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TEST:
UW-Oncoplex™

Type:
Laboratory Developed Test
Related tests:
8d
Looking beyond year 1 in the molecular era of pediatric brain tumor diagnosis: confirmatory testing of germline variants found on tumor sequencing. (PubMed)
Despite this, only a subset of these patients underwent the indicated confirmatory sequencing. Further work is needed to identify barriers and facilitators to this testing, including the role of genetic counseling and consideration of upfront paired somatic-germline testing.
Journal
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UW-Oncoplex™
16d
A CSF LIQUID BIOPSY PLATFORM USING LOW-PASS WHOLE GENOME SEQUENCING FOR MALIGNANT BRAIN TUMORS (ASPHO 2024)
CSF liquid biopsy has potential as a minimally invasive method of disease detection for measuring treatment response and longitudinal disease surveillance. lpWGS on CSF-derived cfDNA can identify tumor-derived sCNVs even when CSF cytology is negative for malignant cells. lpWGS can reveal sCNVs that are clinically actionable without need for a tissue biopsy.
Liquid biopsy • Biopsy • Whole genome sequencing
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IDH1 (Isocitrate dehydrogenase (NADP(+)) 1)
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IDH1 mutation
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UW-Oncoplex™
4ms
Olaparib for the Treatment of Castration Resistant Prostate Adenocarcinoma (clinicaltrials.gov)
P2; N=30 --> 2 | Trial completion date: May 2025 --> Oct 2023 | Recruiting --> Terminated | Trial primary completion date: May 2025 --> Oct 2023; Withdrawal of funding
Trial completion date • Trial primary completion date • Enrollment change • Trial termination
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AR (Androgen receptor)
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UW-Oncoplex™
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Lynparza (olaparib)
10ms
Supratentorial non-RELA, ZFTA-fused Ependymoma – A Characteristic Fusion with a Histopathologic Correlate (AANP 2023)
Subsequent evaluation of the patient's recurrence using a DNA-based targeted NGS panel at the University of Washington (UW OncoPlex) detected a ZFTA::NCOA2 fusion, prompting methylation reanalysis (NIH) using the recently released v12b6 DKFZ classifier, which matched to "Supratentorial Ependymoma, ZFTA fusion-positive". Conclusions While this case is unusual in the lack of traditional ependymal morphology, the morphologic findings are consistent with the underlying ZFTA::NCOA2 fusion.
YAP1 (Yes associated protein 1) • MAML2 (Mastermind Like Transcriptional Coactivator 2) • NCOA2 (Nuclear Receptor Coactivator 2) • RELA (RELA Proto-Oncogene) • ZFTA (Zinc Finger Translocation Associated)
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UW-Oncoplex™
10ms
MLH1 Loss in Primary Prostate Cancer. (PubMed, JCO Precis Oncol)
These cases highlight the challenges in identifying MLH1-deficient prostate cancers using standard MSI testing and commercial sequencing panels, and support the utility of immunohistochemical assays and LMR- or sequencing-based MSI testing for detection of MMRd prostate cancers.
Journal • Tumor mutational burden • PD(L)-1 Biomarker
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TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • MLH1 (MutL homolog 1)
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MSI-H/dMMR • MLH1 mutation
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UW-Oncoplex™
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Keytruda (pembrolizumab)
11ms
3D open-top light-sheet microscopy and 3D microdissection of neuoadjuvant-treated primary prostate cancer reveals latent subclonal mutations. (ASCO 2023)
Patients received 12 weeks of apalutamide, abiraterone acetate plus prednisone, degarelix, and indomethacin followed by radical prostatectomy (RP). The findings show the potential for 3D microdissection of morphologically distinct subclones in samples from neoadjuvant-treated patient, to enable sequencing of specific cellular populations. The sparsity of carcinoma necessitated a spatially targeted approach for extracting material for sequencing. The increased yield from avoiding FFPE processing and carcinoma enrichment from targeted 3D microdissection of carcinoma ROIs enabled the detection of spatially distinct molecular subclones.
