Molecular analysis of CTCs is a challenge since CTCs are very rare in the blood and there are technical limitations in isolating CTCs with sufficient purity. In this study, we developed the process for NGS analysis on very low number of CTCs with high purity, isolated using CytoGen's Smart Biopsyâ„¢ system. Overall, these process could provide information for diagnosis and appropriate treatment of metastatic breast cancer along with the results of our ongoing clinical trials.

2 months ago

Circulating tumor cells • Next-generation sequencing • Tumor cell

KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • NF2 (Neurofibromin 2) • NOTCH3 (Notch Receptor 3) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C)

TP53 mutation • KRAS mutation • BRAF mutation • NF2 mutation • NOTCH3 mutation

Oncomine™ Pan-Cancer Cell-Free Assay • Oncomine™ Comprehensive Assay Plus

3ms

EGFR Sensitive Non-Small Cell Lung Cancer with and without EGFR Amplification Show Similar Sensitivity to First Line Osimertinib. Acquired EGFR Amplification is Rare but Presents a Potential Therapeutic Pitfall without Close Analysis of Next Generation Sequencing Results (USCAP 2024)

These results demonstrate that EGFR amplification in a first-line setting retains sensitivity to the standard of care, osimertinib. Caution should be exhibited when assessing new EGFR amplification for therapeutic decisions, especially when the original biopsy was of poor quality. False negative findings of gene amplification due to low tumor cellularity are known phenomenon in NGS testing.

3 months ago

Clinical • Next-generation sequencing

EGFR (Epidermal growth factor receptor)

EGFR mutation • EGFR amplification • EGFR wild-type

Oncomine™ Comprehensive Assay Plus

Tagrisso (osimertinib)

3ms

Homologous Recombinant Deficiency Does Not Share Morphologic Surrogates of BRCA-mutated High-Grade Serous Carcinoma (USCAP 2024)

BRCA mutation is one cause of HRD and appears that SET morphology associated with HGSC is unique to BRCA-mutation and not under the umbrella of other causes and effects of HRD. HRD in HGSC may produce its own molecular surrogate that is yet to be discovered. Definitive determination of which platform is superior for clinical validation of HRD assessment as a surrogate to Myriad MyChoiceDX gold standard requires matched analysis against Myriad and patient's progression free survival.

3 months ago

BRCA Biomarker

HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)

HRD • BRCA wild-type • BRCA mutation

Myriad myChoice® CDx • Oncomine™ Comprehensive Assay Plus

3ms

Harmonization of tumor mutation burden testing with comprehensive genomic profiling assays: an IQN Path initiative. (PubMed, J Immunother Cancer)

This study estimated TMB cut-off values for commercially available CGP panels. The results showed a good performance of all panels on clinical samples and the calculated cut-offs support better accuracy measures for TSO500. The validated cut-off values can drive clinical interpretation of TMB testing in clinical research and clinical practice.

3 months ago

Journal • Tumor mutational burden • IO biomarker

TMB (Tumor Mutational Burden)

FoundationOne® CDx • TruSight Oncology 500 Assay • Oncomine™ Comprehensive Assay Plus

3ms

Unveiling The Clinical Impact Of Tumor-Based Next-Generation Sequencing In Ovarian Cancer: Insights From Real-World Data (ESGO 2024)

Conclusion Tumor-based NGS frequently provides clinically significant information. It holds the potential to reveal specific therapeutic targets and contribute to clinical decision-making

3 months ago

Real-world evidence • Clinical • Next-generation sequencing • Real-world

FoundationOne® CDx • Oncomine™ Comprehensive Assay v3M • Oncomine™ Comprehensive Assay Plus

5ms

Genomic alteration in sporadic adolescent and young adult-onset colorectal adenocarcinoma. (ASCO-GI 2024)

This study is the comprehensive report hotspot mutations using NGS in sporadic AYA-onset sporadic CRC patients. The most commonly identified gene mutation frequencies among AYA-onset were similar to those reported in adult-onset, except for FBXW7, PIK3CA, NOTCH1, FGFR3, ERBB2, and PTEN mutations that had a slightly higher frequency. Further studies on larger sample set for genetic and epigenetic landscape are required.

