, Mod Pathol)
    These results suggest that high-grade infarct-associated sarcomas of bone, while sharing high levels of structural variations with osteosarcoma, may exhibit potentially less frequent TP53 mutations and more common CDKN2A/B deletions. This points to the possibility that the mutation spectrum and disrupted pathways could be distinct from conventional osteosarcoma.
    Journal • Tumor mutational burden • IO biomarker
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    TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • HRD (Homologous Recombination Deficiency) • HRAS (Harvey rat sarcoma viral oncogene homolog) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • DNMT3A (DNA methyltransferase 1) • MDM2 (E3 ubiquitin protein ligase) • CDKN2B (Cyclin Dependent Kinase Inhibitor 2B) • H3-3A (H3.3 Histone A)
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    TruSight Oncology 500 Assay • OncoScan™ CNV Assay
    5ms
    Genomic instability as a biomarker for advanced cancer of the head and neck (ESMO 2024)
    Genomic instability score based on SNP array copy number alterations profile is associated with worse prognosis in patients with carcinoma of the head and neck. Higher GIS score is found in squamous cell carcinomas and is associated with mutations in genes involved in cell cycle control.
    Metastases
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    TP53 (Tumor protein P53)
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    OncoScan™ CNV Assay
    5ms
    Comparison of microarray and next-generation sequencing-based approaches for detection of homologous recombination deficiency (ESMO 2024)
    The Applied BiosystemsTM OncoScanTM CNV Plus Assay for Research offers a reliable and cost-effective alternative to NGS-based approaches for detection of HRD and can contribute to expanding access to HRD testing for cancer research.
    Next-generation sequencing • PARP Biomarker
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    HRD (Homologous Recombination Deficiency)
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    HRD
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    OncoScan™ CNV Assay • OncoScan™ CNV Plus Assay
    8ms
    Genomic instability in advanced non-small cell lung cancer (NSCLC) treated with maintenance durvalumab in the UNICANCER SAFIR02-Lung/ IFCT1301 trial. (ASCO 2024)
    Genomic instability score based on CGH array-based copy number alterations profile is associated with worse PFS and OS in patients under response to chemotherapy who received durvalumab maintenance.
    Clinical • PD(L)-1 Biomarker • IO biomarker • Metastases
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    PD-L1 (Programmed death ligand 1)
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    OncoScan™ CNV Assay
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    Imfinzi (durvalumab)
    10ms
    Exploiting somatic oncogenic driver alterations in a patient with Li-Fraumeni-Syndrome – Paving the path towards precision medicine (DKK 2024)
    A homozygous loss of 9p21, harboring the CDKN2A gene locus, was identified, providing rationale for a treatment with CDK4/6 inhibitor Palbociclib...OncoScan analysis of this ovarian cancer revealed copy number loss of the BRCA2 gene locus in 13q and a targeted therapy with the PARP-inhibitor Olaparib was initiated recently... Early case evaluation by a multidisciplinary MoFa is critical to increase the awareness of molecular profiling and targeted therapies in patients with CSDs.
    Clinical • PARP Biomarker • BRCA Biomarker
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    TP53 (Tumor protein P53) • BRCA2 (Breast cancer 2, early onset) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A)
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    OncoScan™ CNV Assay
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    Lynparza (olaparib) • Ibrance (palbociclib)
    11ms
    Changes in HRD status during treatment for ovarian high-grade serous carcinoma (SGO 2024)
    This study demonstrates that cases identified as having HRD based on tumor tissue analysis prior to chemotherapy can be identified as not having HRD when tumor tissue collected at the time of IDS is examined. When testing for HRD, it should be recognized that this may change during the course of treatment.
    BRCA Biomarker
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    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)
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    BRCA2 mutation • BRCA1 mutation • HRD • HRD + BRCA1 mutation • BRCA mutation
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    OncoScan™ CNV Assay
    1year
    Moving towards homologous recombination deficiency (HRD) analysis standardization: evaluation of reference materials across leading HRD assays (AMP 2023)
    "We developed the Seraseq HRD reference materials to meet the needs of laboratories looking to analyze HRD in cancer patient samples. The HRD status of each material was evaluated using several assays using different measurement approaches. Although the materials showed similar trends and concordance among formats, there was variability in GIS across the methods tested."
