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    TEST:
    Oncomine Focus Assay

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

    News

    1d
    Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for Detecting ERBB2 and Other Gene Amplifications in Solid Tumors. (PubMed, Cancers (Basel))
    This study highlights the strengths and limitations of amplicon-based NGS assays in detecting amplifications using real-world data.
    Journal • Next-generation sequencing
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    HER-2 (Human epidermal growth factor receptor 2)
    |
    HER-2 amplification
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    Oncomine™ Comprehensive Assay v3M • Oncomine Focus Assay • Oncomine™ Comprehensive Assay Plus
    11d
    Targeted Sequencing in Rosai-Dorfman Disease from Microdissected Specimens Reveals Higher Incidence of MAP2K1 Mutations (ASH 2024)
    The incidence of MAP2K1 mutations was higher in the current study than in previous studies (Garces et al. 2017), though not statistically significant, at 29% (4/14) compared to 16% (8/49; p=0.15).These results highlight the value of stringent tissue microdissection for identifying targetable molecular alterations in RDD and suggest that such approaches may help uncover additional neoplastic drivers and/or mutations implicated in therapeutic resistance.
    KRAS (KRAS proto-oncogene GTPase) • MAP2K1 (Mitogen-activated protein kinase kinase 1)
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    KRAS mutation • KRAS G12D • KRAS G12 • MAP2K1 E203K • KRAS A146P • MAP2K1 G128D
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    Oncomine Focus Assay
    1m
    Negative hyperselection and mechanisms of acquired resistance to first-line chemotherapy plus anti-EGFR in pMMR RAS/BRAF wild-type (wt) metastatic colorectal cancer (mCRC) patients (pts): a translational analysis of the TRIPLETE trial (AIOM 2024)
    TRIPLETE is a phase III trial where 435 pts with RAS/BRAF wt – per local assessment – mCRC were randomized to receive first-line FOLFOX/ panitumumab (pan) or mFOLFOXIRI/pan... In contrast to previous data, negative hyperselection both through tissue and plasma analysis failed to demonstrate a prognostic role among pMMR RAS/BRAF wt mCRC pts treated with first-line chemotherapy plus pan. The confounding effect of the associated chemotherapy is a potential explanation for this finding. Tissue and plasma analyses at baseline failed to provide fully concordant results.
    Clinical • Preclinical • Metastases
    |
    BRAF (B-raf proto-oncogene) • MAP2K1 (Mitogen-activated protein kinase kinase 1)
    |
    BRAF V600E • MSI-H/dMMR • BRAF V600 • BRAF wild-type • RAS mutation • RAS wild-type
    |
    FoundationOne® CDx • Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine Focus Assay
    |
    5-fluorouracil • Vectibix (panitumumab) • leucovorin calcium
    1m
    Comparison of Clinical Sensitivity for Kinase Fusion Detection in Thyroid Carcinoma by Paired Primer Targeted Methods (AMP 2024)
    AFP, the targeted, breakpoint/fusion partner agnostic panel, outperformed 3 other established panels using real-world, fusion-driven thyroid cancers by an average detection frequency of 39%. Such findings demonstrate the importance in sequencing panel selection for fusion-driven thyroid cancer detection, and the potential downstream consequences for diagnostic utility and therapeutic intervention.
    Clinical
    |
    BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • RET (Ret Proto-Oncogene) • FGFR2 (Fibroblast growth factor receptor 2) • 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 • FGFR2 fusion • ALK fusion
    |
    FusionPlex® Dx • Illumina Focus Panel • Oncomine Focus Assay
    2ms
    Integrating Genetic Alterations and Histopathological Features for Enhanced Risk Stratification in Non-Muscle-Invasive Bladder Cancer. (PubMed)
    In multivariate Cox regression, MAI was the strongest predictor for PFS. Integrating genetic alterations and histopathological features may improve risk stratification in NMIBC.
    Journal
    |
    Oncomine Focus Assay
    2ms
    Impact of Comprehensive Genome Profiling on the Management of Advanced Non-Small Cell Lung Cancer: Preliminary Results From the Lung Cancer Cohort of the FPG500 Program. (PubMed, JCO Precis Oncol)
    P=N/A; The early data of the FPG program (NSCLC cohort) support the implementation of CGP and MTB in clinical practice to grant access to patients harboring actionable molecular alterations to the most effective and individualized available treatment options, thus improving their survival outcomes.