5 months ago

Clinical

HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • NRAS (Neuroblastoma RAS viral oncogene homolog) • PTEN (Phosphatase and tensin homolog) • FGFR3 (Fibroblast growth factor receptor 3) • NOTCH1 (Notch 1) • SMAD4 (SMAD family member 4) • FBXW7 (F-Box And WD Repeat Domain Containing 7)

TP53 mutation • KRAS mutation • BRAF mutation • NRAS mutation • PIK3CA mutation • HER-2 mutation • PTEN mutation • SMAD4 mutation

Oncomine™ Comprehensive Assay Plus

7ms

Comprehensive Genomic Profiling of Early Hormone Receptor Positive Breast Cancer Reveals Diverse Genomic Alterations (AMP 2023)

In a retrospective analysis, we used comprehensive genomic profiling in the well-studied early-stage HR+ BC Tamoxifen and Exemestane Adjuvant Multinational (TEAM) trial cohort to characterize genomic alterations that contribute to oncogenesis and may drive recurrence. The genomic landscape of early HR+ BC is diverse and contains many actionable alterations. In addition to activating mutations in well-known BC associated oncogenes, the landscape included high-level CN gain in several RTK genes. The relatively high level of aneuploidy in early-stage HR+ BC was unanticipated and associated with poor risk.

7 months ago

Tumor mutational burden

EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • FGFR2 (Fibroblast growth factor receptor 2) • FGFR1 (Fibroblast growth factor receptor 1) • CDH1 (Cadherin 1) • POLD1 (DNA Polymerase Delta 1) • MAP3K1 (Mitogen-Activated Protein Kinase Kinase Kinase 1) • GATA3 (GATA binding protein 3)

TP53 mutation • TMB-H • HR positive • HER-2 negative • PIK3CA mutation • POLD1 mutation

Oncomine™ Comprehensive Assay Plus

tamoxifen • exemestane

8ms

Molecular Profiling and Human Papillomavirus Identification of Digital Papillary Adenocarcinoma (ASDP 2023)

POLE mutations frequently occurred in DPA and their clinical significance and association with low-risk HPV in DPA warrants further investigation. Poster type: Poster Defense

8 months ago

TP53 (Tumor protein P53) • NF1 (Neurofibromin 1) • POLE (DNA Polymerase Epsilon)

POLE mutation

Oncomine™ Comprehensive Assay Plus

8ms

Biomarker Assessment Through Comprehensive Genomic Profiling (AMP 2023)

In this workshop, hear how one research laboratory is leveraging the Oncomine Comprehensive Assay Plus (OCA+) to perform CGP in-house. Additionally, see results from a multi-site study evaluating performance of OCA+ across several parameters.

8 months ago

Tumor mutational burden

TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)

HRD

Oncomine™ Comprehensive Assay Plus

9ms

Next generation sequencing of breast cancer in the neoadjuvant setting. (PubMed, Pathobiology)

This study showcases the significance of employing comprehensive genomic testing in breast cancer cases, primarily due to the scarcity of specific target assays. The detection of somatic mutations, coupled with the availability of targeted therapies, holds promise as a potential therapeutic avenue to enhance tumor response rates during NAT, or as a complementary treatment following surgery. Moreover, evaluating the TMB in non-pCR samples could serve as a valuable criterion for selecting patients suitable for immunotherapy. Further exploration through clinical trials is imperative to investigate these prospects.

9 months ago

Journal • Tumor mutational burden • BRCA Biomarker • IO biomarker • Next-generation sequencing

HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • MET (MET proto-oncogene, receptor tyrosine kinase) • BRCA1 (Breast cancer 1, early onset) • BRCA (Breast cancer early onset)

TP53 mutation • BRCA mutation

Oncomine™ Comprehensive Assay Plus

10ms

Identification of 'secondary' germline cancer predisposition variants from somatic tumour testing: Should we evolve towards universal screening? (ESMO 2023)

Detected germline mutations included high penetrance cancer predisposing genes as BRCA1. This detection rate reflects the clinical utility, for patients and their families, of using the somatic genomic analysis as a source of information about a potential hereditary cancer predisposition syndrome.

10 months ago

BRCA Biomarker

BRCA1 (Breast cancer 1, early onset) • PMS2 (PMS1 protein homolog 2) • MUTYH (MutY homolog)

BRCA1 mutation

Oncomine™ Comprehensive Assay Plus

10ms

Multicentric evaluation of amplicon-based next-generation sequencing solution for local comprehensive molecular tumor profiling (ESMO 2023)

The high concordance rate with orthogonal methods highlights the assay's potential in guiding clinical decision-making for personalized cancer care. OCA+ may provide comprehensive genomic information for cancer management and may be a valuable tool for further implementing precision medicine in oncology.

10 months ago

Clinical • Tumor mutational burden • Next-generation sequencing

TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)

Oncomine™ Comprehensive Assay Plus

11ms

Next-Generation Sequencing-Guided Therapy for BRAF V600E Mutant Glioblastoma Results in Stable Disease (AMP Europe 2023)

"The patient underwent a standard post-operative treatment with radiation and 12 cycles of temozolomide...Given the presence of BRAF V600E mutation, the patient was started on dabrafenib 150mg BID and trametinib 2mg (10/07/2022). NGS can provide useful data for successful targeted therapy of patients with GBM."

