^
    2ms
    FusionPlexâ„¢-HT and VariantPlexâ„¢-HT: Automation ready solutions for anchored multiplex PCR (AACR 2024)
    When using 50ng SeraSeq® Myeloid DNA input (LGC Clinical Diagnostics, Inc.) and the VariantPlex Core Myeloid panel (37 gene targets), both the lyophilized VariantPlex and VariantPlex-HT detected 100% (22/22) known variants ranging from 3.8% to 20.4% allele frequency (AF). When using low-quality FFPE and the VariantPlex Complete Solid Tumor panel (430 gene targets), both workflows captured 28/28 (AF: 1.4%-20.2%) and 11/11 (AF:1.2%-18.9%) single nucleotide variants (SNVs) and Insertion and Deletions (InDels) when 50ng of SeraSeq compromised FFPE or 200ng Horizon Severe FFPE was used as input, respectively. The FusionPlex-HT workflow consistently showed increased library complexity using the FusionPlex Lung V2 panel with 20ng or 50ng of Seraseq RNA Fusion Mix v4 input.
    Archer® FusionPlex® Lung Kit • Archer® VariantPlex® Solid Tumor Kit • FusionPlex® Pan Solid Tumor v2 panel
    9ms
    Pan-TRK immunohistochemistry as screening tool for NTRK fusions: A diagnostic workflow for the identification of positive patients in clinical practice. (PubMed, Cancer Biomark)
    These data lead to suggest that IHC with VENTANA pan-TRK antibody can be a reliable screening tool for the identification of patients potentially bearing NTRK rearranged tumours.
    Journal
    |
    NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • TPM3 (Tropomyosin 3) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    NTRK1 fusion • NTRK positive • NTRK fusion
    |
    Archer® FusionPlex® Lung Kit
    |
    Vitrakvi (larotrectinib) • Rozlytrek (entrectinib)
    9ms
    Metastatic NSCLC with G719X/S781I EGFR-mutations with acquired BRAF V600E mutation - response to Osimertinib, Dabrafenib and Trametinib (IASLC-WCLC 2023)
    The patient initially received 1st line Erlotinib with remission maintained more than 4 years, despite an early dose reduction due to skin toxicity. Despite loss of the original compound EGFR mutation, the rebiopsy revealed a new pathogenic and druggable driver (BRAF p.V600E), which gave the patient a new possibility of further treatment. Yet, replacing Osimertinib with a BRAF/MEK-Is combination resulted only in mixed response, suggesting that some lesions might have remained, at least in part, dependent on the original EGFR mutations. Indeed, re-challenge with Osimertinib in reduced dose together with continuation of Dabrafenib and Trametinib resulted in SD and reflected spatial and temporal heterogeneity of NSCLC.
    Metastases
    |
    EGFR (Epidermal growth factor receptor) • BRAF (B-raf proto-oncogene)
    |
    BRAF V600E • EGFR mutation • BRAF V600 • EGFR exon 20 insertion • EGFR G719X • EGFR exon 18 mutation
    |
    cobas® EGFR Mutation Test v2 • Oncomine™ Comprehensive Assay v3M • Archer® FusionPlex® Lung Kit
    |
    Mekinist (trametinib) • Tagrisso (osimertinib) • erlotinib • Tafinlar (dabrafenib)
    10ms
    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)
    |
    TruSight Oncology 500 Assay • Archer® FusionPlex® Lung Kit • Oncomine Focus Assay
    over1year
    Clinicopathologic Features and Cytologic Correlation of ALK-rearranged Papillary Thyroid Carcinoma: A series of six cases (USCAP 2023)
    In this case series, all six ALK -rearranged PTCs demonstrated a predominant follicular growth pattern and five of them were diagnosed as infiltrative follicular variant. The nuclear features were subtle and might be present in only focal areas, resulting in a significant rate of false negative diagnosis (33%, 2/6) in pre-operative FNA.
    Clinical
    |
    ALK (Anaplastic lymphoma kinase) • EML4 (EMAP Like 4) • STRN (Striatin)
    |
    ALK positive • ALK rearrangement • ALK fusion • ALK V3a
    |
    VENTANA ALK (D5F3) CDx Assay • Archer® FusionPlex® Lung Kit
    over1year
    Integrated DNA Technologies Acquires ArcherDX Next Generation Sequencing Research Assays from Invitae Corporation (Integrated DNA Technologies Press Release)
    "Integrated DNA Technologies, Inc....announced it closed on the purchase of Next Generation Sequencing (NGS) research assays from Invitae Corporation (NYSE: NVTA) under the trademarked name Archer. The integration of IDT’s portfolio with the acquired NGS research assays—which have been foundational in researching novel cancer fusions—will empower labs with an all-in-one solution to uncover biomarkers and advance cancer discoveries. The transaction enables IDT to expand its existing operations, build upon the legacy Archer portfolio, and welcome more than 100 new associates globally....Transaction Details-IDT purchased Archer NGS research assays—which reported high double-digit growth since 2019—from Invitae for cash consideration of approximately $48 million, subject to certain adjustments. The transaction is structured as an asset deal and includes a license to intellectual property related to the AMP technology."