    Journal • IO biomarker • Metastases
    |
    TruSight Oncology 500 Assay • Archer® FusionPlex® Lung Kit • FusionPlex® Dx • Oncomine Focus Assay
    3ms
    MOLTHY: Spanish Study for Molecular Characterization of Thyroid Carcinoma (clinicaltrials.gov)
    P=N/A; Trial completion date: Mar 2024 --> Mar 2025
    Trial completion date
    |
    PD-L1 (Programmed death ligand 1) • PD-1 (Programmed cell death 1)
    |
    Oncomine Focus Assay • VENTANA pan-TRK (EPR17341) Assay
    3ms
    Application of updated clinical recommendations for the use of NGS (2024) in Russian reality (ESMO Asia 2024)
    The findings were mostly detected in those types of cancer, where NGS could be routinely used due to several potential findings, it can be really important to broadly use this type of testing in other especially rare cancers where the targeted therapy in dot broadly used. Comprehensive NGS testing for current tumor-agnostic biomarkers with co-findings searching for molecular resistance mechanisms may shed some light making the list of biomarkers wider and options for treatment greater.
    Clinical • Next-generation sequencing • Tumor mutational burden • MSi-H Biomarker
    |
    BRAF (B-raf proto-oncogene) • MSI (Microsatellite instability) • RET (Ret Proto-Oncogene) • FGFR (Fibroblast Growth Factor Receptor) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    BRAF V600E • MSI-H/dMMR • BRAF V600 • FGFR mutation • RET mutation
    |
    Oncomine Focus Assay
    3ms
    Validation of thyroid fine needle aspiration rinse with indeterminate cytology results as a suitable sample type for molecular testing (ECP 2024)
    FNA rinses are a suitable source to perform molecular analysis after morphological evaluation maximizing diagnostic efficiency. Additionally, BRAF V600E is not the sole pathogenic alteration in thyroid cancer, so expanding tests to include other molecular alterations may enhance diagnostic utility using this available material.
    Cytology
    |
    KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • NRAS (Neuroblastoma RAS viral oncogene homolog) • HRAS (Harvey rat sarcoma viral oncogene homolog)
    |
    BRAF V600E • KRAS mutation • NRAS mutation • HRAS mutation • NRAS Q61 • NRAS Q61R • HRAS Q61R
    |
    Oncomine Focus Assay
    4ms
    Single-center analysis of a real-world cohort of patients with metastatic urothelial carcinoma evaluated by NGS: molecular landscape and efficacy of targeted therapies. (PubMed, Clin Transl Oncol)
    We recommend that all patients with mUC undergo NGS at diagnosis given the high percentage of patients with pathogenic alterations in our real-world cohort and the efficacy data of patients treated with targeted therapies.
    Real-world evidence • Journal • IO biomarker • Next-generation sequencing • Real-world • Metastases
    |
    Oncomine Focus Assay
    5ms
    Latin-American Non-Small Cell Lung Cancer Patient's Tumors Harbor Many Novels Potentially Actionable/driver Mutations. (IASLC-WCLC 2024)
    ALK (23%) and ROS1 (23%) account for most of these variants, followed by ERBB2 (14%), EGFR (11%), RET (11%), BRAF (8%), MET (7%) and KRAS (3%). Conclusions : The analysis of many Latin America subjects revealed a significant number of clinically actionable but also novel somatic mutations in cancer genes highlighting the importance of including less-represented populations in clinical trials and molecular studies.
    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) • RET (Ret Proto-Oncogene) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    EGFR mutation • ALK mutation
    |
    Oncomine Focus Assay
    5ms
    Clinical utility of liquid biopsy for non-small cell lung cancer patients with ALK fusion variants treated with brigatinib (ESMO 2024)
    Detection rate by ctDNA profiling is higher compared with RNA-based approaches and it is of prognostic significance.