Clinical
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PTEN (Phosphatase and tensin homolog)
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UW-Oncoplex™
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abiraterone acetate • Erleada (apalutamide) • Firmagon (degarelix)
11ms
PSMA expression and response to 177Lu-PSMA-617 (LuPSMA) in men with vs. without DNA damage repair (DDR) mutations. (ASCO 2023)
Background: LuPSMA, a radioligand targeting the cell surface protein PSMA, is approved for men with PSMA-positive metastatic castration resistant prostate cancer (mCRPC) following an androgen receptor (AR)-signaling inhibitor (ARSI) and docetaxel. Mutations in DDR genes were associated with a higher PSA50 response rate following LuPSMA compared to patients without a DDR mutation. There was no difference in baseline PSMA expression based on DDR mutational status, suggesting that higher response rates in the DDR cohort may have been mediated primarily by increased sensitivity to ionizing radiation. Evaluation for associations between DDR mutational status and survival endpoints is needed and will require a larger sample size and longer follow up.
PARP Biomarker • BRCA Biomarker
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BRCA2 (Breast cancer 2, early onset) • FOLH1 (Folate hydrolase 1)
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BRCA2 mutation • FOLH1 expression • FOLH1 positive
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UW-Oncoplex™
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docetaxel • Pluvicto (lutetium Lu 177 vipivotide tetraxetan)
11ms
The somatic mutation profile of breast cancer in Uganda. (ASCO 2023)
We identified a diverse landscape of somatic mutations - the prevalence of BRCA1, BRCA2, and PIK3CA mutations are considerably higher than in other documented populations. A better understanding of the mutational profile can provide biological insights, inform prognosis, and serve as a predictive biomarker. As mutations in BRCA1/2 and PIK3CA can potentially be treated with targeted therapies (e.g.
PARP Biomarker • BRCA Biomarker
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EGFR (Epidermal growth factor receptor) • 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) • FGFR1 (Fibroblast growth factor receptor 1) • CCND1 (Cyclin D1)
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TP53 mutation • BRCA2 mutation • BRCA1 mutation • PIK3CA mutation • BRCA1 expression
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UW-Oncoplex™
1year
AZD1775 in Treating Patients With Advanced Refractory Solid Tumors With CCNE1 Amplification (clinicaltrials.gov)
P2 | N=31 | Completed | Sponsor: National Cancer Institute (NCI) | Suspended ➔ Completed | Trial completion date: Sep 2023 ➔ Oct 2022 | Trial primary completion date: Sep 2023 ➔ Oct 2022
Trial completion date • Trial primary completion date • Trial completion
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CCNE1 (Cyclin E1)
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CCNE1 amplification
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MSK-IMPACT • UW-Oncoplex™
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adavosertib (AZD1775)
1year
Evaluation of the aggressive variant prostate cancer molecular profile (AVPCm) in CLIA environments. (ASCO-GU 2023)
Post-hoc analysis in a phase I/II trial indicated a benefit of carboplatin+cabazitaxel in men with AVPCm+ metastatic castrate resistant prostate cancer (mCRPC). We show the operational characteristics of the AVPCm detection using CLIA certified assays. IHC detected a greater proportion of patients with AVPCm+ tumors than stDNA, likely due, partly, to the challenges of copy number loss detection. ctDNA detected the greatest proportion of AVPCm+ tumors but was not evaluable in two thirds of patients.
TP53 (Tumor protein P53) • PTEN (Phosphatase and tensin homolog) • AR (Androgen receptor) • RB1 (RB Transcriptional Corepressor 1)
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PTEN expression
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UW-Oncoplex™
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carboplatin • cabazitaxel
over1year
Pilot study to evaluate circulating tumor DNA (ctDNA) to PET/CT imaging using 18F-Fluorodeoxyglucose (FDG) and 18F-Fluoroestradiol (FES) PET/CT imaging as biomarkers in patients with metastatic breast cancer (SABCS 2022)
In this pilot study, FDG TLG showed a significant correlation with ctDNA. There is an encouraging association with ctDNA fraction and number of FDG lesions and with ctDNA fraction and extent of FES avid disease (TLER) in the 9 patients that had FES. Research Support: RG1005258 Table 1.
