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    TEST:
    Oncomine Precision Assay

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

    News

    11d
    Fast-tracking NSCLC Standard of Care Genomic Testing with a Formalin-free Fresh EBUS Pathway (BTOG 2024)
    These data clearly show the potential for a fresh EBUS pathway to improve patient care through viability and rapidity of predictive testing for SOC therapy and trial decision-making, benefitting from higher RNA success and markedly reduced TATs. These results also support the use of first-line assessment of fresh EBUS over FFPE, reducing multidisciplinary laboratory work burden and increasing availability of FFPE material for additional predictive biomarker processes.
    Endobronchial ultrasound
    |
    Oncomine Precision Assay
    13d
    Utility of bronchoscopically obtained frozen cytology pellets for next-generation sequencing. (PubMed, BMC Cancer)
    Our study showed that frozen cytology pellets may have equivalent diagnostic value to frozen tissue for NGS analyses. Bronchial cytology specimens are usually used only for cytology, but NGS analysis is possible if enough cells are collected to create pellet specimens. In particular, the frozen cytology pellets obtained by endobronchial ultrasound-guided transbronchial needle aspiration yielded sufficient amounts of DNA.
    Journal • Next-generation sequencing • Cytology
    |
    Oncomine Precision Assay
    2ms
    Next generation liquid biopsy reference material performance across NGS assays and platforms (AACR 2024)
    Remnant samples are typically not an option due to limited yields from a standard blood draw, thus contrived standards are especially needed. Expanded variant content and improvements in the methods used to produce the Seraseq ctDNA Mutation Mix v4 materials will enable advancements in the blood-based NGS clinical diagnostics space.
    Liquid biopsy • Next-generation sequencing • Biopsy
    |
    MSI (Microsatellite instability)
    |
    TruSight Oncology 500 Assay • Oncomine Precision Assay
    2ms
    Increased PI3K pathway activity is associated with recurrent breast cancer in patients with low and intermediate 21-gene recurrence score. (PubMed, J Clin Pathol)
    Higher Ki67 gene expression was associated with recurrences (p=0.042) Increased PI3K pathway activity, independent of PIK3CA mutations, may play a role in the recurrence of early-stage breast cancer with low and intermediate 21-gene RS. Pathway analysis can help to identify high-risk patients in this setting.
    Journal
    |
    ER (Estrogen receptor) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • AR (Androgen receptor)
    |
    PIK3CA mutation
    |
    OncoSignal™ • Oncomine Precision Assay • Oncotype DX Breast Recurrence Score®Test
    3ms
    Genomic Landscape in Solid Tumors: A Real World Data to Evaluate Actionability of a Comprehensive Molecular Profiling Panel in Tumors of Different Origin in a Mexican Cohort (USCAP 2024)
    Our study comprises one of the largest retrospective studies in solid tumors of different sources in the Mexican population, giving new perspectives and evidence about our genomic profiles and mutational prevalence. It also highlights the feasibility of a small NGS panel that represents cost effectiveness for a latin american landscape. Among the comparison between the molecular profiles of the global databases, it is important to distinguish that the allele frequency of EGFR in the Mexican population is significantly higher, similar to the data reported in the Asian population
    Real-world evidence • Clinical • Real-world
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53)
    |
    Oncomine Precision Assay
    3ms
    Association of Clinicopathological and Molecular Features with the Prognosis of KRAS Mutation Subtypes in Lung Adenocarcinoma (USCAP 2024)
    In this study, we found that KRAS-G12D mutation is significantly associated with poor prognosis, remaining significant after adjusting for clinicopathologic characteristics and co-occurring mutations among LUAD patients.
    Clinical
    |
    KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • FGFR3 (Fibroblast growth factor receptor 3) • GNAS (GNAS Complex Locus)
    |
    TP53 mutation • KRAS mutation • PIK3CA mutation • KRAS G12D • KRAS G12
    |
    Oncomine Precision Assay
    4ms
    Comparative Analysis of Ion Torrent Sequencing Platforms: Unveiling Enhanced Performance and Precision with the GenexusTM integrated sequencer in Clinical Applications (ACMG 2024)
    Taken together, our comparison ofIon PGMTM Dx system and GenexusTM integrated sequencer indicates that the latter exhibits superior performance with significantly higher total reads, mapped reads, and mean depth, leading to a faster turnaround time and improved detection of clinically relevant variants. This underscores its potential for enhanced precision in clinical applications.