11 months ago

Clinical

PD-L1 (Programmed death ligand 1) • BRAF (B-raf proto-oncogene) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • TERT (Telomerase Reverse Transcriptase) • SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1)

PD-L1 expression • BRAF V600E • BRAF V600 • TERT mutation • IDH wild-type • TERT promoter mutation

Oncomine™ Comprehensive Assay Plus

Mekinist (trametinib) • Tafinlar (dabrafenib) • temozolomide

11ms

Diagnosis of Metastatic SHH-Activated Medulloblastoma in Adult via Bone Biopsy and Next- Generation Sequencing (AMP Europe 2023)

"NGS can play a pivotal role in providing a definitive diagnosis and guide therapeutic efforts in central nervous system tumors."

11 months ago

Clinical

TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • MYCN (MYCN Proto-Oncogene BHLH Transcription Factor) • PTCH1 (Patched 1) • KDM6A (Lysine Demethylase 6A)

TP53 mutation • TP53 wild-type • PIK3CA E545K • PTCH1 mutation • PIK3CA E545

Oncomine™ Comprehensive Assay Plus

temozolomide • Erivedge (vismodegib)

11ms

Molecular Characteristics of a C11orf95-RELA Fusion Gliosarcoma: A Case Report (AMP Europe 2023)

In this report we present an extremely rare case of C11orf95-RELA fusion supratentorial ependymoma that underwent a complete sarcomatous transformation. The presence of C11orf95-RELA fusion in this case highlights the importance of considering the diagnosis of ependymoma in sarcomatous brain tumors and of performing unbiased molecular studies in these cases. Importantly, this report sheds light on key biological and evolutionary aspects of this rare tumor, such as an aberrant overactivation of the RAS/RAF/MAPK signaling pathway.

11 months ago

Clinical

TP53 (Tumor protein P53) • HRAS (Harvey rat sarcoma viral oncogene homolog) • NF1 (Neurofibromin 1) • BCOR (BCL6 Corepressor) • STAG2 (Stromal Antigen 2) • GFAP (Glial Fibrillary Acidic Protein) • RELA (RELA Proto-Oncogene) • ZFTA (Zinc Finger Translocation Associated)

TP53 mutation • NF1 mutation • HRAS mutation • STAG2 mutation • IDH wild-type

Oncomine™ Comprehensive Assay Plus

11ms

Exploring the use of Genomic Instability Metric (GIM) to determine Homologous Recombination Deficiency (HRD) in cancer (EACR 2023)

Acknowledgements: NSF, MES: D01-395/18.12.2020, D01-278-14.12. 2022, D01-302/17.12.2021, D01 165/28.07.2022; KP-06-OPR03/1719.12.2018/NSF

11 months ago

Tumor mutational burden • PARP Biomarker • MSi-H Biomarker • BRCA Biomarker

TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)

BRCA2 mutation • BRCA1 mutation • TMB-H • MSI-H/dMMR • HRD • TMB-L • HRD + BRCA1 mutation

Oncomine™ Comprehensive Assay Plus

11ms

The determination of Homologous Recombination Deficiency by comprehensive genomic profiling panel associates with clinical outcome in Ovarian Cancer patients. (EACR 2023)

HRD status determined with both assays was associated to Progression-Free Survival (PFS) after first line bevacizumab and platinum-based therapy and Overall Survival (OS) in univariate and multivariate analysis.Results and DiscussionsHRD status obtained by OCA was compared with the reference Myriad assay in 86/97 samples for which both test results were available...In univariate analysis for OS, OCA was prognostic (HR=0.44, p=0.016) but not Myriad (HR 0.71, P=0,3). Multivariate analysis for OS was not performed due to low number of events.ConclusionThese data suggest the feasibility of OCA testing for assessing HRD status, with a good concordance with the gold standard assay and association with clinical outcome.

11 months ago

Clinical data • Clinical • PARP Biomarker • BRCA Biomarker

HRD (Homologous Recombination Deficiency) • BRCA (Breast cancer early onset)

HRD • BRCA mutation

Myriad myChoice® CDx • Oncomine™ Comprehensive Assay Plus

Avastin (bevacizumab)

1year

Multicentric prospective study assessing clinical benefit of targeted treatment for patients with biliary tract cancers (ESMO-GI 2023)

Targeted therapy was actually started for 95 pts (16%), with 15 (16%) pts treated with ivosidenib for IDH1 mutations, 63 (66%) with FGFR2 inhibitors for FGFR2 alterations, 3 (3%) with immune checkpoint inhibitors (ICIs) for MSI-H, 9 (10%) with BRAF+MEK inhibitors for BRAFV600E mutations and 4 (4%) with HER2 inhibitors for HER2 amplification... NGS is feasible in daily clinical practice and it should be performed, as recommended, for all pts affected by advanced BTC, since biomarker-directed treatment for BTCs has clinically meaningful benefit in pretreated patients.

