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TEST:
OncoPanel™ Assay

Type:
Laboratory Developed Test
Evidence

News

3d
Molecular profiling of visible polypoid and invisible conventional intestinal-type low-grade dysplasia in patients with idiopathic inflammatory bowel disease. (PubMed, J Clin Pathol)
Molecular alterations in visible low-grade dysplastic polyps with conventional intestinal-type dysplasia from patients with IBD and sporadic adenomas from non-IBD patients overlap significantly. APC alterations appear to play a major role in the development of visible low-grade dysplastic lesions in patients with IBD, regardless of background colitis. As with IBD-associated colorectal cancers, TP53 mutations are an early event in the development of invisible, low-grade conventional intestinal-type dysplasia in patients with IBD.
Journal
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KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • ARID1A (AT-rich interaction domain 1A) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • TCF7L2 (Transcription Factor 7 Like 2)
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OncoPanel™ Assay
2ms
The Identification of an Activating ESR1 Mutation in an Aggressive Prolactinoma Enabled the Use of Personalized Treatment (ENDO 2024)
Elacestrant, a second-line ER degrader, increases overall free-survival in patients with resistant breast cancer and ESR1Y537S...Abstracts presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.
ER (Estrogen receptor) • SF3B1 (Splicing Factor 3b Subunit 1) • MEN1 (Menin 1)
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ER positive • ER mutation • ER Y537S • SF3B1 mutation • ESR1 mutation
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OncoPanel™ Assay
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Orserdu (elacestrant)
2ms
Characterizing genomic alterations in patients with metastatic urothelial carcinoma (mUC) treated with enfortumab-vedotin (EV) with a focus on 1q23.3. (ASCO 2024)
Our study did not find significant correlations between specific somatic alterations and clinical outcomes in patients with metastatic UC treated with EV though limited by small sample size. The observed trends in alterations of 1q23. 3 and 9p21.
Clinical • Metastases
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CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • MTAP (Methylthioadenosine Phosphorylase) • CDKN2B (Cyclin Dependent Kinase Inhibitor 2B)
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OncoPanel™ Assay
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Padcev (enfortumab vedotin-ejfv)
2ms
Combination therapy • Enrollment closed • Metastases
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PD-L1 (Programmed death ligand 1) • BRCA1 (Breast cancer 1, early onset) • MSI (Microsatellite instability) • CD8 (cluster of differentiation 8) • MLH1 (MutL homolog 1) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • CDK12 (Cyclin dependent kinase 12) • CHEK2 (Checkpoint kinase 2) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD51D (RAD51 paralog D) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • ABRAXAS1 (Abraxas 1 BRCA1 A Complex Subunit 2) • GEN1 (GEN1 Holliday junction 5' flap endonuclease)
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PD-L1 expression • MSI-H/dMMR
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OncoPanel™ Assay
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Opdivo (nivolumab) • docetaxel • goserelin acetate • Firmagon (degarelix) • leuprolide acetate for depot suspension
2ms
Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA. (PubMed, Sci Rep)
The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.
Journal
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OncoPanel™ Assay
2ms
Merestinib In Non-Small Cell Lung Cancer And Solid Tumors (clinicaltrials.gov)
P2; Trial completion date: Mar 2024 --> Oct 2023 | Active, not recruiting --> Terminated; Funding was pulled
Trial completion date • Trial termination
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EGFR (Epidermal growth factor receptor) • ALK (Anaplastic lymphoma kinase) • MET (MET proto-oncogene, receptor tyrosine kinase) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK (Neurotrophic receptor tyrosine kinase)
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MET exon 14 mutation
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OncoPanel™ Assay
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merestinib (LY2801653)
4ms
Investigating clinical trial eligibility criteria to improve MatchMiner trial matching (AACR 2024)
Overall, having similar categories of criteria across trials suggests that common clinical data could be used for many different PM trials. Currently, we are investigating which categories are most relevant for trial matching and the use of AI for structuring unstructured clinical data.
Clinical
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OncoPanel™ Assay
4ms
A novel microtubule disruptor exerts broad anticancer efficacy with a tolerable safety profile (AACR 2024)
Our studies have elaborated the mechanism of AUS_001 as an inhibitor of tubulin polymerization. The favorable safety profile of AUS_001, along with its ability to circumvent Pgp-mediated multidrug resistance, provides potential for efficacy against multiple cancers where microtubule destabilization is proven to be an effective target.