    Clinical • Tumor mutational burden • Liquid biopsy • Biopsy
    |
    ALK (Anaplastic lymphoma kinase) • TMB (Tumor Mutational Burden) • EML4 (EMAP Like 4)
    |
    ALK positive • ALK fusion • EML4-ALK variant 1
    |
    TruSight Oncology 500 Assay • Oncomine Focus Assay • TruSight Oncology 500 ctDNA v2
    |
    Alunbrig (brigatinib)
    5ms
    Characterizing the genomic landscape of breast cancer in an Irish cohort of patients (ESMO 2024)
    We present the largest study of BC variant frequencies in a cohort of Irish breast cancer patients to date and confirm NGS is feasible and identifies clinically relevant and actionable variants. We confirm that the frequency of PIK3CA alterations, in addition to codon specificity, are comparable to those observed in European and US cohorts and demonstrate that the detection of clinically relevant biomarkers is not confined to ER positive HER2 negative BC. The tissue failure rate (19%) underscores the need for cfDNA testing to identify the expanding range of actionable targets in BC to improve access to emerging targeted therapies and biomarker-driven clinical trials.
    Clinical • BRCA Biomarker
    |
    HER-2 (Human epidermal growth factor receptor 2) • ER (Estrogen receptor) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • AKT1 (V-akt murine thymoma viral oncogene homolog 1)
    |
    HER-2 positive • ER positive • HER-2 amplification • HER-2 negative • PIK3CA mutation • HER-2 S310F • ESR1 mutation • AKT1 mutation • HER-2 D769Y • HER-2 L869R • ER positive + HER-2 negative • HER-2 negative + ER positive • HER-2 negative + ER positive + ESR1 mutation
    |
    Oncomine Focus Assay
    5ms
    Feasibility and Impact of Embedding an Extended DNA and RNA Tissue-Based Sequencing Panel for the Routine Care of Patients with Advanced Melanoma in Spain. (PubMed, Int J Mol Sci)
    For patients with a given genetic profile, the melanoma survival and recurrence-free survival rates were equivalent, but not for stage and LDH values. This expanded knowledge of molecular alterations has helped to more comprehensively characterize our patients and has provided relevant information for deciding the best treatment strategy.
    Journal • Metastases
    |
    EGFR (Epidermal growth factor receptor) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • NRAS (Neuroblastoma RAS viral oncogene homolog) • HRAS (Harvey rat sarcoma viral oncogene homolog) • MAP2K1 (Mitogen-activated protein kinase kinase 1) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)
    |
    Oncomine Focus Assay • Oncomine Solid Tumor DNA Kit
    5ms
    Fusion partner agnostic approaches improve detection of targetable gene fusions in thyroid cancers (ETA 2024)
    Additional work will need to quantify the diagnostic utility of agnostic sequencing approaches against both broad scale and hot-spot panels as they relate to metrics of cost-effectiveness and theranostic consequence. Word count: 395/400
    BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2)
    |
    FusionPlex® Dx • Oncomine Focus Assay
    6ms
    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
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    Oncomine Focus Assay • Oncomine™ Comprehensive Assay Plus
    6ms
    Retrospective Analysis to Optimize the Detection of MET Exon 14 Skipping Mutations in Non-Small Cell Lung Cancer. (PubMed, Diagnostics (Basel))
    Specimens with low ratios (average ratio: 0.12% for nine cases) may yield false-positive results. Our results suggested that monitoring read counts and ratios and validating the results with RT-PCR are crucial to prevent false positives.
    Journal • Retrospective data
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    MET (MET proto-oncogene, receptor tyrosine kinase)
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    Oncomine Focus Assay
    7ms
    Genetic profiles of oligometastatic non-small cell lung cancer and corresponding brain metastases. (PubMed, Eur J Cardiothorac Surg)
    In oligometastatic non-small cell lung cancer, brain metastases retain the main genetic alterations of the primary tumors. Patients may profit from targeted inhibition of mutated KRAS. Additional private genetic alterations in the brain metastases are dismal.