1 year ago

Clinical • MSi-H Biomarker • IO biomarker

MSI (Microsatellite instability) • FGFR2 (Fibroblast growth factor receptor 2) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1)

BRAF V600E • MSI-H/dMMR • HER-2 amplification • BRAF V600 • IDH1 mutation • FGFR2 mutation

FoundationOne® CDx • Archer® FusionPlex® Oncology Research Kit • Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine™ Comprehensive Assay Plus

Tibsovo (ivosidenib)

1year

Fully automated comprehensive genomic profiling for detection of cancer variants, gene fusions, and complex oncology endpoints (AACR 2023)

The Genexus System combines minimal touch points and a rapid turnaround time to enable comprehensive genomic profiling for research assays such as OCA Plus for detection of rare variants and low-level fusion transcripts. Further, by providing accurate characterization of key oncology research endpoints, the Genexus System can accelerate research in oncology. For research use only.

1 year ago

Tumor mutational burden

HER-2 (Human epidermal growth factor receptor 2) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • HRD (Homologous Recombination Deficiency)

HER-2 amplification

Oncomine™ Comprehensive Assay Plus

over1year

Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment. (PubMed, J Pers Med)

A total of 100% of the variants in the diagnostic samples and 80% of the variants in the AcroMetrix™ assessment sample were detected by both panels, and the panels reported highly similar variant allele frequency. A proportion of 14/19 (74%) samples were classified in the same TMB category; (4) Comparable results were obtained using OCAP and TSO500, suggesting that both panels could be applied to screen patients for enrolment in personalized cancer treatment trials.

over 1 year ago

Journal • Tumor mutational burden

TMB (Tumor Mutational Burden)

TruSight Oncology 500 Assay • Oncomine™ Comprehensive Assay Plus

over1year

Next-Generation Sequencing (NGS) of Multivergent Morphologies in Colorectal Carcinomas (CRCs) Identifies Unique Targetable Alterations (USCAP 2023)

Multivergent morphology is rare in CRC but is highly predictive of the presence of targetable molecular alterations. In such cases, NGS of multiple areas with different morphology may identify potential therapeutic targets that would otherwise be missed. While most cases have recognizable driver alterations, the less common targetable alterations frequently identified in these cases could open up additional trial options for salvage therapy.

over 1 year ago

Tumor mutational burden • MSi-H Biomarker • BRCA Biomarker • IO biomarker • 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) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • FGFR2 (Fibroblast growth factor receptor 2) • PTEN (Phosphatase and tensin homolog) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • DNMT3A (DNA methyltransferase 1) • ARID1A (AT-rich interaction domain 1A) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha) • NF1 (Neurofibromin 1) • JAK2 (Janus kinase 2) • POLE (DNA Polymerase Epsilon) • GNAQ (G Protein Subunit Alpha Q) • RUNX1 (RUNX Family Transcription Factor 1) • PBRM1 (Polybromo 1) • BAP1 (BRCA1 Associated Protein 1) • PALB2 (Partner and localizer of BRCA2) • KMT2A (Lysine Methyltransferase 2A) • BCL6 (B-cell CLL/lymphoma 6) • TET2 (Tet Methylcytosine Dioxygenase 2) • TOP2A (DNA topoisomerase 2-alpha) • ETV6 (ETS Variant Transcription Factor 6) • MLH1 (MutL homolog 1) • KMT2D (Lysine Methyltransferase 2D) • PTCH1 (Patched 1) • SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily A, member 4) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • RNF43 (Ring Finger Protein 43) • CDK12 (Cyclin dependent kinase 12) • SMAD4 (SMAD family member 4) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • KMT2C (Lysine Methyltransferase 2C) • PMS2 (PMS1 protein homolog 2) • WT1 (WT1 Transcription Factor) • ATRX (ATRX Chromatin Remodeler) • B2M (Beta-2-microglobulin) • CDH1 (Cadherin 1) • CHEK2 (Checkpoint kinase 2) • CREBBP (CREB binding protein) • SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1) • BCOR (BCL6 Corepressor) • FAT1 (FAT atypical cadherin 1) • PIK3R1 (Phosphoinositide-3-Kinase Regulatory Subunit 1) • RBM10 (RNA Binding Motif Protein 10) • RAD51C (RAD51 paralog C) • RAD50 (RAD50 Double Strand Break Repair Protein) • GLI1 (GLI Family Zinc Finger 1) • PIK3CB (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) • STAG2 (Stromal Antigen 2) • CUL4A (Cullin 4A) • EP300 (E1A binding protein p300) • IL7R (Interleukin 7 Receptor) • RAD51D (RAD51 paralog D) • RICTOR (RPTOR Independent Companion Of MTOR Complex 2) • SETBP1 (SET Binding Protein 1) • ARID2 (AT-Rich Interaction Domain 2) • MSH3 (MutS Homolog 3) • NOTCH4 (Notch 4) • GNAS (GNAS Complex Locus) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • NCOR1 (Nuclear Receptor Corepressor 1) • PIM1 (Pim-1 Proto-Oncogene) • CASP8 (Caspase 8) • PPM1D (Protein Phosphatase Mg2+/Mn2+ Dependent 1D) • PPP2R2A (Protein Phosphatase 2, Regulatory Subunit B, Alpha) • DICER1 (Dicer 1 Ribonuclease III) • FANCM (FA Complementation Group M) • KMT2B (Lysine Methyltransferase 2B) • POT1 (Protection of telomeres 1) • PRDM1 (PR/SET Domain 1) • AMER1 (APC Membrane Recruitment Protein 1) • CHD4 (Chromodomain Helicase DNA Binding Protein 4) • CSMD3 (CUB And Sushi Multiple Domains 3) • FANCD2 (FA Complementation Group D2) • LATS1 (Large Tumor Suppressor Kinase 1) • TAP1 (Transporter 1) • ACVR2A (Activin A Receptor Type 2A) • CUL4B (Cullin 4B) • DSC1 (Desmocollin 1) • MAP2K4 (Mitogen-Activated Protein Kinase Kinase 4) • RASA1 (RAS P21 Protein Activator 1) • SLX4 (SLX4 Structure-Specific Endonuclease Subunit) • USP9X (Ubiquitin Specific Peptidase 9 X-Linked)