    Clinical
    |
    EGFR (Epidermal growth factor receptor) • NRAS (Neuroblastoma RAS viral oncogene homolog)
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine Precision Assay
    4ms
    Rapid detection of mutations in CSF-cfTNA with the Genexus Integrated Sequencer. (PubMed, J Neurooncol)
    In summary, our results indicate that CSF-cfTNA analysis with the Genexus-OPA can provide clinically relevant information in patients with brain metastases with short TAT.
    Journal
    |
    ER (Estrogen receptor) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • CCDC170(Coiled-Coil Domain Containing 170)
    |
    EGFR mutation • PIK3CA mutation • EGFR exon 19 deletion • EGFR T790M • ER D538G
    |
    Oncomine Precision Assay
    6ms
    Analytical Performance and Concordance with Next-Generation Sequencing of a Rapid, Multiplexed dPCR Panel for the Detection of DNA and RNA Biomarkers in Non-Small-Cell Lung Cancer. (PubMed, Diagnostics (Basel))
    The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and exceeded 99.0% in aggregate. The assay demonstrated >97% concordance with respect to the comparator method.
    Journal • Next-generation sequencing • Discordant
    |
    ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    NTRK1 fusion • MET exon 14 mutation
    |
    FusionPlex® Dx • Oncomine Precision Assay
    6ms
    COMPARISON OF ENDOBRONCHIAL ULTRASOUND (EBUS) FINE NEEDLE ASPIRATION (FNA) AND FINE NEEDLE BIOPSY (FNB) FOR CANCER DIAGNOSIS: A SINGLE CENTRE PROSPECTIVE STUDY (BTS WM 2023)
    Conclusion FNB provides a better quality specimen with preserved architecture than FNA. FNB samples were more suitable for NGS testing in lung cancer diagnosis.
    Clinical • Endobronchial ultrasound • Biopsy
    |
    Oncomine Precision Assay
    6ms
    Dideoxy Sequencing Enhances Detection of KIT Variants in GISTs Initially Evaluated by NGS Hotspot Panels (AMP 2023)
    Our results suggest that short read NGS-based assays may miss a significant number of clinically actionable KIT variants, and that follow-up of KIT and PDGFRA NGS-negative cases by alternative testing modalities should be considered.
    Next-generation sequencing
    |
    BRAF (B-raf proto-oncogene) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha)
    |
    BRAF V600E • BRAF V600 • KIT exon 11 mutation • KIT exon 9 mutation • KIT exon 17 mutation
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine Precision Assay
    6ms
    Validation of Genexus Purification Instrument for DNA and RNA extraction from formalin fixed paraffin embedded tissues for use with patient NGS testing. (AMP 2023)
    GeneXus Purification Instrument provides a convenient automated workflow for NA isolation and quantification. In comparison with manual NA extraction using the AllPrep DNA/RNA FFPE kit, we observed lower DNA yield, better preservation of DNA and RNA integrity, and higher sequencing quality of NAs purified with GPI.
    Clinical • Next-generation sequencing
    |
    Oncomine Precision Assay
    6ms
    Rapid and Automated Genomic Profiling of Lung Cancer Solid Tumor and Liquid Biopsy (AMP 2023)
    We demonstrated that OPA on the automated GeneXus sequencer can profile well-established biomarkers in NSCLC research samples with minimal sample input and rapid turnaround time. These improvements were developed to test the feasibility of implementing a fast and automated workflow with minimal hands-on time to help achieve the goals of precision medicine research for NSCLC. The development of a single assay capable of supporting tissue and liquid biopsy profiling will advance research into precision medicine for NSCLC.