Clinical
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PGP overexpression
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OncoPanel™ Assay
4ms
Evolution of clinically relevant variants in advanced pediatric sarcomas (AACR 2024)
Interestingly, in three cases there was emergence of a new variant activating the RAF/MAPK or AKT pathway.Conclusion Pediatric sarcomas display a range of genomic changes over time. Given the observed changes in oncogenic alterations, there may be utility to repeat sequencing of relapsed tumor biopsies to understand these changes.
Clinical • Metastases
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TP53 (Tumor protein P53) • STAG2 (Stromal Antigen 2)
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OncoPanel™ Assay
4ms
Small molecule allosteric regulators of eIF4E activity target proteomic dysregulation and demonstrate potent antiproliferative activity in multiple myeloma models whilst sparing normal immune cells (AACR 2024)
Furthermore, CD4+ T-cells isolated from fresh PBMCs demonstrated proliferative responses following stimulation (ImmunoCultâ„¢) in the presence of PIC eIF4E regulators. The impact on key oncogenic drivers and potent antiproliferative activity in multiple myeloma models with minimal effects on normal immune cell populations suggests that targeting eIF4E activity with PIC allosteric eIF4E regulators could offer an attractive therapeutic strategy in multiple myeloma.
Immune cell
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MYC (V-myc avian myelocytomatosis viral oncogene homolog) • CD4 (CD4 Molecule) • EIF4EBP1 (Eukaryotic translation initiation factor 4E binding protein 1)
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MYC expression
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OncoPanel™ Assay
4ms
Genomic analysis of primary epithelial neoplasms of the seminal vesicle identifies a subset of mucinous cystic tumours driven by KRAS mutations. (PubMed)
Our results suggest that primary low-grade mucinous neoplasms of the seminal vesicle may represent a distinct entity equivalent to appendiceal counterparts, driven by gain-of-function variants of RAS GTPases. The remaining tumours showed genomic features that closely resembled those of neoplasms with comparable phenotypes and/or biological characteristics arising in other sites, suggesting that they could be managed similarly, with special considerations related to their anatomical location.
Journal
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OncoPanel™ Assay
4ms
Molecular and Clinical Characterization of Oncocytic Intraductal Papillary Neoplasms of the Pancreas (USCAP 2024)
The presence of a PRKACA/B fusion appears to contribute to oncocytic morphology, but 71% of fusion-positive cases had mixed epithelial subtypes. Rare cases harbored concurrent fusion and driver mutation associated with IPMN. Though fusion-positive lesions were more commonly seen in the non-recurrence group, they also comprised >50% of cases with disease recurrence.
Clinical
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KRAS (KRAS proto-oncogene GTPase) • RNF43 (Ring Finger Protein 43) • SMAD4 (SMAD family member 4) • GNAS (GNAS Complex Locus) • PRKACA (Protein Kinase CAMP-Activated Catalytic Subunit Alpha)
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KRAS mutation • RNF43 mutation • SMAD4 deletion • GNAS mutation • KRAS deletion
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OncoPanel™ Assay
4ms
Trial primary completion date
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CCND1 (Cyclin D1) • CDK4 (Cyclin-dependent kinase 4) • CDK6 (Cyclin-dependent kinase 6)
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CCND1 amplification • CDK4 amplification • CCND1 mutation
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OncoPanel™ Assay
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Verzenio (abemaciclib)
5ms
Association of a gene-expression subtype to outcome and treatment response in patients with recurrent/metastatic head and neck squamous cell carcinoma treated with nivolumab. (PubMed, J Immunother Cancer)
P3; These data highlight the presence of underlying biological differences able to predict survival and response following treatment with immunotherapy in platinum-refractory R/M HNSCC that could have translational implications improving treatment selection.