TMB-H • MSI-H/dMMR • POLE mutation • RNF43 mutation • PMS2 mutation

Oncomine™ Comprehensive Assay Plus

over1year

Molecular Landscape of Hepatocellular Carcinoma (HCC) and the Recurrence Risk Assessment Score (RRAS): Correlating Molecular Signatures to RRAS (USCAP 2023)

HCCs with RRAS of 4 were more likely to harbor TP53 alterations and those with scores of <4 were more likely to have CTNNB1 alterations, though neither alteration seems to correlate with recurrence. Conversely, higher accumulation of genetic and chromosomal gains and losses were associated with recurrence and not RRAS. In the setting of a cohort with demonstrated concordance between RRAS of 4 and recurrence, the lack of significant association with molecular findings suggests that RRAS may be a prognostic factor independent of molecular typing.

over 1 year ago

TP53 (Tumor protein P53) • TERT (Telomerase Reverse Transcriptase) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)

TERT mutation • TERT promoter mutation

Oncomine™ Comprehensive Assay Plus

over1year

Characterization of Homologous Recombination Deficiency-Associated Pancreatic Ductal Adenocarcinoma Using Oncomine Comprehensive Assay Plus NGS-Based Cancer Panel (USCAP 2023)

In contrast to 14.5-16.5% through NGS panels and 24-44% through WES or WGS reported in the literatures, our HRD assessment using Oncomine Plus NGS-based cancer panel revealed a high prevalence of 33% in our PDAC cohort, suggesting NGS-based panel method could be a potential powerful tool for HRD estimate. Interestingly, our HRD-associated PDAC cohort showed a different distribution of concurrent variants compared to TCGA PDAC, which might be suggestive of the biologic differences between HRD-associated PDAC cohort and non-HRD-associated PDAC cohort.

over 1 year ago

Tumor mutational burden • PARP Biomarker • MSi-H Biomarker • BRCA Biomarker • Next-generation sequencing

KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • ATM (ATM serine/threonine kinase) • HRD (Homologous Recombination Deficiency) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • ARID1A (AT-rich interaction domain 1A) • PALB2 (Partner and localizer of BRCA2) • RNF43 (Ring Finger Protein 43) • CDK12 (Cyclin dependent kinase 12) • SMAD4 (SMAD family member 4) • CHEK2 (Checkpoint kinase 2) • RAD51 (RAD51 Homolog A) • FANCA (FA Complementation Group A) • RAD51B (RAD51 Paralog B) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD50 (RAD50 Double Strand Break Repair Protein) • RAD51D (RAD51 paralog D) • CHEK1 (Checkpoint kinase 1) • BARD1 (BRCA1 Associated RING Domain 1) • MRE11A (MRE11 homolog, double strand break repair nuclease) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • RAD54L (DNA Repair And Recombination Protein RAD54) • FANCF (FA complementation group F) • FANCL (FA Complementation Group L) • HDAC2 (Histone deacetylase 2) • FANCD2 (FA Complementation Group D2) • FANCE (FA Complementation Group E) • FANCC (FA Complementation Group C)

KRAS mutation • TMB-H • MSI-H/dMMR • HRD • KRAS Q61H

Oncomine™ Comprehensive Assay Plus

over1year

Somatic Genomic Alteration Prevalence and Association with Tumor Grade Reclassification in Prostate Cancer Patients Undergoing Active Surveillance (USCAP 2023)