    Journal • Metastases
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    KRAS (KRAS proto-oncogene GTPase)
    |
    Oncomine Focus Assay
    7ms
    Negative hyperselection and mechanisms of acquired resistance to first-line chemotherapy plus anti-EGFR in pMMR RAS/BRAF wild-type (wt) metastatic colorectal cancer (mCRC) patients (pts): A translational analysis of the TRIPLETE trial (ESMO-GI 2024)
    TRIPLETE is a phase III trial where 435 pts with RAS/BRAF wt mCRC were randomized to receive first-line FOLFOX/panitumumab (pan) or mFOLFOXIRI/pan. Pts enrolled in the TRIPLETE trial with available tissue and plasma at baseline (BP), and plasma at the time of disease progression (PDP) were included... In contrast to previous data, negative hyperselection both through tissue and plasma analysis failed to demonstrate a prognostic role among pMMR RAS/BRAF wt mCRC pts treated with first-line chemotherapy plus pan. The confounding effect of the associated chemotherapy is a potential explanation for this finding.
    Preclinical • Clinical • Metastases
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    BRAF (B-raf proto-oncogene) • MAP2K1 (Mitogen-activated protein kinase kinase 1)
    |
    FoundationOne® CDx • Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine Focus Assay
    |
    5-fluorouracil • Vectibix (panitumumab) • leucovorin calcium
    8ms
    Clinical impact of panel gene sequencing on therapy of advanced cancers of the digestive system: a retrospective, single center study. (PubMed)
    Actionable genetic alterations are frequently detected by panel gene sequencing in patients with advanced cancers of the digestive tract, providing clinical benefit in selected cases. However, for the majority of identified actionable alterations, sufficient clinical evidence for targeted treatments is still lacking.
    Journal • Retrospective data • Metastases
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    Oncomine Focus Assay
    8ms
    Effect of screening with a pan-TRK immunohistochemistry-based algorithm on NTRK fusion detection rates. (ASCO 2024)
    In our experience, the comprehensive screening approach based on morphological and clinical/ molecular inclusion criteria, along with the use of immunohistochemical techniques (pan-TRK antibody), significantly enhances the detection rate of NTRK fusions (5. 8% vs. 0.
    MSI (Microsatellite instability) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • ETV6 (ETS Variant Transcription Factor 6) • LMNA (Lamin A/C) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    Oncomine Focus Assay • VENTANA pan-TRK (EPR17341) Assay
    8ms
    Negative hyperselection and mechanisms of acquired resistance to first-line chemotherapy plus anti-EGFR in patients (pts) with pMMR RAS/BRAF wild-type (wt) metastatic colorectal cancer (mCRC): A translational analysis of the TRIPLETE trial. (ASCO 2024)
    TRIPLETE is a phase III trial where 435 pts with untreated RAS/BRAF wt – per local assessment - mCRC were randomized to receive first-line FOLFOX/panitumumab (pan) or mFOLFOXIRI/pan... Inconsistently with previous data, negative hyperselection both through tissue and plasma analysis failed to demonstrate a prognostic role among pMMR RAS/BRAF wt mCRC pts treated with first-line chemotherapy plus pan. The confounding effect of the associated chemotherapy backbone is a potential explanation for this finding. FFPE tissue and plasma analyses at baseline failed to provide fully concordant results.
    Preclinical • Clinical • Metastases
    |
    HER-2 (Human epidermal growth factor receptor 2) • BRAF (B-raf proto-oncogene) • MAP2K1 (Mitogen-activated protein kinase kinase 1)
    |
    FoundationOne® CDx • Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine Focus Assay
    |
    5-fluorouracil • Vectibix (panitumumab) • leucovorin calcium
    10ms
    Tumor genomic heterogeneity in non-small cell lung cancer (NSCLC) patients from Latin America (AACR 2024)
    The prevalence of mutations and fusions in the eight most relevant NSCLC genes (EGFR, KRAS, ALK, MET, RET, BRAF, ROS1 and ERBB2) varies based on sociodemographic, clinical and lifestyle characteristics. Clear distinctions emerged in the prevalence of EGFR, KRAS and ERBB2 mutations among the three countries (EGFR: 20.9%, 17.6%, 35.3%; KRAS: 21.8%, 15.6%, 10.3%; ERBB2: 2.8%, 3.3%, 4.4% for Brazil, Chile, and Peru, respectively). Furthermore, distinct association patterns were identified between the prevalence of genetic alterations and the studied factors, with attributes such as sex, tobacco use and ethnicity mostly influencing the occurrence of EGFR, ALK and ROS1 alterations.