    Liquid biopsy • Biopsy
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • MET (MET proto-oncogene, receptor tyrosine kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • FGFR1 (Fibroblast growth factor receptor 1)
    |
    TP53 mutation • KRAS mutation • EGFR mutation • PIK3CA mutation • MET exon 14 mutation • ROS1 fusion • FGFR1 fusion
    |
    Oncomine Precision Assay
    7ms
    Preceding plasma EGFR vs upfront tissue NGS for advanced NSCLC in the Chinese population: A single centre experience in Hong Kong (ESMO Asia 2023)
    The liquid-first approach enhances the yield of rare mutations by tissue NGS which is resource-dependent. It benefits regions where tissue biopsy is a rate limiting factor and EGFR mutations are prevalent.
    Clinical • Next-generation sequencing • Metastases
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    TP53 mutation • BRAF mutation • PIK3CA mutation • EGFR T790M • EGFR exon 20 insertion • MET exon 14 mutation • MET mutation • EGFR exon 20 mutation • EGFR negative • EGFR mutation + PIK3CA mutation • EGFR exon 20 insertion + EGFR T790M • HER-2 exon 23 mutation
    |
    cobas® EGFR Mutation Test v2 • Oncomine Precision Assay
    7ms
    Multigene panel next generation sequencing in metastatic colorectal cancer in an Australian population. (PubMed, PLoS One)
    In addition to identifying patients with genomic alterations suitable for clinically proven standard of care therapeutic options, the 50 gene NGS panel has significant potential in identifying potentially actionable non-tier 1 mutations and therefore may become future standard clinical practice.
    Journal • Next-generation sequencing • Metastases
    |
    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) • MET (MET proto-oncogene, receptor tyrosine kinase) • RAS (Rat Sarcoma Virus)
    |
    TP53 mutation • BRAF V600E • HER-2 amplification • PIK3CA mutation • BRAF V600 • MET amplification • RAS mutation • RAS wild-type • MET mutation
    |
    Oncomine Precision Assay
    8ms
    Utility of multigene panel next-generation sequencing in routine clinical practice for identifying genomic alterations in newly diagnosed metastatic nonsmall cell lung cancer. (PubMed, Intern Med J)
    In addition to identifying patients with genomic alterations suitable for clinically proven standard-of-care therapeutic options, the 45-gene NGS panel has significant potential in identifying potentially actionable non-Tier 1 mutations that may become future standard clinical practice in NSCLC.
    Journal • PD(L)-1 Biomarker • Next-generation sequencing • Metastases
    |
    EGFR (Epidermal growth factor receptor) • PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    PD-L1 expression • KRAS mutation • EGFR mutation • KRAS G12C • MET exon 14 mutation • MET mutation • KRAS G12
    |
    Oncomine Precision Assay
    9ms
    Pulmonary Adenocarcinoma: ALK, ROS1 and RET imbalance sequencing concomitant with other target mutations (ECP 2023)
    Possible novel fusion mutations (3'/5' imbalance) detections requires confirmatory analyses. Tumoral cells that contain a gene fusion are often expected to have elevated expression of the 3' assay compared to the 5' assay, and these cases have to be confirmed though the other methods – IHC and FISH, to complete Molecular Pathology Reports for target therapies prescription.
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • RET (Ret Proto-Oncogene) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • EML4 (EMAP Like 4) • CCDC6 (Coiled-Coil Domain Containing 6)
    |
    KRAS mutation • EGFR mutation • RET fusion • ALK rearrangement • RET mutation • MET mutation
    |
    Oncomine Precision Assay
    9ms
    Performance evaluation of different genomic testing workflows for the detection of gene-fusions in non-small cell lung cancer (ECP 2023)
    Clinical testing laboratories may benefit from improved understanding of strengths and limitations of different workflows. It is important to keep these in mind when reporting results.
    ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2)
    |
    NTRK1 fusion • NTRK2 fusion • ROS1 fusion
    |
    TruSight Oncology 500 Assay • Idylla™ GeneFusion Assay • Oncomine Precision Assay
    9ms
    Molecular heterogeneity of Primary liver carcinomas: early study (ECP 2023)
    HCC CK19+/CK7+ targeted therapy might benefit from a CTNNB1, TP53, ALK, EGFR, MAP2K2, RET, PTEN, and IDH2 panel, standardized for PLC spectrum. This knowledge would allow better understanding the clinical course and PLC heterogeneity, together with improving tumor classification and treatment.
    EGFR (Epidermal growth factor receptor) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • PTEN (Phosphatase and tensin homolog) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • FGFR3 (Fibroblast growth factor receptor 3) • FGFR1 (Fibroblast growth factor receptor 1) • ERBB3 (V-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha) • FGFR4 (Fibroblast growth factor receptor 4) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • MAP2K2 (Mitogen-activated protein kinase kinase 2) • KRT19 (Keratin 19)
    |
    TP53 mutation • EGFR mutation • PIK3CA mutation • KIT mutation • ALK mutation • AR mutation • PDGFRA mutation • ERBB3 mutation • EGFR mutation + PIK3CA mutation • EGFR mutation + ALK mutation
    |
    Oncomine Precision Assay
    9ms
    Lung cancer molecular approach by NGS/MPS: the experience of IAP‐PM using different NGS platforms (ECP 2023)
    The frequency of targetable mutations and complex mutation detection increased. The use of more sensitive technologies helps pathologists respond faster, more proficiently, with less likelihood of errors due to automation with less sample requirement.
    Next-generation sequencing
    |
    Oncomine Precision Assay
    9ms
    Genomic screening by multi-gene assay for perioperative targeted therapy in patients with early-stage non-small cell lung cancer: LC-SCRUM-Advantage/MRD (ESMO 2023)
    Conclusions Multi-PCR panel showed a high success rate and a short TAT in genomic screening by preoperative biopsy tumor samples. Multi-PCR panel would help to better detect actionable oncogenic drivers in patients with early-stage NSCLC.
    Clinical
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • RET (Ret Proto-Oncogene) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    KRAS mutation • EGFR mutation • KRAS G12C • EGFR L858R • EGFR exon 19 deletion • KRAS G12D • RET fusion • KRAS G12
    |
    AmoyDx® Pan Lung Cancer PCR Panel • Oncomine Precision Assay
    9ms
    Validation of MET amplification using next-generation sequencing in lung adenocarcinoma (ESMO 2023)
    Conclusions The detection of MET amplification by NGS did not show satisfactory concordance with the results obtained by FISH, likely due to the high heterogeneity in MET gene copy number enumeration. As a result, complementary determination by FISH is necessary, given the lack of standardized criteria for establishing CNAs positivity by NGS.
    Next-generation sequencing
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    KRAS G12C • EGFR L858R • MET amplification • MET exon 14 mutation • KRAS G12 • KRAS Q61H
    |
    Oncomine Precision Assay
    9ms
    Molecular Characterization and Prognosis of Patients with KRAS Mutant Non-small Cell Lung Cancer (IASLC-WCLC 2023)
    In our cohort, the most frequent KRAS mutation found was G12C and the most frequent co-mutation was TP53. We found a high response rate and a long PFS of KRAS mutant patients treated with chemoimmunotherapy or immunotherapy. Further prospective studies are needed to derive definitive conclusions.
    Clinical • PD(L)-1 Biomarker • IO biomarker
    |
    PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A)
    |
    PD-L1 expression • TP53 mutation • KRAS mutation • KRAS G12D • KRAS G12V
    |
    Oncomine™ Comprehensive Assay v3M • Oncomine Precision Assay
    9ms
    Usefulness of Bronchoscopic Cytology Pellets for Next Generation Sequencing (IASLC-WCLC 2023)
    In NGS, bronchoscopic cytology pellets may have an equivalent diagnostic value to frozen tissue. Especially, the cytology pellet from EBUS-TBNA yielded sufficient amounts of DNA.