We provide a first assessment of somatic genomic alterations in PCa in a large multi-institutional cohort of patients on active surveillance. Potentially owing to the low prevalence of pathogenic genomic alterations (7.9%), no association between pathogenic genomic alterations and grade reclassification was identified.

over 1 year ago

Clinical • BRCA Biomarker

TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • PTEN (Phosphatase and tensin homolog) • FGFR1 (Fibroblast growth factor receptor 1) • ATM (ATM serine/threonine kinase) • CHEK2 (Checkpoint kinase 2) • SPOP (Speckle Type BTB/POZ Protein) • APEX1 (Apurinic/Apyrimidinic Endodeoxyribonuclease 1)

BRCA2 mutation • BRCA1 mutation • ATM mutation • FGFR1 amplification

Oncomine™ Comprehensive Assay Plus

over1year

Evaluation of clinical benefit and progression-free survival ratio of targeted treatments in a prospective cohort study of patients with biliary tract cancers. (ASCO-GI 2023)

Targeted therapy was actually started for 48 pts (14 %), with 9 pts treated with ivosidenib, 32 with FGFR2 inhibitors, 2 with PD-L1 inhibitor, 6 with BRAF+MEK inhibitor and 1 with an HER2 inhibitor)... Expanded sequencing for BTCs is feasible in real-life and can improve treatment strategy. Analysis of PFS ratio and of treatment outcomes shows clinically meaningful benefit of targeted treatment in pretreated patients.

over 1 year ago

Clinical • PD(L)-1 Biomarker • MSi-H Biomarker • BRCA Biomarker • IO biomarker

BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • FGFR2 (Fibroblast growth factor receptor 2) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1)

BRAF V600E • BRCA2 mutation • BRCA1 mutation • MSI-H/dMMR • HER-2 amplification • BRAF V600 • IDH1 mutation • FGFR2 mutation • FGFR2 fusion • BRCA2 amplification

FoundationOne® CDx • Oncomine™ Comprehensive Assay Plus

Tibsovo (ivosidenib)

over1year

Serial genomic analysis of circulating tumor cells, circulating free DNA and change of immune-related gene signature in triple negative and HER2 positive advanced, metastatic breast cancer (SABCS 2022)

Our study suggest that serial follow up CTC and ctDNA,immune-related gene signature is feasible and reflect the general characteristics of baselinecharacteristics and dynamic molecular alteration of breast cancer. Further analysis with largerpatient sample and correlation with tumor tissue is warranted in the future.

over 1 year ago

Tumor mutational burden • Gene Signature • Circulating tumor cells • BRCA Biomarker

HER-2 (Human epidermal growth factor receptor 2) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MYCN (MYCN Proto-Oncogene BHLH Transcription Factor) • FGFR4 (Fibroblast growth factor receptor 4) • EPCAM (Epithelial cell adhesion molecule)

HER-2 positive • TP53 mutation • BRCA1 mutation • FGFR4 mutation

Oncomine™ Comprehensive Assay Plus

over1year

Fibroblast growth factor receptor (FGFR) inhibitor rogaratinib in patients with advanced pretreated squamous-cell non-small cell lung cancer over-expressing FGFR mRNA: The SAKK 19/18 phase II study. (PubMed, Lung Cancer)

Despite preliminary signals of activity, rogaratinib failed to improve PFS in patients with advanced SQCLC overexpressing FGFR mRNA. FGFR inhibitors in SQCLC remain a challenging field, and more in-depth understanding of pathway crosstalks may lead to the development of drug combinations with FGFR inhibitors resulting in improved outcomes.

over 1 year ago

Journal • P2 data

FGFR1 (Fibroblast growth factor receptor 1) • FGFR (Fibroblast Growth Factor Receptor)

FGFR overexpression

Oncomine™ Comprehensive Assay Plus

rogaratinib (BAY 1163877)

2years

Serial genomic analysis of circulating tumor cells and circulating tumor DNA in triple-negative and HER2-positive advanced, metastatic breast cancer. (ASCO 2022)

Our study suggest that serial follow up CTC and ctDNA is feasible and reflect the general characteristics of baseline characteristics and dynamic molecular alteration of breast cancer. Further analysis with larger patient sample and correlation with tumor tissue is warranted in the future.

2 years ago

Tumor mutational burden • Circulating tumor cells • BRCA Biomarker • Circulating tumor DNA

HER-2 positive • TP53 mutation • BRCA1 mutation

Oncomine™ Comprehensive Assay Plus

2years

Molecular analyses of metastatic collecting ducts renal cell carcinoma from the phase 2 prospective trial of cabozantinib as first-line treatment (BONSAI trial Meeturo 2). (ASCO 2022)

Our findings for the first time define specific molecular signatures that differentiate therapy-specific outcomes in first-line mCDC, warranting further investigation of their involvement in the tumor biology.