    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) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    KRAS mutation • EGFR mutation • HER-2 mutation
    |
    Oncomine Focus Assay
    10ms
    Clinical and Genetic Characteristics of Early and Advanced Gastric Cancer. (PubMed)
    Among these patients, five harbored mutated PIK3CA, while the remaining patient had a mutation in ALK. AGC patients more frequently exhibited alterations of PIK3CA, KRAS, and ERBB2 as somatic oncogenic drivers, and displayed a higher prevalence of cumulative genetic events, including increased rates of PIK3CA mutations, enhanced detection of immunotherapy biomarkers, and mutations of the ESR1 gene.
    Journal • IO biomarker • Metastases
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    Oncomine Focus Assay
    10ms
    Cytomorphology of Non-Small Cell Lung Carcinoma with MET Exon 14 Skipping Mutations (USCAP 2024)
    One patient received Capmatinib and one patient Pembrolizumab. This study showed that NSCLC with METex14 are poorly differenciated tumors with necrotic background,multinucleation,atypical mitoses,and pleomorphic/sarcomatoid features. Larger studies are needed to confirm our preliminary findings. Routine NGS testing on cytological specimens is feasible and essential for METex14 testing and select patients with advanced lung NSCLC for targeted therapies.
    PD(L)-1 Biomarker • IO biomarker
    |
    HER-2 (Human epidermal growth factor receptor 2) • PD-L1 (Programmed death ligand 1) • MET (MET proto-oncogene, receptor tyrosine kinase) • NKX2-1 (NK2 Homeobox 1)
    |
    TP53 mutation • HER-2 amplification • HER-2 mutation • MET amplification • MET exon 14 mutation • MET mutation • TP53 amplification
    |
    Oncomine Focus Assay
    |
    Keytruda (pembrolizumab) • Tabrecta (capmatinib)
    10ms
    Fibromatosis of the Breast: Clinicopathologic Features and Treatment Outcomes (USCAP 2024)
    β-catenin nuclear immunoreactivity is not a consistent feature in fibromatosis of the breast. Given that these lesions are managed via active surveillance, we in turn have relied less on β-catenin expression and more on morphologic assessment and, if needed, NGS to render the diagnosis of fibromatosis.
    Clinical
    |
    APC mutation • CTNNB1 mutation
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    Oncomine Focus Assay
    1year
    Brazilian Multicenter Comparative Study to Characterize the Analytical Sensitivity and Expert's Concordance, using Target-directed Sequencing of FFPE Samples (AMP 2023)
    The high concordance rate of the clinical reports emitted by the participants shows that NGS data is reliably generated and interpreted in Brazil. Oncology patients may benefit from having their samples analyzed faster locally, rather than sending them abroad. We obtained important agreement levels between the results of the labs, evidencing a high accuracy in the detection and reporting of genetic variants.
    Clinical • Discordant
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    Oncomine Focus Assay
    1year
    A Retrospective Study Comparing Operational Metrics between Different Diagnostic Approaches for Molecular Testing in Lung and Colon Cancers (AMP 2023)
    Based on these findings, SGP has a shorter TAT but lower alteration detection rate for NSCLC compared to OFA and SO-NGS. OFA and SONGS have comparable alteration detection rates, but their TAT is statistically higher compared to SGP. SGP does not detect all recommended alterations per oncology guidelines.
    Retrospective data
    |
    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) • NRAS (Neuroblastoma RAS viral oncogene homolog) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    KRAS G12C • KRAS G12
    |
    Oncomine Focus Assay
    1year
    Large-Scale Comparative Analysis of Gene Fusion Detection across Solid Tumors Using AMPâ„¢ and Amplicon-Based Assays (AMP 2023)
    Our results suggest that different gene fusions have higher frequency than previously reported in the literature across different tumor types (mostly thoracic). They also support the rationale to adopt AMP assay for fusion detection given its higher sensitivity compared to amplicon-based sequencing. Novel fusions and variants of unknown significance detected merit further characterization.