    Next-generation sequencing • Cytology
    |
    Oncomine Precision Assay
    10ms
    Study of Liquid-Based Cytology Using Next-Generation Sequencing as a Liquid Biopsy Application in Patients with Advanced Oncological Disease. (PubMed, Biomedicines)
    Liquid-based cytology can be used as a component of liquid biopsy, as it allows the identification of actionable mutations in patients with advanced oncological disease. Our findings expand the utility of liquid biopsy from different body fluids or cell aspirates.
    Journal • Liquid biopsy • Next-generation sequencing • Metastases • Biopsy • Cytology
    |
    Oncomine Precision Assay
    12ms
    An Observational Study to Evaluate the Clinical Utility of the Oncomine Precision Assay Within the Exactis Network (clinicaltrials.gov)
    P=N/A; N=200 --> 100
    Enrollment change • Metastases
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    Oncomine Precision Assay
    1year
    Comparison between liquid biopsy and tissue NGS in two cohorts of advanced NSCLC. (ASCO 2023)
    To our knowledge, this is the first retrospective observational study where liquid biopsy and tissue NGS are compared in two different cohorts of patients with advanced NSCLC. Time to obtain results was shorter for blood NGS than tissue sequencing, and liquid biopsy provided molecular information in cases in which tissue NGS is not available. Further studies to identify patients in which liquid biopsy could replace tissue analysis are needed.
    Liquid biopsy • Next-generation sequencing • Metastases • Biopsy
    |
    Guardant360® CDx • FoundationOne® Liquid CDx • Oncomine Focus Assay • Oncomine Precision Assay
    1year
    A nation-wide genomic screening project for further development of targeted therapies in treatment-refractory non–small-cell lung cancer (LC-SCRUM-TRY). (ASCO 2023)
    Genotype-matched targeted therapies to overcome treatment-resistance have not been established, except osimertinib against EGFR T790M mutation... LC-SCRUM-TRY contributes to the clinical development of precision medicine to overcome drug resistance, especially for EGFR-mutated NSCLC resistant to EGFR-TKI. This screening platform also help to practice precision medicine for patients initially diagnosed as driver-negative. Clinical trial information: UMIN000041957.
    HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3)
    |
    BRAF V600E • EGFR mutation • KRAS G12C • BRAF V600 • EGFR L858R • EGFR exon 19 deletion • MET amplification • EGFR T790M • MET exon 14 mutation • EGFR C797S • KRAS G12 • HER-2 exon 20 mutation • EGFR L718Q • EGFR A750P • HER-2 exon 23 mutation
    |
    Guardant360® CDx • Oncomine Precision Assay
    |
    Tagrisso (osimertinib)
    1year
    EGFR assessment using next generation sequencing as a reflex testing on surgically resected non-squamous non-small cell lung carcinoma. (ASCO 2023)
    Genomic alteration should be systematically evaluated using an NGS reflex testing in surgically resected NS-NSCLC, since future adjuvant therapeutic decision making may consider the presence of compound EGFR mutations as well as co-occuring mutations in other genes, especially in TP53.
    PD(L)-1 Biomarker • IO biomarker • Next-generation sequencing • Reflex
    |
    EGFR (Epidermal growth factor receptor) • PD-L1 (Programmed death ligand 1) • TP53 (Tumor protein P53) • MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    PD-L1 expression • TP53 mutation • EGFR mutation • EGFR L858R • EGFR expression • MET exon 14 mutation • MET mutation • EGFR exon 18 mutation
    |
    Oncomine Precision Assay
    1year
    Evaluation of two clinically focused targeted NGS systems for liquid biopsy testing shows a high level of concordance in resulting actionable mutations (AACR 2023)
    The high concordance of the independent workflows for the detection of nucleic acid variants in circulation demonstrates the capability of both systems to be used for testing of clinical specimens. Specifically, actionable variants in the four major mutation classes were successfully detected in the reference and test specimen set. As a part of clinical validation, orthogonal testing of variants will need to be conducted.