2 years ago

P2 data • Clinical

Oncomine™ Comprehensive Assay Plus

Cabometyx (cabozantinib tablet)

2years

Shannon entropy of mutational signatures predict sensitivity of signature detection in targeted sequencing (AACR 2022)

For research use only. Not for use in diagnostic procedures.

2 years ago

Tumor mutational burden • MSi-H Biomarker

HRD (Homologous Recombination Deficiency)

MSI-H/dMMR

Oncomine™ Comprehensive Assay Plus

over2years

Oncocyte announces development and co-marketing agreement with Thermo Fisher Scientiﬁc to expand access to precision oncology (Oncocyte Press Release)

"Oncocyte Corporation...announced a development and co-marketing agreement for two distributed in vitro diagnostic (IVD) assays on Thermo Fisher Scientific’s Ion Torrent™ Genexus™ System...Under the terms of the collaboration, Oncocyte will clinically validate Thermo Fisher’s existing Oncomine Comprehensive Assay Plus* on the Genexus System, paving the way toward IVD clearance for use in tumor profiling and future submissions as a companion diagnostic...Oncocyte will also develop its 27-gene expression DetermaIO™ test as a distributed kit on the Genexus."

over 2 years ago

Licensing / partnership

Oncomine™ Comprehensive Assay v3M • DetermaIO™ • Oncomine™ Comprehensive Assay Plus

over2years

Histologic, Immunohistochemical and Molecular Stratification of Thymic Neuroendocrine Neoplasms (USCAP 2022)

In our cohort, all LCNEC were reclassified as G2/G3 WD-NET by morphology and Ki67 index using WHO GEP NEN criteria. G3 WD-NET appears along a molecular spectrum with G2 WD-NET, and biologically distinct from high grade NEC in the thymus. Thymic NENs may be stratified into at least 3 molecular subgroups, including a subset of G3 WD-NET with RAS/MAPK pathway mutations, with potential therapeutic implications.

over 2 years ago

TP53 (Tumor protein P53) • NRAS (Neuroblastoma RAS viral oncogene homolog) • HRAS (Harvey rat sarcoma viral oncogene homolog) • KDR (Kinase insert domain receptor) • SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1) • TSC1 (TSC complex subunit 1) • FGF4 (Fibroblast growth factor 4) • ENO1 (Enolase 1) • CHD4 (Chromodomain Helicase DNA Binding Protein 4) • DAXX (Death-domain associated protein) • MEN1 (Menin 1) • MAP2K7 (Mitogen-Activated Protein Kinase Kinase 7)

NRAS mutation • TP53 wild-type • HRAS mutation • TSC1 mutation • MTOR mutation • TP53 expression • ENO1 deletion

Oncomine™ Comprehensive Assay Plus

over2years

[VIRTUAL] A Targeted Next-Generation Sequencing Assay to Characterize Homologous Recombination Deficiency (HRD) Reveals Associations between Homologous Recombination Repair Genes and Genomic Instability (AMP 2021)

HRD is an emerging biomarker for sensitivity to cisplatin and for inhibitors of poly (ADPribose) polymerase (PARP)... We developed a comprehensive genomic profiling assay that determines genomic %LOH to characterize HRD. We established that tumor samples with BRCA1/2 alterations exhibit significantly higher %LOH relative to samples without HRR alterations. Further, samples with biallelic BRCA1/2 mutations have higher %LOH relative to monoallelic mutations.

over 2 years ago

PARP Biomarker • BRCA Biomarker • Next-generation sequencing

BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD52 (RAD52 Homolog DNA Repair Protein)

BRCA2 mutation • BRCA1 mutation • HRD • BRIP1 mutation • RAD52 mutation

Oncomine™ Comprehensive Assay Plus

cisplatin

over2years

[VIRTUAL] Splice Site and Exon Deletion Variants Detection with Oncomine RNA Sequencing Panel (AMP 2021)

We demonstrated exon deletion and splice site detection technology with an expanded RNA sequencing Oncomine panel that includes more than 1,000 gene fusion targets and assays for novel fusion detection. The approach is compatible with Ion systems, requires low input material, and retains simple workflows and fast turn-around time.

over 2 years ago

BRCA Biomarker

EGFR (Epidermal growth factor receptor) • BRAF (B-raf proto-oncogene) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • BRCA1 (Breast cancer 1, early onset) • FGFR2 (Fibroblast growth factor receptor 2) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • RELA (RELA Proto-Oncogene)