    M&A
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    Archer® FusionPlex® Comprehensive Thyroid & Lung (CTL) Kit • Archer® FusionPlex® Acute Lymphoblastic Leukemia (ALL) • Archer® FusionPlex® Lung Kit • Archer® FusionPlex® Lymphoma • Archer® FusionPlex® Myeloid Kit • Archer® FusionPlex® Oncology Research Kit • Archer® FusionPlex® Sarcoma kit • Archer® VariantPlex® Comprehensive Thyroid and Lung (CTL) kit • Archer® VariantPlex® Myeloid panel • Archer® VariantPlex® Solid Tumor Kit • FusionPlex® Dx • FusionPlex® Pan Solid Tumor v2 panel • FusionPlex™ Heme v2 panel • FusionPlex™ Pan-Heme panel • LiquidPlex™
    over1year
    Clinical and Molecular Characterization of Thoracic Inflammatory Myofibroblastic Tumors (IASLC-ACLC 2022)
    In Taiwan, the patients with thoracic IMT were young, and had early stages of disease status. ALK rearrangement and NTRK3 overexpression were the major genetic alterations. Different partners of ALK arrangement could be detected.
    Clinical
    |
    ALK (Anaplastic lymphoma kinase) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • EML4 (EMAP Like 4) • TPM3 (Tropomyosin 3) • DCTN1 (Dynactin Subunit 1) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    ALK positive • ALK rearrangement • NTRK expression
    |
    VENTANA ALK (D5F3) CDx Assay • Archer® FusionPlex® Lung Kit
    over1year
    MET Amplification Prediction in Non-Small Cell Lung Carcinoma Using RNA-Based Next-Generation Sequencing (AMP 2022)
    In this study, simple NGS output data analysis from RNA-based NGS assay allowed reliable prediction of MET highamplification status in NSCLC. Although copy number variation analysis is usually restricted to DNA panels, this study shows that focused analysis can be useful to triage and select samples with candidate MET gene amplifications from an RNA-based NGS assay.
    Next-generation sequencing
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    HER-2 amplification • MET amplification • MET-H
    |
    Archer® FusionPlex® Lung Kit
    over1year
    Is next generation sequencing the new golden standard for ALK testing? The diagnostic journey of an atypical case (ECP 2022)
    The unusual loss of the red signal suggested the presence of an atypical rearrangement in the 5' part of the ALK gene which required additional investigation. Using a NGS panel we identified an atypical EML4-ALK fusion which was not detected by break-apart conventional FISH. We highlight the need for a new gold standard for ALK rearrangements testing represented by RNA NGS, a more sensitive approach that could identify patients with rare molecular phenotypes and increase the addressability of targeted therapies.
    Clinical • Next-generation sequencing
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • EML4 (EMAP Like 4)
    |
    ALK positive • ALK rearrangement • EML4-ALK fusion • ALK fusion • EGFR negative
    |
    Vysis ALK Break Apart FISH Probe Kit • Archer® FusionPlex® Lung Kit
    almost2years
    Adding Alectinib Rescues Progression on Osimertinib Due to Acquired ALK p.R1275Q Variant in EGFR p.L858R-mutated NSCLC (IASLC-WCLC 2022)
    The patient was unfit for platin-based doublet chemotherapy but was offered Pemetrexed, continuing Osimertinib in standard doses...This variant is characteristic for neuroblastomas and known to be Crizotinib-resistant... Liquid biopsy-guided approach at progression in elderly patients with reduced PS may offer a feasible and effective therapy, as in this case by combining ALK- and EGFR-TKI. The treatment is ongoing and current progression-free survival is now 8 months, which is the longest under the whole treatment course. Effective combination of Osimertinib and Alectinib has been reported in single cases of disseminated EGFR-mutant NSCLC becoming resistant to Osimertinib through acquired ALK-fusions.
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53)
    |
    TP53 mutation • KRAS mutation • EGFR mutation • EGFR L858R • ALK fusion • ALK mutation • KRAS G12R • KRAS G12 • ALK R1275Q
    |
    Oncomine™ Comprehensive Assay v3M • Archer® FusionPlex® Lung Kit • Oncomine™ Lung cfDNA Assay
    |
    Xalkori (crizotinib) • Tagrisso (osimertinib) • Alecensa (alectinib) • pemetrexed
    almost2years
    Simultaneous Detection of FGFR Gene Aberrations in Squamous Non-small Cell Lung Cancer Using Targeted DNA- and RNA-based NGS (IASLC-WCLC 2022)
    Our data provide insight into the presence of various molecular aberrations simultaneously on DNA and RNA level alongside with the FGFR1 amplification and protein expression. TP53 mutations approved to be most common in analysed Sq-NSCLC tumors, while the FGFR fusions and pathogenic variants were rare. Our results highlight the necessity of detailed and extended molecular analysis (i.e.