    Clinical • Liquid biopsy • Next-generation sequencing • Biopsy • Discordant
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • NRAS (Neuroblastoma RAS viral oncogene homolog) • EML4 (EMAP Like 4) • FGFR (Fibroblast Growth Factor Receptor)
    |
    KRAS mutation • EGFR mutation • BRAF mutation • NRAS mutation • HER-2 mutation • MET exon 14 mutation • EML4-ALK fusion • ALK fusion
    |
    GeneStrat® test • Oncomine Precision Assay
    1year
    Performance of a 24-hour turnaround, guideline-complete NSCLC assay, optimized for sparse samples (AACR 2023)
    Here we demonstrate that the HDPCR NSCLC Tumor Profiling Panel provides comparable performance to validated NGS assays with a turnaround that enables adherence to guideline-recommended treatment, and a low sample requirement that maximizes the number of patients for molecular testing. The standard protocols used by the assay and the use of a cloud based analysis pipeline enables easy deployment of this assay in any lab.
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2)
    |
    Oncomine Precision Assay
    1year
    Impact of TP53/KRAS mutations on Overall Survival of Metastatic non-Small Cell Lung Cancer Patients (pts) Treated with Systemic First-line Therapy (ELCC 2023)
    TP53 mutations could represent a potential biomarker for treatment selection for pts with low PDL1 expression treated with chemo-immunotherapy. Prospective validation is needed.
    Clinical • PD(L)-1 Biomarker • IO biomarker • Metastases
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    PD-L1 expression • TP53 mutation • KRAS mutation • TP53 mutation + KRAS mutation • PD-1-L • PD-L1-L • TP53 mutation + PD-L1 expression
    |
    VENTANA PD-L1 (SP263) Assay • Oncomine Precision Assay
    over1year
    Ultrafast Gene Fusion Assessment for Nonsquamous NSCLC. (PubMed, JTO Clin Res Rep)
    UFGFA using NGS and reverse-transcriptase polymerase chain reaction approaches had an equal level of detection of gene fusion but with some technique-specific limitations. Nevertheless, UFGFA detection in routine clinical care is feasible with both systems allowing faster initiation of therapy and a broad degree of screening.
    Journal
    |
    ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    MET exon 14 mutation • ALK fusion • NTRK positive • NTRK fusion
    |
    Idylla™ GeneFusion Assay • Oncomine Precision Assay
    over1year
    Rapid In-House Liquid Biopsy to Support Community Oncology Practice (USCAP 2023)
    Liquid biopsy is a valuable tool to support precision oncology practice. The immediate intra-institutional availability of this modality significantly reduces barriers and time to results. This study demonstrates the feasability of liquid biopsy performed within a community-based pathology practice.
    Liquid biopsy • Biopsy
    |
    Oncomine Precision Assay
    over1year
    Utility of Urine Cytology Specimens for Molecular Profiling in Detection of High-Grade Urothelial Carcinoma (USCAP 2023)
    This validation study supports the feasibility of applying NGS testing to leftover fixed urine cytology specimens. In addition, the potential utility of urine NGS testing as an adjunct to urine cytology in the early detection of HGUC for cases in which cytology is negative and/or atypical/suspicious should be investigated further.
    Cytology
    |
    HER-2 (Human epidermal growth factor receptor 2) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • FGFR3 (Fibroblast growth factor receptor 3) • HRAS (Harvey rat sarcoma viral oncogene homolog)
    |
    FGFR3 S249C • HER-2 S310F • FGFR3 Y373C • FGFR3 fusion • NRAS G12 • HRAS G12S • EGFR fusion
    |
    Oncomine Precision Assay
    over1year
    Genomic Profiling of Metastatic Tumors in Pleural Effusion Specimens: Comparison of Fresh Supernatant, Fresh Cell Pellet, and Cell Block Material for Testing (USCAP 2023)
    In our validation study, leftover supernatants from refrigerated unfixed cytology PE specimens proved to be a reliable and accurate alternative source to cell blocks for genomic profiling in metastatic disease. In our hands, cell pellets revealed slightly better results than supernatants due to a higher concordance rate and less read coverage needed for the NGS test.