NTRK1 fusion • NTRK2 fusion • MET exon 14 mutation • FGFR2 fusion • ALK fusion

Oncomine™ Comprehensive Assay Plus

over2years

Oncomine™ Comprehensive Assay v3 vs. Oncomine™ Comprehensive Assay Plus. (PubMed, Cancers (Basel))

Moreover, results showed that a region of PTEN is poorly covered by the OCA-Plus assay, hence, we implemented rescue filters for those variants. In conclusion, the OCA-Plus can reflect the mutational profile of genomic variants compared with OCAv3 of 144 overlapping genes, without compromising performance.

over 2 years ago

Journal • Tumor mutational burden

TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • PTEN (Phosphatase and tensin homolog)

Oncomine™ Comprehensive Assay v3M • Oncomine™ Comprehensive Assay Plus

over2years

Association of tumour mutational burden (TMB) with outcomes in stage IIIA(N2) non-small cell lung cancer (NSCLC) patients treated with neoadjuvant chemotherapy and durvalumab: prospective analysis of the multicenter single-arm phase II trial SAKK16/14 (DGHO 2021)

Here, we evaluate the association of tumor TMB with clinical outcome in resectable stage IIIA(N2) non-small cell lung cancer (NSCLC) patients undergoing neoadjuvant chemo-immunotherapy with three cycles of cisplatin/docetaxel followed by treatment with the PD-L1 antibody durvalumab. Our results suggest that TMB is not associated with clinical outcome after neoadjuvant sequential chemo-immunotherapy with durvalumab in patients with resectable stage IIIA(N2) NSCLC.

over 2 years ago

P2 data • Clinical • Tumor mutational burden • PD(L)-1 Biomarker • IO biomarker

TMB (Tumor Mutational Burden)

TMB-H

FoundationOne® CDx • Oncomine™ Comprehensive Assay Plus

cisplatin • Imfinzi (durvalumab) • docetaxel

almost3years

[VIRTUAL] SAKK 16/14 - T - Cell Receptor Repertoire Metrics Predict Response to Neoadjuvant Durvalumab in Patients With Stage IIIA(N2) NSCLC (IASLC-WCLC 2021)

"Here, we performed TCR sequencing in patients from the phase 2 trial SAKK 16/14 undergoing neoadjuvant chemotherapy with three cycles of cisplatin/docetaxel followed by treatment with the PD-L1 antibody durvalumab. In contrast, TMB was not associated with EFS, MPR or nodal clearance (p=0.91, p=0.47, p=0.52). Conclusion Our results show that TCR repertoire measured in peripheral blood samples and tumor tissue may provide a useful tool for predicting risk of recurrence after neoadjuvant sequential chemo-immunotherapy with durvalumab in patients with resectable stage IIIA(N2) NSCLC."

almost 3 years ago

Clinical

TMB (Tumor Mutational Burden)

FoundationOne® CDx • Oncomine™ BCR IGH-LR Assay • Oncomine™ BCR IGH-SR Assay • Oncomine™ Comprehensive Assay Plus

cisplatin • Imfinzi (durvalumab) • docetaxel

3years

[VIRTUAL] The RODILIA pilot study for molecular screening of patients with metaplastic breast cancer (ESMO-BC 2021)

Mutational and copy number alterations conveyed complementary information in MPBC cooperating in activation of cancer pathways.These findings suggest to further study the value of CNAs in MPBC biological processes, especially immunogenicity, which cannot be explained by the low TMB and MSI found. Extended data with matched immune profile will be presented at the meeting.

3 years ago

Clinical • Tumor mutational burden

TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • PTEN (Phosphatase and tensin homolog) • FGFR3 (Fibroblast growth factor receptor 3) • mTOR (Mechanistic target of rapamycin kinase) • FGFR4 (Fibroblast growth factor receptor 4) • TGFB1 (Transforming Growth Factor Beta 1)

TP53 mutation • TMB-L • NFE2L2 mutation • MTOR mutation

Oncomine™ Comprehensive Assay Plus

over3years

[VIRTUAL] An Extended Targeted RNA Sequencing for Fusion Detection with Oncomine Comprehensive Assay Plus (IASLC-WCLC 2020)

We also sequenced 2 ALK fusion FFPE samples and a single RET fusion FFPE sample, and obtained positive calls with the exon tiling method, concordant to the detected fusion isoforms in the samples. Conclusion We present a design and study results for an extended, multiplexed RNA panel for fusions and intragenic rearrangements that retains the simple workflow and fast turn-around time of previous Oncomine fusion panels and significantly expands the scope of fusion isoform detection including methods to detect novel gene fusions in a partner agnostic manner.

over 3 years ago

ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine 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) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • NTRK (Neurotrophic receptor tyrosine kinase)

NTRK1 fusion • NTRK2 fusion • RET fusion • MET exon 14 mutation • ALK fusion • RET rearrangement • NTRK fusion

Oncomine™ Comprehensive Assay Plus

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