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Company:
Thermo Fisher ScientificType:
Laboratory Developed Test
Related tests:
1m
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
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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) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
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KRAS mutation • EGFR mutation • HER-2 mutation
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Oncomine Focus Assay
2ms
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
2ms
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
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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)
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TP53 mutation • HER-2 amplification • HER-2 mutation • MET amplification • MET exon 14 mutation • MET mutation • TP53 amplification
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Oncomine Focus Assay
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Keytruda (pembrolizumab) • Tabrecta (capmatinib)
2ms
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
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APC mutation • CTNNB1 mutation
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Oncomine Focus Assay
6ms
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
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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) • NRAS (Neuroblastoma RAS viral oncogene homolog) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK (Neurotrophic receptor tyrosine kinase)
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KRAS G12C • KRAS G12
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Oncomine Focus Assay
6ms
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 • 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)
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ROS1 fusion • ROS1 positive • FGFR fusion
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Oncomine Focus Assay
6ms
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
8ms
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
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ALK (Anaplastic lymphoma kinase)
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ALK rearrangement • ALK fusion
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VENTANA ALK (D5F3) CDx Assay • Oncomine Focus Assay
8ms
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
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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)
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Oncomine™ Pan-Cancer Cell-Free Assay • PATHWAY antiHer2/neu (4B5) Rabbit Monoclonal Primary Antibody • Oncomine Focus Assay
9ms
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
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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)
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BRAF mutation • PIK3CA mutation • NTRK1 fusion • NTRK3 fusion • RET fusion • RAS mutation • RET mutation • RET M918T • NTRK fusion
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Oncomine Focus Assay
9ms
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
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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)
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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
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Idylla™ GeneFusion Assay • Oncomine Focus Assay
9ms
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
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MET (MET proto-oncogene, receptor tyrosine kinase)
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MET exon 14 mutation
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Guardant360® CDx • ArcherMET • Oncomine Focus Assay
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Tepmetko (tepotinib)
9ms
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
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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) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
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KRAS mutation • EGFR mutation • KRAS G12C • HER-2 amplification • ALK fusion • ROS1 fusion • KRAS G12 • KRAS amplification
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Guardant360® CDx • FoundationOne® Liquid CDx • Oncomine Focus Assay
9ms
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
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HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden)
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TP53 mutation • HER-2 mutation • HER-2 A775_G776insYVMA • HER-2 A775
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FoundationOne® CDx • Guardant360® CDx • FoundationOne® Liquid CDx • Oncomine Focus Assay
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Kadcyla (ado-trastuzumab emtansine) • Enhertu (fam-trastuzumab deruxtecan-nxki)
9ms
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
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EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • EML4 (EMAP Like 4) • KIF5B (Kinesin Family Member 5B)
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KRAS mutation • EGFR mutation • BRAF mutation • ALK fusion • KIF5B-RET fusion • ALK-KIF5B fusion
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Oncomine Focus Assay
9ms
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
10ms
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
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MAP2K1 (Mitogen-activated protein kinase kinase 1) • SRSF2 (Serine and arginine rich splicing factor 2)
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IDH2 mutation • SRSF2 mutation • MAP2K1 C121S • IDH2 R140Q • SRSF2 P95L • IDH2 mutation + SRSF2 mutation
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Oncomine Focus Assay • Oncomine Myeloid Assay GX • TruSight Myeloid Sequencing Panel
10ms
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
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)
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TruSight Oncology 500 Assay • Archer® FusionPlex® Lung Kit • Oncomine Focus Assay
10ms
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)
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KRAS mutation • EGFR mutation • BRAF mutation • PIK3CA mutation • KRAS G12
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Oncomine Focus Assay
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Keytruda (pembrolizumab) • Opdivo (nivolumab) • Tecentriq (atezolizumab)
10ms
Multigenic testing of somatic mutations in solid tumor cells (EACR 2023)
In 10% of cases, an increase in the number of copies of the EGFR and KRAS genes was found, and in 10% of cases, a fusion gene (RNA) MET- MET.M13M15, TMPRSS2-ERG.The identified genome changes were processed by the server through the FDA, NCCN, EMA, ESMO registries to search for the most appropriate therapy options that exist in world practice for a specific type and localization of the established mutation.ConclusionConclusion. For personalized prescription of targeted drugs, it is more efficient to use multigene diagnostics for a comprehensive study of the mutational status of a tumor.