    Next-generation sequencing
    |
    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) • NRAS (Neuroblastoma RAS viral oncogene homolog) • 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) • FGFR3 (Fibroblast growth factor receptor 3) • FGFR1 (Fibroblast growth factor receptor 1) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha) • FGFR (Fibroblast Growth Factor Receptor) • NRG1 (Neuregulin 1) • GNAQ (G Protein Subunit Alpha Q) • AKT1 (V-akt murine thymoma viral oncogene homolog 1) • GNA11 (G Protein Subunit Alpha 11) • FOXL2 (Forkhead Box L2)
    |
    TP53 mutation • KRAS mutation • EGFR mutation • BRAF mutation • PIK3CA mutation • FGFR1 amplification • ALK fusion • ROS1 fusion • FGFR fusion • FGFR1 fusion • FGFR1 expression • TP53 expression • FGFR3 amplification • FGFR3 expression
    |
    Archer® FusionPlex® Lung Kit
    almost2years
    Analysing the molecular landscape of squamous cell carcinoma through simultaneous targeted DNA and RNA-based next-generation sequencing (ERS 2022)
    Our results highlight the necessity of detailed molecular analysis (i.e. RNA-Seq, WES) especially of tumors negative for FGFR1 amplification and FGFR protein expression. The research was co-financed by the NCBR and CelonPharmaS.A – project “Celonko”
    Next-generation sequencing
    |
    ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • FGFR2 (Fibroblast growth factor receptor 2) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • FGFR1 (Fibroblast growth factor receptor 1) • GNAQ (G Protein Subunit Alpha Q) • AKT1 (V-akt murine thymoma viral oncogene homolog 1)
    |
    TP53 mutation • FGFR1 amplification • FGFR2 fusion • ROS1 fusion • FGFR fusion • FGFR1 fusion • FGFR1 expression
    |
    Archer® FusionPlex® Lung Kit
    2years
    Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers. (PubMed, Virchows Arch)
    "Our results show that kinase fusions (20/30, 67%) and most importantly targetable NTRK1 fusions (7/30, 23%) are frequent in CRCs with dMLH1/BRAFV600Ewt/MLH1ph/RASwt. NGS was the most comprehensive method in finding the fusions, of which a subset can be screened by Idylla or IHC, provided that the result is confirmed by NGS."
    Journal
    |
    BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • RET (Ret Proto-Oncogene) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • MLH1 (MutL homolog 1) • TPM3 (Tropomyosin 3) • LMNA (Lamin A/C)
    |
    BRAF V600E • BRAF V600 • NTRK1 fusion • RET fusion • ALK rearrangement • BRAF wild-type • ALK fusion • BRAF fusion • MLH1 mutation • TPM3-NTRK1 fusion • LMNA-NTRK1 fusion • NTRK expression
    |
    Idylla™ GeneFusion Assay • Archer® FusionPlex® Lung Kit • VENTANA pan-TRK (EPR17341) Assay
    over2years
    [VIRTUAL] CANTRK: A Canadian Ring Study to Optimize Detection of NTRK Gene Fusions by Next-Generation Sequencing (NGS) (AMP 2021)
    The CANTRK study demonstrated a high level of agreement in detection of NTRK fusions by NGS RNA testing across different NGS panels. Fusions not detected by certain panels were due either to absence of targets in amplicon primer panels, or potential bioinformatic challenges. Issues encountered during the study, such as defining quality criteria for reporting a positive result, types of results requiring confirmation, and reporting requirements, will be used to formulate a best practice guideline for analysis and reporting of gene fusions detected by NGS methods.
    Next-generation sequencing
    |
    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) • ETV6 (ETS Variant Transcription Factor 6) • TPM3 (Tropomyosin 3) • LMNA (Lamin A/C) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    NTRK1 fusion • NTRK3 fusion • NTRK2 fusion • ALK fusion • ETV6-NTRK3 fusion • ROS1 fusion • TPM3-NTRK1 fusion • LMNA-NTRK1 fusion • ALK-ROS1 fusion • NTRK fusion
    |
    Oncomine™ Comprehensive Assay v3M • Archer® FusionPlex® Lung Kit • Oncomine Focus Assay • Oncomine Precision Assay
    over2years
    Evaluating Targeted Next-Generation Sequencing (NGS) Assays and Reference Materials for NTRK Fusion Detection. (PubMed, J Mol Diagn)
    The NTRK fusion detection rate in QC-validated clinical samples was 100% for all assays. This comparison of the strengths and limitations of four RNA-based NGS assays will inform physicians and pathologists regarding optimal assay selection to support identification of patients with NTRK fusion-positive tumors.