Journal • P3 data • Tumor mutational burden • PD(L)-1 Biomarker • IO biomarker • Metastases
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PD-L1 (Programmed death ligand 1) • TMB (Tumor Mutational Burden)
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OncoPanel™ Assay
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Opdivo (nivolumab)
5ms
Idiopathic erythrocytosis: a germline disease? (PubMed, Clin Exp Med)
We identified recurrent germline variants in 42 (75%) patients occurring mainly in JAK/STAT, Hypoxia and Iron metabolism pathways, among them: JAK3-V722I and HIF1A-P582S; a high fraction of patients (48.2%) resulted also mutated in homeostatic iron regulatory gene HFE-H63D or C282Y. By generating cellular models, we showed that JAK3-V722I causes activation of the JAK-STAT5 axis and upregulation of EPAS1/HIF2A, while HIF1A-P582S causes suppression of hepcidin mRNA synthesis, suggesting a major role for these variants in the onset of IE.
Journal • Tumor mutational burden
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TMB (Tumor Mutational Burden) • DNMT3A (DNA methyltransferase 1) • JAK2 (Janus kinase 2) • ASXL1 (ASXL Transcriptional Regulator 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • HIF1A (Hypoxia inducible factor 1, alpha subunit) • WT1 (WT1 Transcription Factor) • EPAS1 (Endothelial PAS domain protein 1) • JAK3 (Janus Kinase 3)
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TMB-H • DNMT3A mutation • TMB-L • JAK2 V617F • JAK2 mutation • JAK3 mutation • HIF1A P582S
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OncoPanel™ Assay
5ms
Clinical and genomic predictors of adverse events in newly diagnosed glioblastoma. (PubMed, Clin Cancer Res)
Genomic biomarkers based on functional variant analysis of a routine clinical panel may help identify adverse events in GBM, particularly seizures. Identifying these risk factors could improve the management of patients through better supportive care and consideration of prophylactic therapies.
Journal • Adverse events
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EGFR (Epidermal growth factor receptor) • TP53 (Tumor protein P53) • RB1 (RB Transcriptional Corepressor 1) • GNA11 (G Protein Subunit Alpha 11) • SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily A, member 4) • SETD2 (SET Domain Containing 2, Histone Lysine Methyltransferase) • TCF3 (Transcription Factor 3) • BRD4 (Bromodomain Containing 4)
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IDH wild-type
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OncoPanel™ Assay
5ms
Enrollment change • Trial withdrawal • Metastases
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BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset)
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BRCA1 mutation • BRCA2 deletion • BRCA1 deletion
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OncoPanel™ Assay
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Lynparza (olaparib)
5ms
Trial suspension • Tumor mutational burden
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HRD (Homologous Recombination Deficiency) • CD4 (CD4 Molecule)
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HRD
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OncoPanel™ Assay
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Lynparza (olaparib) • Xofigo (radium Ra-223 dichloride)
5ms
Implementing Tumour-First Genetic Testing and Parent-of-Origin-Aware Genomic Analysis into the Diagnostic Pipeline for Hereditary Breast Cancer (ACMG 2024)
By implementing next-generation sequencing into the diagnostic pipeline for breast cancer, we can identify more patients with hereditary breast cancer and expedite familial screening for breast cancer prevention. This pilot program will offer valuable insights for future implementation of tumour genetic testing on a larger scale in the province. Additionally, the results will provide evidence supporting the adoption of POAga as an alternative cascade genetic testing approach, leading to a 50% increase in efficiency, reduced financial burden, and emotional benefits for patients and their families.
Genomic analysis • BRCA Biomarker • Omic analysis
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BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • BRCA (Breast cancer early onset)
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BRCA2 mutation • BRCA1 mutation • BRCA mutation
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OncoPanel™ Assay
6ms
Prevalence and Therapeutic Targeting of High Level ERBB2 Amplification in Non-Small Cell Lung Cancer. (PubMed)
High level ERBB2 amplification reliably predicts HER2 amplification in NSCLC patients and HER2 ADC is effective therapy in this population.