Tumor cell
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EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • FGFR3 (Fibroblast growth factor receptor 3) • SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily A, member 4) • FGFR4 (Fibroblast growth factor receptor 4) • CREBBP (CREB binding protein) • ERG (ETS Transcription Factor ERG) • JAK3 (Janus Kinase 3)
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KRAS mutation • BRAF mutation • PIK3CA mutation • PIK3CA E542K • IDH1 R132H • BRAF G469V • PIK3CA E545 • IDH1 R132 • JAK3 mutation • PIK3CA E542 • PIK3CA H1047L • TMPRSS2-ERG fusion
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Oncomine Focus Assay
12ms
Genomic profiling in advanced NSCLC in Italy: First results of NERoNE (NSCLC Emilia Romagna Next Generation Sequencing Evaluation) project. (ASCO 2023)
NERoNE evaluates data from NGS profiling of three OU mapping key actionable molecular alterations in a large population of aNSCLC also accounting for PDL1 status. This preliminary analysis will be the starting point for further evaluations in order to improve the personalized approach to aNSCLC. >*For 15 pts PDL1 expression was not known.
PD(L)-1 Biomarker • IO biomarker • Next-generation sequencing • Metastases
|
EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • PD-L1 (Programmed death ligand 1) • 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) • FGFR1 (Fibroblast growth factor receptor 1) • NTRK (Neurotrophic receptor tyrosine kinase)
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PD-L1 expression • BRAF V600E • KRAS mutation • EGFR mutation • KRAS G12C • BRAF V600 • EGFR expression • MET exon 14 mutation • RET rearrangement • KRAS G12 • EGFR exon 18 mutation • FGFR1 expression
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Oncomine™ Dx Target Test • Oncomine™ Comprehensive Assay v3M • Oncomine Focus Assay
12ms
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
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Guardant360® CDx • FoundationOne® Liquid CDx • Oncomine Focus Assay • Oncomine Precision Assay
12ms
An exploratory analysis of lung cancer survival using NGS genetic predictors and partial least squares. (ASCO 2023)
Though alterations in the EGFR and ALK genes usually present a favorable prognosis, our work suggests that some of their variants are associated with a poor survival. This study also reveals other mutations like alterations on PIK3CA and CTNNB1 genes, which may impact lung cancer prognosis and will require further exploration.
Next-generation sequencing
|
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) • EML4 (EMAP Like 4) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • FUS (FUS RNA Binding Protein)
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PIK3CA mutation • CTNNB1 mutation • KRAS exon 2 mutation • KRAS exon 3 mutation • BRAF exon 15 mutation
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Oncomine Focus Assay
12ms
Survival outcomes in ALK-positive NSCLC patients (p) treated 1st line brigatinib and impact of the ALK fusion variant. (ASCO 2023)
In this interim analysis we were unable to demonstrate a significant difference in survival outcomes according to variant type. Clinical trial information: NCT04223596.
Clinical
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KRAS (KRAS proto-oncogene GTPase) • ALK (Anaplastic lymphoma kinase) • EML4 (EMAP Like 4) • HIP1 (Huntingtin Interacting Protein 1)
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KRAS mutation • KRAS G12C • ALK positive • ALK rearrangement • ALK fusion • KRAS G12
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Oncomine Focus Assay
|
Alunbrig (brigatinib)
12ms
MOLTHY: Spanish Study for Molecular Characterization of Thyroid Carcinoma (clinicaltrials.gov)
P=N/A; Recruiting --> Active, not recruiting
Enrollment closed
|
PD-L1 (Programmed death ligand 1) • PD-1 (Programmed cell death 1)
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Oncomine Focus Assay • VENTANA pan-TRK (EPR17341) Assay
1year
The Glioma-IRE project - Molecular profiling in patients with glioma: steps toward an individualized diagnostic and therapeutic approach. (PubMed, J Transl Med)
Routine timely molecular profiling in patients with glioma should be implemented to offer patients an individualized diagnostic approach and provide them with advanced targeted therapy options if available.
Journal
|
Oncomine Focus Assay
1year
Performance Characteristics of Oncomine Focus Assay for Theranostic Analysis of Solid Tumors, A (21-Months) Real-Life Study. (PubMed, Diagnostics (Basel))
RNA analysis of 55 clinical samples revealed 7 alterations. This is the first study showing the long-term robustness of the Oncomine Focus assay in clinical routine practice.
Journal
|
Oncomine Focus Assay
1year
Cell-free DNA as a predictive and prognostic marker in adjuvant-treated non-small cell lung cancer (ELCC 2023)
Conclusions The use of liquid biopsy in early stages and the follow-up of patients with NSCLC is a potential tool for detecting tumor recurrence, as demonstrated by the increase in cfDNA concentration, mutated allele frequency and gene dosage after relapse. A long-term follow-up is required to assess the consistency and robustness of results.