    EGFR (Epidermal growth factor receptor) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • PTEN (Phosphatase and tensin homolog) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • FGFR (Fibroblast Growth Factor Receptor) • WT1 (WT1 Transcription Factor) • BCOR (BCL6 Corepressor) • EWSR1 (EWS RNA Binding Protein 1) • TFE3 (Transcription Factor Binding To IGHM Enhancer 3) • NTRK (Neurotrophic receptor tyrosine kinase) • PDGFB (Platelet Derived Growth Factor Subunit B) • STAT6 (Signal transducer and activator of transcription 6) • PLAG1 (PLAG1 Zinc Finger) • RSPO3 (R-Spondin 3) • MAML2 (Mastermind Like Transcriptional Coactivator 2) • NCOA3 (Nuclear Receptor Coactivator 3)
    |
    ROS1 fusion • ROS1 positive • FGFR fusion
    |
    Oncomine Focus Assay
    over1year
    Anaplastic lymphoma kinase (ALK) status in non-small cell lung cancer (NSCLC), a prospective study/review of 2445 cases (ECP 2023)
    Conclusion Our study confirms that compared to IHC, NGS is a more accurate first line testing platform for the detection of consensus ALK fusion status. However access to IHC may be required to mitigate the higher tissue requirements of NGS and access to FISH may be beneficial to resolve atypical results.
    Review • Clinical
    |
    ALK (Anaplastic lymphoma kinase)
    |
    ALK rearrangement • ALK fusion
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    VENTANA ALK (D5F3) CDx Assay • Oncomine Focus Assay
    over1year
    NGS mutational status on first diagnostic tissue and liquid biopsy in breast cancer (ECP 2023)
    ER/PGR/Ki67 percentage; cerbB2 ASCO/CAP/2018score. Tissue biopsies(24) and plasma(8) served for DNA/RNA extraction: RecoverAll/Total/Nucleic/Acid/Isolation/kit and Thermo-Fisher, MagMAXCell-free/Total/Nucleic/Acid/Kit. DNA/RNA concentration: Invitrogen, Qubit/RNA/HS/Assay/kit, Qubit-1X-ds-DNA-HS-Assay and Qubit-4-Fluorometer.
    Liquid biopsy • Next-generation sequencing • Biopsy
    |
    HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • AKT1 (V-akt murine thymoma viral oncogene homolog 1)
    |
    Oncomine™ Pan-Cancer Cell-Free Assay • PATHWAY antiHer2/neu (4B5) Rabbit Monoclonal Primary Antibody • Oncomine Focus Assay
    over1year
    Next-generation sequencing enables identification of RET rearrangements in papillary thyroid cancer (ESMO 2023)
    Conclusions Molecular screening in non-BRAF PTC patients is useful to identify patients harboring RET fusions who may benefit from targeted therapies. As other potentially actionable gene fusions are also found in these patients, routine implementation of NGS analysis warrants a comprehensive biomarker study.
    Next-generation sequencing
    |
    KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • NRAS (Neuroblastoma RAS viral oncogene homolog) • RET (Ret Proto-Oncogene) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • EML4 (EMAP Like 4) • TERT (Telomerase Reverse Transcriptase) • CCDC6 (Coiled-Coil Domain Containing 6) • ETV6 (ETS Variant Transcription Factor 6) • STRN (Striatin) • NCOA4 (Nuclear Receptor Coactivator 4)
    |
    BRAF V600E • KRAS mutation • BRAF V600 • RET fusion • RET rearrangement • KRAS G12 • NRAS Q61 • KRAS G12S • NRAS Q61R • NCOA4-RET fusion • TERT mutation • TERT promoter mutation • NRAS G12S • RET expression
    |
    Idylla™ GeneFusion Assay • Oncomine Focus Assay
    over1year
    MOLTHY project (TTCC-2020-02): A Spanish observational study for MOLecular characterization of THYroid carcinoma (ESMO 2023)
    RET-mutant MTC correlates with better OS, as previous studies have demonstrated with RET M918T carriers. NGS, FISH and IHC comparison is underway.