Journal
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OncoPanel™ Assay
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Gilotrif (afatinib) • Kadcyla (ado-trastuzumab emtansine) • Enhertu (fam-trastuzumab deruxtecan-nxki)
6ms
Trial completion date • IO biomarker • Metastases
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HER-2 (Human epidermal growth factor receptor 2) • PGR (Progesterone receptor) • TMB (Tumor Mutational Burden)
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HR positive • HER-2 amplification • HER-2 negative • ER positive + PGR positive • PGR positive
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MSK-IMPACT • OncoPanel™ Assay
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Opdivo (nivolumab) • Yervoy (ipilimumab)
6ms
A multicohort phase 2 trial of ADT, docetaxel plus nivolumab in patients with de novo metastatic hormone-sensitive prostate cancer enriched for inflamed tumors and DNA damage repair defects. (ASCO-GU 2024)
After January 2022, the addition of standard of care abiraterone/prednisone was allowed after 7 months of study treatment at investigator discretion. Clinical trial information: NCT04126070.PD-L1 Combined Positive Score (CPS) ≥ 1 and/or CD T cell density ≥ 200. Homozygous deletions and/or deleterious mutations in a DDR gene, including and not limited to BRCA2, ATM, CHECK2, BRCA1, PALB2, RAD51D, ATR, NBN, PMS2, GEN1, MLH1, MSH2, MSH6, RAD51C, MRE11A, BRIP1, FAM175A, and CDK12.
P2 data • Clinical • PD(L)-1 Biomarker • BRCA Biomarker • IO biomarker • Metastases
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PD-L1 (Programmed death ligand 1) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • CD8 (cluster of differentiation 8) • PALB2 (Partner and localizer of BRCA2) • MLH1 (MutL homolog 1) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • CDK12 (Cyclin dependent kinase 12) • PMS2 (PMS1 protein homolog 2) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD51C (RAD51 paralog C) • RAD51D (RAD51 paralog D) • MRE11A (MRE11 homolog, double strand break repair nuclease) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • ABRAXAS1 (Abraxas 1 BRCA1 A Complex Subunit 2) • GEN1 (GEN1 Holliday junction 5' flap endonuclease)
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PD-L1 expression • ATM mutation • PALB2 mutation • BRIP1 mutation • RAD51C mutation • RAD51D mutation • PMS2 mutation • MRE11A mutation • NBN mutation
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OncoPanel™ Assay
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Opdivo (nivolumab) • docetaxel • abiraterone acetate
7ms
Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy. (ASCO-GI 2024)
In 2022, 151,030 new CRC and 65,950 new EC cases were diagnosed in the USA. Extrapolating our findings to this larger population, use of NGS mutational signature analysis instead of IHC would amount to about 1510 additional MMR-D CRC cases and 3297 additional MMR-D endometrial cases identified each year for whom first-line ICI therapy is preferred. Our findings support revisiting guideline recommendations for diagnostic testing of MMR to incorporate both IHC and targeted NGS tumor panel testing using sensitive and specific mutation signature calling algorithms.
Clinical • IO biomarker • Mismatch repair
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MSI (Microsatellite instability)
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OncoPanel™ Assay
7ms
COMRADE: Testing the Safety of Different Doses of Olaparib Given Radium-223 for Men With Advanced Prostate Cancer With Bone Metastasis (clinicaltrials.gov)
P1/2; Trial completion date: Nov 2023 --> Nov 2024 | Trial primary completion date: Nov 2023 --> Nov 2024
Trial completion date • Trial primary completion date • Tumor mutational burden
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HRD (Homologous Recombination Deficiency) • CD4 (CD4 Molecule)
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HRD
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OncoPanel™ Assay
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Lynparza (olaparib) • Xofigo (radium Ra-223 dichloride)
7ms
Antineoplastic activity of GP-2250 in-vitro and in mouse xenograft models. (PubMed, Anticancer Drugs)
GP-2250 demonstrated cytotoxic activity in vitro and reduced the tumor volume in a variety of human cancer cell lines in a xenograft mouse model. Given these results, as well as evidence of synergism with other anticancer drugs, GP-2250 shows promise as a new therapeutic agent for treating human cancers and is being evaluated in a phase 1 dose-escalation study (NCT03854100).
Journal • Preclinical
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OncoPanel™ Assay
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misetionamide (GP-2250)
7ms
Prognostic impact of tumor mutational burden at baseline in IDH-wildtype glioblastoma (SNO 2023)
In summary, there is no significant association between TMB at baseline and poor survival outcomes in IDH-wildtype GBM. Further research is needed to explore the potential implications of TMB as a prognostic marker and its relevance for personalized treatment strategies in GBM patients.