Clinical
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TP53 (Tumor protein P53) • CCND2 (Cyclin D2)
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TP53 mutation
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Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine Focus Assay
1year
KRAS mutation, the molecular landscape of lung adenocarcinoma in the Portuguese population (ESMO-TAT 2023)
1,98% (2pts) had 2 KRAS different mutation observed c.34G>T p.Gly12Cys+c.37G>A p.Gly13Ser and c.35G>T p.Gly12Val+c427G>A p.Glu143Lys where the combinations. Conclusions Our representative population presented a slight raise in the frequency of the G12C mutation, showing that approximately 36% of Portuguese pts with NSCLC harbor the G12C variant, thus potentially responsive to the new anti-KRAS agents.
Clinical • PD(L)-1 Biomarker • IO biomarker
|
EGFR (Epidermal growth factor receptor) • PD-L1 (Programmed death ligand 1) • KRAS (KRAS proto-oncogene GTPase)
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KRAS mutation • KRAS G12C • KRAS G12
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Oncomine Focus Assay
over1year
The Utility of Molecular Testing as a Diagnostic Aid in Small Biopsies of Well-Differentiated Hepatocellular Lesions (USCAP 2023)
Our findings suggest that targeted molecular testing has potential value in distinguishing well-differentiated HCC from benign lesions in small needle biopsies. All HCC cases demonstrated CTNNB1 and/or TERT promoter mutations, and while CTNNB1 mutations were infrequent in this small cohort of WDHL/Ns, the presence of TERT promoter mutation would strongly favor a diagnosis of HCC. A negative result, particularly in a small molecular panel is less informative; however, these small samples may be insufficient for larger, more comprehensive molecular testing.
Biopsy
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TERT (Telomerase Reverse Transcriptase)
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CTNNB1 mutation • TERT mutation • TERT promoter mutation • CTNNB1 expression • CTNNB1 exon 3 mutation
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Oncomine Focus 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
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MET (MET proto-oncogene, receptor tyrosine kinase) • MAP2K1 (Mitogen-activated protein kinase kinase 1) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)
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MET exon 14 mutation
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Oncomine Focus Assay • Oncomine Precision Assay
over1year
HER2 copy number and resistance mechanisms in patients with HER2-positive advanced gastric cancer receiving initial trastuzumab-based therapy in JACOB trial. (PubMed, Clin Cancer Res)
HER2 CNV-high assessed by NGS may be associated with better ORR, PFS, OS in a JACOB subgroup, especially if combined with HER2 3+. The negative prognostic role of AMNESIA requires further clinical validation.
Journal
|
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) • MET (MET proto-oncogene, receptor tyrosine kinase)
|
HER-2 positive • KRAS mutation • EGFR mutation • HER-2 amplification • PIK3CA mutation • HER-2 expression • MET amplification • EGFR amplification • MET mutation • HER-2-H
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Oncomine Focus Assay
|
Herceptin (trastuzumab) • Perjeta (pertuzumab)
over1year
Identification of prognostic factors in classic Hodgkin lymphoma by integrating whole slide imaging and next generation sequencing. (PubMed, Mol Omics)
Moreover, patients with MUM1+ cells above 21.8% showed a statistically significantly higher PFS when combined with amplification of the AR gene (p < 0.001) and wild-type KRAS (p < 0.001). The integration of WSI analysis and DNA sequencing could be useful to improve our understanding of the biology of cHL and define risk subgroups.
Journal • Next-generation sequencing
|
KRAS (KRAS proto-oncogene GTPase) • FGFR2 (Fibroblast growth factor receptor 2) • AR (Androgen receptor) • CD20 (Membrane Spanning 4-Domains A1) • NF1 (Neurofibromin 1) • TNFRSF8 (TNF Receptor Superfamily Member 8) • CDK4 (Cyclin-dependent kinase 4) • IRF4 (Interferon regulatory factor 4)
|
KRAS wild-type • RAS wild-type
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Oncomine Focus Assay
over1year
MOLTHY PROJECT: A SPANISH OBSERVATIONAL STUDY FOR MOLECULAR CHARACTERIZATION OF THYROID CARCINOMA (ATA 2022)
A comparison of different molecular testing technique will be explored, with the aim to propose a diagnostic decision‐making in advanced TC, especially for NTRK and RET alterations. (NCT04970134)
Observational data • Clinical
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RET (Ret Proto-Oncogene) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK (Neurotrophic receptor tyrosine kinase)
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RET rearrangement • NTRK expression
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Oncomine Focus Assay
over1year
A Single-Institution Cohort Study on Her2-Low Expression in Hormone-Receptor Positive Metastatic Breast Cancer Treated with Cyclin-Dependent Kinase Inhibition by Palbociclib (AMP 2022)
Concurrent hormone therapy: letrozole (47), fulvestrant (20). Her2- low disease was present in more than one-third of patients treated with palbociclib for metastatic breast cancer, and was found in various tumor tissue sites. Clinical benefit of palbociclib was high in our cohort, and lower in the small number of patients who also presented with BRCA mutations.