Clinical • Circulating tumor DNA
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ER (Estrogen receptor)
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ER expression
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UW-Oncoplex™
over1year
AZD1775 in Treating Patients With Advanced Refractory Solid Tumors With CCNE1 Amplification (clinicaltrials.gov)
P2; Trial completion date: Sep 2022 --> Sep 2023 | Trial primary completion date: Sep 2022 --> Sep 2023
Trial completion date • Trial primary completion date
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CCNE1 (Cyclin E1)
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CCNE1 amplification
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FoundationOne® CDx • UW-Oncoplex™
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adavosertib (AZD1775)
over1year
Olaparib for the Treatment of Castration Resistant Prostate Adenocarcinoma (clinicaltrials.gov)
P2, N=30, Recruiting, University of Washington | Not yet recruiting --> Recruiting
Enrollment open
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AR (Androgen receptor)
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UW-Oncoplex™
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Lynparza (olaparib)
almost2years
Combination therapy • Trial completion date • Trial completion
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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) • NRAS (Neuroblastoma RAS viral oncogene homolog) • CDH1 (Cadherin 1) • RAF1 (Raf-1 Proto-Oncogene Serine/Threonine Kinase) • RAS (Rat Sarcoma Virus)
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EGFR mutation • BRAF mutation • NRAS mutation • HER-2 mutation • CDH1 expression • CDH1 mutation
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FoundationOne® CDx • UW-Oncoplex™
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Gilotrif (afatinib) • capecitabine
over2years
Validating cell-free DNA from supernatant for molecular diagnostics on cytology specimens. (PubMed, Cancer Cytopathol)
This study confirmed that cfDNA from supernatant is a viable alternative to FFPE cell blocks for molecular biomarker testing using both amplicon-based and capture-based assays with potential for decreasing additional tissue sampling and faster turnaround time.
Journal
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UW-Oncoplex™
almost3years
[VIRTUAL] Concordance of DNA damage repair (DDR) gene mutations in paired primary and metastatic prostate cancer (PC) samples. (ASCO 2021)
These data provide evidence that primary prostate tissue accurately reflect the mutational status of actionable DDR genes in men with metastatic PC, supporting the hypothesis that DDR alterations are early truncal events . After excluding likely CHIP events, ctDNA profiling accurately captured these truncal DDR mutations, while also detecting reversion alterations that may suggest potential resistance mechanisms.
PARP Biomarker • BRCA Biomarker
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BRCA2 (Breast cancer 2, early onset)
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UW-Oncoplex™
3years
[VIRTUAL] Nivolumab (NIVO) and ipilimumab (IPI) treatment in prostate cancer with an immunogenic signature: cohort 1 of the NEPTUNES multi-centre, two-stage biomarker-selected Phase II trial (AACR 2021)
NIVO + IPI demonstrated significant activity in biomarker selected, pre-treated pts with mCRPC. The safety profile is consistent with this dosing schedule. Accrual to expansion cohort 2 started in September 2020.
Late-breaking abstract • P2 data • Clinical • PD(L)-1 Biomarker • BRCA Biomarker
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BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • CD8 (cluster of differentiation 8) • CDK12 (Cyclin dependent kinase 12) • CD4 (CD4 Molecule) • FOXP3 (Forkhead Box P3)
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MSI-H/dMMR
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UW-Oncoplex™
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Opdivo (nivolumab) • Yervoy (ipilimumab)
5years
Clinical determinants for successful circulating tumor DNA analysis in prostate cancer. (PubMed, Prostate)
"Disease burden, including a PSA >10 ng/mL, is strongly associated with detecting somatic mutations from cfDNA specimens."
Journal • Clinical
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UW-Oncoplex™
5years
DNA Damage Repair Alterations are Frequent in Prostatic Adenocarcinomas with Focal Pleomorphic Giant Cell Features. (PubMed, Histopathology)
"These data are consistent with emerging data showing that DNA repair alterations are enriched among castration-resistant prostate cancer and aggressive subsets of primary tumours. Given that these patients are potential candidates for poly(ADP-ribose) polymerase inhibitor and/or immune checkpoint blockade, and have a poor prognosis with standard therapy, we recommend that tumour and germline DNA sequencing with or without mismatch repair protein immunohistochemistry be considered for all prostatic adenocarcinomas with focal pleomorphic giant-cell features."
Journal
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BRCA2 (Breast cancer 2, early onset) • MSH2 (MutS Homolog 2)
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UW-Oncoplex™