Tumor mutational burden
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TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • MLH1 (MutL homolog 1) • MSH6 (MutS homolog 6) • MSH2 (MutS Homolog 2) • PMS2 (PMS1 protein homolog 2)
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MSH2 mutation • MLH1 mutation • PMS2 mutation • IDH wild-type
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OncoPanel™ Assay
7ms
Classification of diffuse glioma subtypes using a next-generation sequencing panel in accordance with the 2021 World Health Organization criteria (SNO 2023)
Cox multivariate regression analysis of 341 GBM patients (median survival=15.9 months) revealed that older age, lack of MGMT promoter methylation, and impaired performance status (Karnofsky performance scale < 80) were significantly associated with survival outcome (HRage=1.40, Page=7.64×10-3, HRMGMT=1.43, PMGMT=6.98×10-3, and HRKPS=1.79, PKPS=3.05×10-6). In summary, by utilizing the AMC OncoPanel and the 2021 WHO criteria, we successfully classified diffuse glioma into three distinct.
Tumor mutational burden • Next-generation sequencing
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EGFR (Epidermal growth factor receptor) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NOTCH1 (Notch 1) • MGMT (6-O-methylguanine-DNA methyltransferase) • ATRX (ATRX Chromatin Remodeler) • FUBP1 (Far Upstream Element Binding Protein 1)
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TP53 mutation • EGFR mutation • IDH1 mutation • MGMT promoter methylation • IDH wild-type
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OncoPanel™ Assay
7ms
Targeting the DNA damage response in glioblastoma propagating cells: from molecular mechanisms to precision medicine (SNO 2023)
Finally, we have also identified group-specific therapeutic strategies combining repositioned FDA-approved drugs with the inhibition of crucial DDR factors. Our long-term goals are i) to understand the molecular basis behind the differential response to DNA damage and replication stress developed by G1 and G3 cells and ii) to propose group-specific, DDR-based combination therapies that prevent treatment resistance and promote long-lasting treatment.
OncoPanel™ Assay
8ms
Comprehensive clinicogenomic characterization of inflammatory breast cancer (SABCS 2023)
Taken together, this study provides a comprehensive landscape of somatic alterations in a large cohort of patients with metastatic IBC and non-IBC. Our data support a lack of major genomic differences other than enrichments in TP53 mutations and an associated LumB-like histopathology. These results both reinforce the importance of TP53 mutations in IBC biology and suggest additional analyses beyond somatic DNA-level changes are warranted.
Tumor mutational burden
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HER-2 (Human epidermal growth factor receptor 2) • ER (Estrogen receptor) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • PGR (Progesterone receptor) • TMB (Tumor Mutational Burden) • FGFR1 (Fibroblast growth factor receptor 1) • CCND1 (Cyclin D1) • GATA3 (GATA binding protein 3)
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HER-2 positive • TP53 mutation • HR positive • ER negative
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OncoPanel™ Assay
8ms
Using Tumor/Germline paired data to recalibrate rescue of somatic variants in Tumor-only NGS (AMP 2023)
Somatic databases such as COSMIC and polymorphism databases such as gnomAD provide convenient means to distinguish somatic versus germline mutations in Tonly tests without a matched germline sample. Careful validation of the data from these databases was essential to ensure that the results were accurate and specific. By using data from the T/G pipeline, we recalibrated the COSMIC and gnomAD cut-offs in our T-only pipeline to ≥10 instances and ≥1%, respectively.
Next-generation sequencing
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OncoPanel™ Assay
8ms
Evaluation of Assay-Specific Single Nucleotide Polymorphism B-allele Frequency Performance Metrics Informs Accurate Allele-Specific Copy Number Variant Calling in Tumor Only Panel NGS Data (AMP 2023)
These data highlight the utility of evaluation of SNP performance in targeted NGS assays using exclusively tumor-only data. Identification of high-quality informative SNP loci can aid in tumor purity estimation and in the interpretation of ASCN variants, as well as provide informative inputs for machine learning-based algorithms trained on a ground truth of CMA data.