    Pleural effusion • Cell block • Metastases
    |
    MET (MET proto-oncogene, receptor tyrosine kinase) • MAP2K1 (Mitogen-activated protein kinase kinase 1) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)
    |
    MET exon 14 mutation
    |
    Oncomine Focus Assay • Oncomine Precision Assay
    over1year
    An Observational Study to Evaluate the Clinical Utility of the Oncomine Precision Assay Within the Exactis Network (clinicaltrials.gov)
    P=N/A, N=200, Recruiting, Exactis Innovation | Trial primary completion date: Aug 2022 --> Apr 2023
    Trial primary completion date • Metastases
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    Oncomine Precision Assay
    over1year
    Oncomine Precision Assay GX on Genexus Integrated Sequencer to Rescue Quantitative or Quality Insufficient Sample of Non-Small Cell Lung Cancer (AMP 2022)
    In this study, we challenged OPA with QNS samples, and OPA successfully detected SNVs and CNVs with an at least 83% concordance rate, compared to reference methods. We demonstrated that OPA can be a valuable, rapid method for molecular testing of advanced NSCLC cases with scant tissue.
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53)
    |
    TP53 mutation • KRAS mutation • EGFR mutation • KRAS G12A • KRAS G12 • EGFR E746
    |
    Idylla™ KRAS Mutation Test • Oncomine Precision Assay
    over1year
    Efficient Biorepository Development Using Oncomine Precision Assay and the Genexus Integrated NGS Platform (AMP 2022)
    The combination of OPA with the Genexus integrated sequencer enabled high-volume, fast, and accurate sample screening with low input and limited handson-time. Sequencing results provided novel insights into the distribution of specific variants across cancer types and the cooccurrence and mutual exclusivity of certain variants. The technology now enables laboratories to efficiently generate their own sample biorepositories to support their assay development and validation requirements.
    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) • ALK (Anaplastic lymphoma kinase) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • FGFR1 (Fibroblast growth factor receptor 1) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2)
    |
    NTRK1 fusion • ALK fusion • FGFR1 fusion
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    Oncomine Precision Assay
    over1year
    Ultra-fast gene fusion assessment as a reflex testing in daily clinical practice for advanced non-small cell lung cancer patients (ECP 2022)
    Ultra-fast gene fusion evaluation using NGS or RT-PCR approaches should be developed as a reflex testing for NS-NSCLC at diagnosis in order to treat these patients according to the international recommendations and guidelines.
    Clinical
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    ALK (Anaplastic lymphoma kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK (Neurotrophic receptor tyrosine kinase)
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    ROS1 positive • MET positive
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    Oncomine Precision Assay
    over1year
    Adenosquamous carcinoma of the lung - biopsy: MET exon 14 skipping mutation (ECP 2022)
    MET-TKIs, capmatinib and tepotinib, for NSCLCs with METex14 marked a new step of MET-targeted therapy. METex14 alterations - point mutations/deletions/insertions/com-plex mutations lead to MET receptor decreased degradation, fol-lowed by MET signalling and tumourigenesis. The evaluation methods for METex14 include differential MET exon expression, quantitative reverse transcription polymerase chain reaction (qRT-PCR) or direct RNA sequencing.
    MET (MET proto-oncogene, receptor tyrosine kinase) • TTF1 (Transcription Termination Factor 1) • NKX2-1 (NK2 Homeobox 1)
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    MET amplification • MET exon 14 mutation • MET mutation • MET expression
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    Idylla™ GeneFusion Assay • Oncomine Precision Assay
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    Tepmetko (tepotinib) • Tabrecta (capmatinib)
    almost2years
    Amplicon-Based Next-Generation Sequencing Rescues “Quantity Not Sufficient” NSCLC Samples and Provides Clinical Information (IASLC-WCLC 2022)
    Our results show that amplicon-based NGS on the OPA-Genexus system can rescue QNS samples using minimal tissue input and provide treatment options for NSCLC patients that may not otherwise have been eligible for targeted therapy.
    Clinical • 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) • ALK (Anaplastic lymphoma kinase) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha)
    |
    Oncomine Precision Assay