    Observational data • Clinical
    |
    BRAF (B-raf proto-oncogene) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • RET (Ret Proto-Oncogene) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    BRAF mutation • PIK3CA mutation • NTRK1 fusion • NTRK3 fusion • RET fusion • RAS mutation • RET mutation • RET M918T • NTRK fusion
    |
    Oncomine Focus Assay
    over1year
    Liquid biopsies (LBx) and tissue biopsies (TBx) for identifying MET exon 14 (METex14) skipping in advanced NSCLC: Analyses from the phase II VISION study of tepotinib (ESMO 2023)
    Differences in populations identified by TBx and LBx should be considered when interpreting trial data. Table: 1382P
    P2 data • Liquid biopsy • Metastases • Biopsy
    |
    MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    MET exon 14 mutation
    |
    Guardant360® CDx • ArcherMET • Oncomine Focus Assay
    |
    Tepmetko (tepotinib)
    over1year
    Clinical Utility of Combined Plasma and Tissue NGS in Patients with Advanced, Treatment-Naïve, Non-small Cell Lung Cancer (IASLC-WCLC 2023)
    Combined tissue and plasma NGS can increase the detection of AA in patients with newly diagnosed aNSCLC when AA are not detected by one of these assays. Due to discordant data observed, plasma NGS should be considered when AA are not detected by tissue, and viceversa.
    Clinical • Next-generation sequencing • Metastases
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    KRAS mutation • EGFR mutation • KRAS G12C • HER-2 amplification • ALK fusion • ROS1 fusion • KRAS G12 • KRAS amplification
    |
    Guardant360® CDx • FoundationOne® Liquid CDx • Oncomine Focus Assay
    over1year
    Real-World Characteristics and Outcomes of ERBB2-Mutant Non-small Cell Lung Cancer in Latin America Patients (IASLC-WCLC 2023)
    42.8% of pts received antibody-drug conjugates targeting ERBB2 in further lines of therapy, trastuzumab emtansine (37.1%) and Trastuzumab Deruxtecan (5.7%). ERBB2 mts in NSCLC are rare. In this comprehensive retrospective real-world multicenter cohort of Latin American NSCLC pts, the frequency of ERBB2 mutations was identified in 2,8% of patients. The most common ERBB2 mutation identified was A775_G776insYVMA, similar to what is reported in the literature.
    Real-world evidence • Clinical • Tumor mutational burden • PD(L)-1 Biomarker • IO biomarker • Real-world
    |
    HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden)
    |
    TP53 mutation • HER-2 mutation • HER-2 A775_G776insYVMA • HER-2 A775
    |
    FoundationOne® CDx • Guardant360® CDx • FoundationOne® Liquid CDx • Oncomine Focus Assay
    |
    Kadcyla (ado-trastuzumab emtansine) • Enhertu (fam-trastuzumab deruxtecan-nxki)
    over1year
    Molecular profiling of advanced urothelial carcinoma in Ireland through next generation sequencing (ECP 2023)
    Conclusion While the identification of 11 cases of UC with FGFR3 alterations is in keeping with published research and of potential therapeutic benefit, this study also supports the evidence of a spectrum of other genetic mutations of potential clinical significance, including co-mutations, most notably PIK3CA and ERBB2. The location of the mutations identified in our study is in keeping with The Cancer Genome Atlas (TCGA) findings and suggestive of APOBEC mutagenic activity, potentially predictive of prognosis and therapeutic response.
    Tumor mutational burden • Next-generation sequencing • Metastases
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    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • FGFR3 (Fibroblast growth factor receptor 3) • FGFR1 (Fibroblast growth factor receptor 1) • HRAS (Harvey rat sarcoma viral oncogene homolog) • MAP2K1 (Mitogen-activated protein kinase kinase 1) • TACC3 (Transforming acidic coiled-coil containing protein 3) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)
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    KRAS mutation • PIK3CA mutation • KIT mutation • FGFR3 mutation • FGFR1 mutation • HRAS mutation • FGFR1 fusion • FGFR3 fusion
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    Oncomine Focus Assay
    over1year
    Routine next generation sequencing testing on lung adenocarcinoma pap-stained (OH-fixed) cytological samples (ECP 2023)
    7 studies were invalid for both ADN&RNA,in 5 for DNA, one for ARN and in two cases without CNV detection.T% median was 90%(mean 75.4%). Among patients with invalid results 10 were rebiopsied. Thirty two patients have no genomic aberrations (24.4%).Co-ocurring molecular alterations-rate was 47,5%.Molecular alterations in KRAS and EGFR genes were the most frequent identified in 37(33%) and 22(16%) cases respectively.