Next-generation sequencing
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OncoPanel™ Assay
8ms
Clinical Implementation of Matched Tumor/Germline Sequencing Improves Accuracy of Tumor Genomic Profiling and Therapeutic Recommendations (AMP 2023)
Matched T/G sequencing enables definitive reporting of tumor-specific variants, more accurate TMB calculation, and appropriate classification of germline pathogenic/likely pathogenic findings. These improved genomic results enable more specific targeted and immunotherapy recommendations for patients and inform inherited cancer risk. Operationally, implementation of matched T/G sequencing can enable expansion of panel testing to whole-exome or whole-genome approaches.
Clinical • Tumor mutational burden • IO biomarker
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TMB (Tumor Mutational Burden)
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OncoPanel™ Assay
9ms
Validation of targeted next-generation sequencing of cell-free DNA from archival cerebrospinal fluid specimens for the detection of somatic variants in cancer involving the leptomeninges: Cytopathologic and radiographic correlation. (PubMed, Cancer Cytopathol)
These data highlight the stability of cfDNA in CSF, which allows for cytopathologic evaluation before triage for next-generation sequencing assays. For a subset of cases in which clinical suspicion is high but cytologic or radiographic studies are inconclusive, the detection of pathogenic somatic variants in CSF cfDNA may aid in the diagnosis of leptomeningeal metastases.
Journal • Next-generation sequencing
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OncoPanel™ Assay
9ms
A Genomic Score to Predict Local Control among Patients with Brain Metastases Managed with Radiation. (PubMed, Int J Radiat Oncol Biol Phys)
Utilizing a targeted panel of genes with a known role in cancer pathogenesis, we developed a genomic score that can be calculated from an extracranial or intracranial site to quantify local recurrence risk following brain-directed radiation. Prior attempts to develop a biomarker-based radiation response signature have not focused on patients with BrM and have primarily relied on RNA-based measures of radiosensitivity, limiting their utility in real-world clinical practice for this patient population. To our knowledge, this represents the first study to systemically correlate DNA-based alterations with radiation-based outcomes among patients with BrM. If validated, Brain-RPS has potential to facilitate clinical trials aimed at genome-based personalization of radiation treatment among patients with BrM.
Journal
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PALB2 (Partner and localizer of BRCA2) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • PAX5 (Paired Box 5) • MDM4 (The mouse double minute 4) • AURKA (Aurora kinase A) • MYCL (MYCL Proto-Oncogene BHLH Transcription Factor) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • PRDM1 (PR/SET Domain 1) • CDKN1B (Cyclin dependent kinase inhibitor 1B)
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OncoPanel™ Assay
9ms
Genomic Predictors of Leptomeningeal Disease Development among Patients with Brain Metastases. (PubMed, Int J Radiat Oncol Biol Phys)
Utilizing a targeted panel of genes with a known role in cancer pathogenesis, we identified genomic alterations in three genes as being predictive of LMD development. If validated in independent datasets, development of clinical trials exploring inhibition of pathways affected by these genomic alterations may be warranted with the goal of LMD prevention and targeted treatment among particularly high-risk cohorts. To our knowledge, this represents the first study to identify potentially actionable alterations as predictive of leptomeningeal disease development among patients with brain metastases.
Journal
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SF3B1 (Splicing Factor 3b Subunit 1) • CDH1 (Cadherin 1) • MAPK1 (Mitogen-activated protein kinase 1)
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OncoPanel™ Assay
9ms
Immune checkpoint inhibitor-induced diabetes mellitus comprises multiple clinical endotypes with distinct immunologic features (SITC 2023)
Conclusions Our analysis identified several risk factors for ICI-DM that may identify patients at higher risk for ICI-DM. The results from our multi-modal strategy – combining clinical, genetic and translational approaches – to dissecting ICI-DM pathogenesis provides a roadmap on how to dissect the mechanistic determinants of ICI toxicities more broadly.
Checkpoint inhibition • Clinical • IO biomarker
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OncoPanel™ Assay
10ms
Genomic Predictors of Leptomeningeal Disease Development among Patients with Brain Metastases (ASTRO 2023)
Utilizing a targeted panel of genes with a known role in cancer pathogenesis, we identified genomic alterations in three genes as being predictive of LMD development. If validated in independent datasets, development of clinical trials exploring inhibition of pathways affected by these genomic alterations may be warranted with the goal of LMD prevention and targeted treatment among particularly high-risk cohorts. To our knowledge, this represents the first study to identify potentially actionable alterations as predictive of leptomeningeal disease development among patients with brain metastases.