    Journal • Next-generation sequencing
    |
    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 • NTRK3 fusion • NTRK2 fusion • NTRK positive • NTRK fusion
    |
    TruSight Oncology 500 Assay • Archer® FusionPlex® Lung Kit • Oncomine Focus Assay • Oncomine Precision Assay
    over2years
    [VIRTUAL] Targeting ROS1 Gene Rearrangement by Crizotinib as Neoadjuvant Treatment Before Definitive Radiotherapy in Locally Advanced NSCLC (IASLC-WCLC 2021)
    "The rapidly achieved partial remission points towards a potential future for ROS1-TKIs used as neoadjuvant treatment in locally advanced ROS1-rearranged NSCLC before definitive, curatively intended radiotherapy or surgery. However, this needs to be further substantiated in randomized trials."
    Clinical
    |
    EGFR (Epidermal growth factor receptor) • ALK (Anaplastic lymphoma kinase) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • CD74 (CD74 Molecule) • NKX2-1 (NK2 Homeobox 1)
    |
    EGFR mutation • HER-2 mutation • ALK positive • ROS1 fusion • ROS1 positive • ROS1 rearrangement • ALK-ROS1 fusion
    |
    Archer® FusionPlex® Lung Kit
    |
    Xalkori (crizotinib)
    over2years
    [VIRTUAL] Impact of Real - World DNA - and RNA - Based Rebiopsy Testing in EGFR - Mutated NSCLC Progressing on Osimertinib. (IASLC-WCLC 2021)
    "The patient received stereotactic radiosurgery (SRS) against two intracranial processes followed by Erlotinib and achieved intra- and extracranial partial response (PR)...Based on these results no additional targeted treatment options were possible, and chemotherapy with Carboplatin/Pemetrexed was initiated while continuing Osimertinib, achieving only short-term stabilization of the disease. However, additional NGS analysis of RNA isolated from the hepatic metastasis showed ANK3-RET fusion on chromosome 10q (breakpoint chr10: 61994446, chr10: 43612032), and RET-TKI was initiated (Pralsetinib)...2. Complementary RNA-based testing is important to implement as a standard diagnostic strategy to better uncover the molecular evolution in advanced EGFR-mutated NSCLC and contribute to identification of further targeted treatment possibilities when progression during Osimertinib occur."
    EGFR (Epidermal growth factor receptor) • RET (Ret Proto-Oncogene) • PTEN (Phosphatase and tensin homolog) • MDM2 (E3 ubiquitin protein ligase)
    |
    EGFR mutation • EGFR exon 19 deletion • EGFR T790M • RET fusion • PTEN mutation • MDM2 amplification • EGFR E746
    |
    Oncomine™ Comprehensive Assay v3M • Archer® FusionPlex® Lung Kit • Oncomine™ Lung cfDNA Assay
    |
    Tagrisso (osimertinib) • erlotinib • carboplatin • pemetrexed • Gavreto (pralsetinib)
    over2years
    [VIRTUAL] FGFR1 gene aberrations and FGFR1 protein expression in squamous non-small cell lung cancer (Sq-NSCLC). (ERS 2021)
    Research in progress. Co-funded by the National Centre for Research and Development and CelonPharma within the Strategmed programme.
    EGFR (Epidermal growth factor receptor) • 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) • 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) • NRG1 (Neuregulin 1)
    |
    NTRK1 fusion • NTRK3 fusion • EGFR expression • FGFR1 amplification • ALK fusion • ROS1 fusion • NRG1 fusion • FGFR1 fusion • FGFR1 expression
    |
    Archer® FusionPlex® Lung Kit
    almost3years
    [VIRTUAL] Prevalence of NTRK1/2/3 fusions in dMMR/MSI metastatic colorectal cancer (ESMO 2021)
    Frequency of NTRK1/2/3 fusions was 5.8% in our dMMR/MSI mCRCs cohort. These fusions were not restricted to sporadic cases. The diagnostic accuracy of pan-TRK IHC was low.
    IO biomarker
    |
    KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • MSI (Microsatellite instability) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • EML4 (EMAP Like 4) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • ETV6 (ETS Variant Transcription Factor 6) • MLH1 (MutL homolog 1) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • TPM3 (Tropomyosin 3) • LMNA (Lamin A/C) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    BRAF V600E • KRAS mutation • MSI-H/dMMR • BRAF V600 • NTRK1 fusion • NTRK3 fusion • NTRK2 fusion • MSH2 mutation • EML4-NTRK3 fusion • NTRK positive • MSH6 expression • NTRK fusion
    |
    Archer® FusionPlex® Lung Kit • VENTANA pan-TRK (EPR17341) Assay