    Next-generation sequencing
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • EML4 (EMAP Like 4) • KIF5B (Kinesin Family Member 5B)
    |
    KRAS mutation • EGFR mutation • BRAF mutation • ALK fusion • KIF5B-RET fusion • ALK-KIF5B fusion
    |
    Oncomine Focus Assay
    over1year
    Severe Systemic Auto-Inflammation in an Elderly Woman with Clonal Hematopoiesis (AMP Europe 2023)
    The discovery of clonal hematopoiesis in this elderly woman with a wide spectrum of severe auto-inflammatory conditions supports a potentially intriguing link between somatic blood mutations and her adult- onset rheumatologic disorders. Mechanistically, disrupted SRSF2-mediated splicing may be driving aberrant antigen presentation by bone marrow-derived dendritic cells in her skin and other organs. Causal relationships between somatic blood mutations and autoimmune/auto-inflammatory conditions have been established in patients with hematologic malignancies and conditions like VEXAS syndrome.
    Clinical
    |
    MAP2K1 (Mitogen-activated protein kinase kinase 1) • SRSF2 (Serine and arginine rich splicing factor 2)
    |
    IDH2 mutation • SRSF2 mutation • MAP2K1 C121S • IDH2 R140Q • SRSF2 P95L • IDH2 mutation + SRSF2 mutation
    |
    Oncomine Focus Assay • Oncomine Myeloid Assay GX • TruSight Myeloid Sequencing Panel
    over1year
    Efficient Lung Cancer Molecular Diagnostics by Combining Next-Generation Sequencing with Reflex Idylla GeneFusion Assay Testing (AMP Europe 2023)
    DNA-only <50 gene NGS panels can identify oncogenic mutations in the majority of lung tumor cases. In contrast, FISH testing for ALK and ROS1 rearrangement is overwhelmingly negative and does not justify their use for initial testing. Instead, NGS negative lung tumor specimens can be reflexed to the Idylla GeneFusion assay, which provides results within 4 hours.
    Next-generation sequencing • Reflex
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    ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • FGFR3 (Fibroblast growth factor receptor 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • TACC3 (Transforming acidic coiled-coil containing protein 3)
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    NTRK1 fusion • ALK positive • ALK rearrangement • MET exon 14 mutation • ALK fusion • ROS1 fusion • ROS1 positive • ROS1 rearrangement • MET mutation • FGFR3 fusion
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    Idylla™ GeneFusion Assay • Oncomine Focus Assay
    over1year
    Unexpected finding of a rare pathogenic germline BRCA1 variant in an intrahepatic cholangiocarcinoma using the Oncomine Focus DNA assay: clinical and diagnostic implications. (PubMed, Mol Biol Rep)
    This case highlights the diagnostic capabilities of CGP, now widely used in both clinical practice and academic setting. The incidental involvement of BRCA1 focuses attention on the role of BRCA genes in biliary tract cancers. Finally, as an orthogonal test confirmed the germline origin of BRCA1 c.5278-2del variant, the germline implications of CGP need to be considered.
    Journal • BRCA Biomarker
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    BRCA1 (Breast cancer 1, early onset) • BRCA (Breast cancer early onset)
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    TruSight Oncology 500 Assay • Archer® FusionPlex® Lung Kit • Oncomine Focus Assay
    over1year
    The impact of genetic disorders on the effectiveness of immunotherapy in patients with advanced NSCLC (EACR 2023)
    68 patients (median age 63 years, 37 women, 31 men, 15 non-smokers) received immunotherapy: 1st line (pembrolizumab alone or in combination with chemotherapy, n=44) or 2nd line (atezolizumab or nivolumab, n=24). KRAS mutations had no effect on OS. The combined analysis of all genetic abnormalities showed no impact on PFS and OS.ConclusionIt appears that the effectiveness of immunotherapy is not greatly affected by KRAS mutations and other genetic disorders in patients with NSCLC who do not show abnormalities in the EGFR, ALK, and ROS1 genes.
    Clinical • PD(L)-1 Biomarker • IO biomarker • Metastases
    |
    EGFR (Epidermal growth factor receptor) • 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)
    |
    KRAS mutation • EGFR mutation • BRAF mutation • PIK3CA mutation • KRAS G12
    |
    Oncomine Focus Assay
    |
    Keytruda (pembrolizumab) • Opdivo (nivolumab) • Tecentriq (atezolizumab)