Clinical
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SF3B1 (Splicing Factor 3b Subunit 1) • CDH1 (Cadherin 1) • MAPK1 (Mitogen-activated protein kinase 1)
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OncoPanel™ Assay
10ms
A Genomic Score to Predict Local Control among Patients with Brain Metastases Managed with Radiation (ASTRO 2023)
Utilizing a targeted panel of genes with a known role in cancer pathogenesis, we developed a genomic score that can be calculated from an extracranial or intracranial site to quantify local recurrence risk following brain-directed radiation. Prior attempts to develop a biomarker-based radiation response signature have not focused on patients with BrM and have primarily relied on RNA-based measures of radiosensitivity, limiting their utility in real-world clinical practice for this patient population. To our knowledge, this represents the first study to systemically correlate DNA-based alterations with radiation-based outcomes among patients with BrM.
Clinical
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PALB2 (Partner and localizer of BRCA2) • PAX5 (Paired Box 5) • MDM4 (The mouse double minute 4) • AURKA (Aurora kinase A) • MYCL (MYCL Proto-Oncogene BHLH Transcription Factor) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • PRDM1 (PR/SET Domain 1) • CDKN1B (Cyclin dependent kinase inhibitor 1B)
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OncoPanel™ Assay
10ms
CTNNB1 and APC Mutations in Sinonasal Myxoma: Expanding the Spectrum of Tumors Driven By WNT/β-catenin Pathway. (PubMed, Am J Surg Pathol)
Our findings expand the spectrum of tumors with underlying WNT/β-catenin pathway and highlight the histologic, clinical, and genetic differences of SNM compared with desmoid fibromatosis. APC deletion raises the possibility of underlying germline alteration and familial adenomatous polyposis.
Journal
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APC (APC Regulator Of WNT Signaling Pathway)
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APC mutation
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OncoPanel™ Assay
10ms
EVOLUTION OF CLINICALLY ACTIONABLE VARIANTS IN ADVANCED PEDIATRIC AND AYA BONE SARCOMAS (CTOS 2023)
In EWS we observed a predominant pattern of emergence of new biological and/or actionable variants over time with emergence of new STAG2 or TP53 mutations occurring in 26% of patients, confirming the importance of these genes in resistant disease. In OS, we observed mixed patterns of change including persistence, emergence and disappearance of variants, suggesting the previously described unstable genome in OS impacts key oncogenes and potentially targetable genes. Given the observed patterns of genomic change in OS and EWS, there may be utility to repeat sequencing of relapsed tumor biopsies.
Clinical • Metastases
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TP53 (Tumor protein P53) • MYC (V-myc avian myelocytomatosis viral oncogene homolog) • FGFR1 (Fibroblast growth factor receptor 1) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • RB1 (RB Transcriptional Corepressor 1) • CCND1 (Cyclin D1) • MCL1 (Myeloid cell leukemia 1) • CDK4 (Cyclin-dependent kinase 4) • STAG2 (Stromal Antigen 2) • CCND3 (Cyclin D3) • FLCN (Folliculin)
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TP53 mutation • MYC amplification • STAG2 mutation
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OncoPanel™ Assay
11ms
Three-dimensional nuclear architecture distinguishes thyroid cancer histotypes. (PubMed, Int J Cancer)
Of note, next-generation thyroid oncopanel sequencing was unable to distinguish the thyroid cancer histotypes in our study cohort. In summary, our data suggest that 3D nuclear architecture can be a powerful analytical tool to diagnose and guide clinical management of NIFTP.
Journal
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BRAF (B-raf proto-oncogene)
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BRAF mutation
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OncoPanel™ Assay
11ms
PREDiCTl: PRecision Oncology Evidence Development in Cancer Treatment - Liquid (clinicaltrials.gov)
P=N/A; Trial completion date: Jun 2023 --> Jun 2025 | Trial primary completion date: Jun 2023 --> Jun 2025
Real-world evidence • Trial completion date • Trial primary completion date • Circulating tumor DNA • Real-world • Metastases
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FoundationOne® Liquid CDx • OncoPanel™ Assay