Clinical • BRCA Biomarker
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HER-2 (Human epidermal growth factor receptor 2) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • BRCA (Breast cancer early onset)
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HR positive • HER-2 amplification • PIK3CA mutation • HER-2 expression • HER-2 underexpression • KIT mutation • BRCA mutation
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PATHWAY antiHer2/neu (4B5) Rabbit Monoclonal Primary Antibody • Oncomine Focus Assay
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Ibrance (palbociclib) • fulvestrant • letrozole
over1year
A Custom NGS Panel for NSCLC: Making NGS Available and Affordable in India (AMP 2022)
This panel designed specifically for NSCLC can be implemented for clinical use based on the performance characteristics. It carries the advantages of not only cost effectiveness, simple design, and workflow, but also has the potential to be spiked with evolving biomarkers of interest.
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) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • MET (MET proto-oncogene, receptor tyrosine kinase) • NRAS (Neuroblastoma RAS viral oncogene homolog) • PTEN (Phosphatase and tensin homolog) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • STK11 (Serine/threonine kinase 11) • RB1 (RB Transcriptional Corepressor 1) • KEAP1 (Kelch Like ECH Associated Protein 1) • AKT1 (V-akt murine thymoma viral oncogene homolog 1)
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BRAF V600E • KRAS mutation • EGFR mutation • KRAS G12C • BRAF V600 • HER-2 mutation • KRAS G12 • HER-2 exon 20 mutation • HER-2 exon 23 mutation
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Oncomine Focus Assay
over1year
Evaluating the Utility of Thermo Fisher Oncomine NGS Panels in Determining Copy Number Variation among Solid Tumors (AMP 2022)
Thirty-three of 34 tumor samples with copy number gains called by NGS were confirmed by an orthogonal method. Investigation of the only false-positive calling by NGS showed that the sample exhibited a much higher MAPD score, approaching the manufacturer's established cut-off. Overall, the analytical specificity of OCAv3 and OFA in detecting copy number gain is greater than 95%.
Next-generation sequencing
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EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • FGFR3 (Fibroblast growth factor receptor 3) • MYCN (MYCN Proto-Oncogene BHLH Transcription Factor)
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Oncomine™ Comprehensive Assay v3M • Oncomine Focus Assay
over1year
Molecular Profiling Project (clinicaltrials.gov)
P=N/A, N=500, Recruiting, National Cancer Centre, Singapore | Trial completion date: Dec 2022 --> Dec 2025 | Trial primary completion date: Dec 2022 --> Dec 2024
Trial completion date • Trial primary completion date
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Oncomine™ Comprehensive Assay v3M • Oncomine Focus Assay
over1year
Mutations detected by Next Generation Sequencing in primary and metastatic melanoma samples and correlation with clinico-histopathological parameters (ECP 2022)
We present the preliminary results of our retro-spective study on 114 melanoma samples. We correlated their molecular status with different clinico-pathological parameters. BRAF mutated melanomas seem to can give rise to multifocal metastatic disease, even in the absence of TERTp mutation.
Next-generation sequencing
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BRAF (B-raf proto-oncogene) • NRAS (Neuroblastoma RAS viral oncogene homolog)
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BRAF mutation • NRAS mutation • TERT mutation
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Oncomine Focus Assay
over1year
Costs of Next-Generation Sequencing Assays in Non-Small Cell Lung Cancer: A Micro-Costing Study. (PubMed, Curr Oncol)
Trusight Tumor 170 Kit was the most expensive NGS assay for NSCLC diagnostics; however, an economic evaluation is required to identify the most cost-effective NGS assay. Our study results could help inform decisions to select a robust platform for NSCLC diagnostics from fine needle aspirates, and future economic evaluations of the NGS platforms to guide treatment selections for NSCLC patients.
Journal • Next-generation sequencing
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Oncomine Focus Assay • TruSight Tumor 170 Assay
over1year
Incidence of NTRK genes fusion in adult brain tumours: A prospective cohort of 140 patients with cerebral gliomas and brain metastases (ESMO 2022)
The treatment of patients with TRK fusion cancer with a first-generation TRK inhibitor (such as larotrectinib or entrectinib) is associated with high response rates (>75%), regardless of tumour histology and presence of metastases, and acceptable toxicity profile. These are composed of 63 BM and 30 gliomas. Conclusions Due to the size of the population analysed, this study will provide pioneering data on the incidence of NTRK gene fusions in brain tumors, which could strongly support the relevance of innovative clinical trials with specific targeted therapies (larotectinib, entrectinib) in this patients's population.
Clinical
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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 fusion
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Oncomine Focus Assay
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Vitrakvi (larotrectinib) • Rozlytrek (entrectinib)
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