    ATM (ATM serine/threonine kinase) • HRD (Homologous Recombination Deficiency) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD51D (RAD51 paralog D)
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    HRD
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    TruSight Oncology 500 Assay • AmoyDx® HRD Focus Panel • OncoScan™ CNV Assay • TruSight Oncology 500 HRD Assay
    1year
    Deletions of CDKN2A and MTAP Detected by Copy-Number Variation Array Are Associated with Loss of p16 and MTAP Protein in Pleural Mesothelioma. (PubMed, Cancers (Basel))
    Both p16 and MTAP IHC showed high concordance with Oncoscan CNV arrays (kappa = 0.952, p < 0.0001, and kappa = 0.787, p < 0.0001 respectively). We recommend combined MTAP and p16 immunohistochemistry to confirm the diagnosis of PM.
    Journal
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    CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • MTAP (Methylthioadenosine Phosphorylase)
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    CDKN2A deletion • MTAP deletion • MTAP negative
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    OncoScan™ CNV Assay
    1year
    RediScore: Prospective validation of a pipeline for homologous recombination deficiency analysis. (PubMed, Oncol Lett)
    "GIS was positive in 40% of the BRCA1/2-negative cases. The RediScore bioinformatics algorithm developed for GIS calculation in combination with NGS BRCA1/2 analysis is a viable and effective approach for HRD calculation in patients with ovarian cancer, offering a positive prediction for PARP inhibitor responsiveness in 55% of the patients."
    Journal
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    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)
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    HRD • HRD + BRCA1 mutation • BRCA mutation
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    Myriad myChoice® CDx • OncoScan™ CNV Assay • Oncomine™ BRCA Research Assay
    over1year
    Molecular Analysis Of BRCA And HRD Status From Small Biopsies In High Grade Serous Carcinoma. A Real-World Comparative Analysis. (ESGO 2023)
    sBRCA and HRD analysis from SES was successful in 88% and 96% of samples and there were no differences regarding the timing of surgery or NACT. Conclusion Careful planning of UGB and stepwise tissue diagnosis with respect to influencing factors can increase the success rate of genomic analyses in HGSOC and could be a feasible alternative to SES.
    Real-world evidence • Clinical • Real-world • Biopsy
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    HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)
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    HRD
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    OncoScan™ CNV Assay • Oncomine™ BRCA Research Assay
    over1year
    Using Chromosome Microarray to Resolve Difficult ERBB2 FISH Results: Example Cases (AMP Europe 2023)
    CMA can help us understand and resolve challenging ERBB2 results. Further studies are warranted to examine the utility of CMA in facilitating ERBB2 testing, especially in cases with unusual results.
    Clinical
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    HER-2 (Human epidermal growth factor receptor 2) • TYK2 (Tyrosine Kinase 2)
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    HER-2 amplification
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    PathVysion HER-2 DNA Probe Kit • OncoScan™ CNV Assay
    over1year
    The application of a multigene NGS assay in homologous recombination deficiency tracking. (ASCO 2023)
    A high rate of HR mutations was detected in ovarian, breast and prostate which is consistent with the PARPi approval in these tumor types. The presence of BRCA1/2 mutations was highly associated with increased LOH value whereas it did not correlate to other HR mutations. Additionally, the pancancer presence of HR gene alterations indicates that the use of such genes as biomarkers of platinum and PARPi treatments should be evaluated in a wider range of tumor types.
    Tumor mutational burden • PARP Biomarker • BRCA Biomarker • IO biomarker • Next-generation sequencing
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    KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • HRD (Homologous Recombination Deficiency) • ARID1A (AT-rich interaction domain 1A) • BAP1 (BRCA1 Associated Protein 1) • PALB2 (Partner and localizer of BRCA2) • ATRX (ATRX Chromatin Remodeler) • CHEK2 (Checkpoint kinase 2) • RAD51 (RAD51 Homolog A) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD50 (RAD50 Double Strand Break Repair Protein) • 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)) • WRN (WRN RecQ Like Helicase)
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    TP53 mutation • KRAS mutation • BRCA2 mutation • BRCA1 mutation • HRD • ATM mutation • ARID1A mutation • PALB2 mutation • BAP1 mutation • BRIP1 mutation • RAD50 mutation • BARD1 mutation • BLM mutation • MRE11A mutation • NBN mutation • CHEK1 expression
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    OncoScan™ CNV Assay
    almost2years
    Multi-site evaluation of FFPE homologous recombination deficiency reference materials (AACR 2023)
    GIS varied for each material across assays, but HRD status was consistent, confirming the wide applicability of the new reference materials.  We have developed the Seraseq HRD reference materials to meet the needs of laboratories looking to analyze HRD in cancer patient samples. These reference materials facilitate standardization and quality control in HRD testing by clinical labs for current and new PARP inhibitor treatment stratification in expanded patient populations that may include those with WT BRCA1/2 genes.
    PARP Biomarker • BRCA Biomarker
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    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • ATM (ATM serine/threonine kinase) • HRD (Homologous Recombination Deficiency) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD51D (RAD51 paralog D)
    |
    HRD • ATM mutation • RAD51C mutation • RAD51D mutation
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    TruSight Oncology 500 Assay • OncoScan™ CNV Assay • SOPHiA DDM HRD Solution
    almost2years
    Sarcomatous Transformation in Hemosiderotic Fibrolipomatous Tumor (HFLT): A Potential Role for TERT Promoter Mutations (USCAP 2023)
    We have identified TERT promoter mutation in 2 HFLT with progression to myxoid sarcoma. Of note, in one of these cases the mutation was detected only in the sarcomatous component, while the conventional HFLT component was wild-type. Conventional HFLT/PHAT and MIFS were consistently negative.
    TERT (Telomerase Reverse Transcriptase)
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    TERT mutation • TERT promoter mutation
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    OncoScan™ CNV Assay
    over2years
    TOWARD A NEW GENOMIC AND CLINICO-PATHOLOGIC CLASSIFICATION OF UTERINE ADENOSARCOMAS (CTOS 2022)
    Post-operative doxorubicine or platinum-based chemotherapy and radiotherapy can be offered to patients at high risk of relapse (myometrial invasion, high grade, presence of SO)... To our knowledge, this is one of the largest retrospective cohorts of uterine AS. Histopathological classification of AS into 4 groups, taking into account the morphologic grade and the presence of SO might predict clinical behavior and correlates with the genomic copy number landscape. Presence of SO, regardless of histologic grade was significantly associated with recurrence.
    OncoScan™ CNV Assay
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    doxorubicin hydrochloride
    over2years
    OpenHRD - an open source platform for calculation of homologous recombination deficiency scores from OncoScan microarrays (ECP 2022)
    Several studies have shown that HRD is a reliable marker for treatment decisions in PARPi therapy. In this study we provided a simple, standardized, web based system to analyse HRD, which is able to process the microarray scan raw image data and generate reliable HRD score values. Initial validation of the HRD platform has been performed in ovarian cancer, and extension to prostate and pancreatic cancer is ongoing.
    PARP Biomarker
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    HRD (Homologous Recombination Deficiency)
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    HRD
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    Myriad myChoice® CDx • OncoScan™ CNV Assay
    over2years
    The Geneva HRD test: clinical validation on 469 samples from the PAOLA-1 trial (ECP 2022)
    On the PAOLA-1 samples, the Geneva test yielded a similar hazard ratio as the Myriad test with respect to the addition of Olaparib or placebo to the Bevacizumab main-tenance treatment (HR=0.32 vs 0.31). The proposed test is a viable alternative to the Myriad myChoice HRD test and can be easily deployed in a clinical labora-tory. The performance is similar to the commercial test in terms of hazard ratio but the lower failure rate of the Geneva HRD test allows a 10% increase (375 vs 340) in the number of patients that will receive a conclusive laboratory result.
    Clinical
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    Myriad myChoice® CDx • OncoScan™ CNV Assay
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    Avastin (bevacizumab) • Lynparza (olaparib)