A prospective validation of nomograms based on BC-116 and BC-106 urine peptide biomarker panels for bladder cancer diagnostics and monitoring

Purpose: Non-invasive urine-based biomarkers for bladder cancer (BC) diagnosis and surveillance can potentially improve current diagnostic and monitoring protocols by guiding cystoscopy. Here, we aim to access the diagnostic performance of nomograms based on published biomarker panels for BC detection (BC-116) and monitoring of recurrence (BC-106) in combination with cytology, in two prospectively collected patient cohorts. Experimental Design: 602 recruited patients were screened for presence of BC, out of which 551 were found eligible for further analysis. For the primary setting, urine samples from 73 eligible patients were analyzed from those diagnosed with primary BC (n=27) and benign urological disorders (n=46). For the surveillance setting, 478 eligible patients were considered (83 BC recurrences; 395 negative for recurrence). Urine samples were analyzed with capillary electrophoresis coupled to mass spectrometry and the biomarker score was estimated via a support vector machine-based software. Results: Validation of the BC-116 biomarker panel resulted in 89% sensitivity and 67% specificity (AUCBC-116=0.82), similar to the published estimates. The nomogram based on cytology and BC-116 resulted in good (AUCNom116=0.85) but not significantly better performance than the BC-116 alone (P=0.5672). BC-106 biomarker panel showed 89% sensitivity and 32% specificity for surveillance, while improved performance was achieved when a nomogram including BC-106 and cytology was evaluated (AUCNom106=0.82), significantly outperforming both cytology (AUCcyt=0.72;P=0.0022) and BC-106 alone (AUCBC-106=0.67;P=0.0012). Conclusions: BC-116 biomarker panel is a useful test for detecting primary BC. BC-106 classifier integrated with cytology and showing >95% negative predictive value, might be useful for decreasing the number of cystoscopies during surveillance.

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Diagnostic Performance of Oncuria™, a Urinalysis Test for Bladder Cancer

10.21203/rs.3.rs-253377/v1 ◽

2021 ◽

Author(s):

Yosuke Hirasawa ◽

Ian Pagano ◽

Runpu Chen ◽

Yijun Sun ◽

Yunfeng Dai ◽

...

Keyword(s):

Bladder Cancer ◽

Diagnostic Performance ◽

Clinical Laboratory ◽

Demographic Data ◽

Roc Curves ◽

Low Grade ◽

Linear Discriminant ◽

Non Invasive ◽

Diagnostic Panel ◽

Parallel Measurement

Abstract Background: Due to insufficient accuracy, urine-based assays currently have a limited role in the management of patients with bladder cancer. The identification of multiplex molecular signatures associated with disease has the potential to address this deficiency and to assist with accurate, non-invasive diagnosis and monitoring. Methods: To evaluate the performance of Oncuria™, a multiplex immunoassay for bladder detection in voided urine samples. The test was evaluated in a multi-institutional cohort of 362 prospectively collected subjects presenting for bladder cancer evaluation. The parallel measurement of 10 biomarkers (A1AT, APOE, ANG, CA9, IL8, MMP9, MMP10, PAI1, SDC1 and VEGFA) was performed in an independent clinical laboratory. The ability of the test to identify patients harboring bladder cancer was assessed. Bladder cancer status was confirmed by cystoscopy and tissue biopsy. The association of biomarkers and demographic factors was evaluated using linear discriminant analysis (LDA) and predictive models were derived using supervised learning and cross-validation analyses. Diagnostic performance was assessed using ROC curves.Results: The combination of the 10 biomarkers provided an AUROC 0.93 [95% CI: 0.87 – 0.98], outperforming any single biomarker. The addition of demographic data (age, sex, and race) into a hybrid signature improved the diagnostic performance AUROC 0.95 [95% CI: 0.90 – 1.00]. The hybrid signature achieved an overall sensitivity of 0.93, specificity of 0.93, PPV of 0.65 and NPV of 0.99 for bladder cancer classification. Sensitivity values of the diagnostic panel for high-grade bladder cancer, low-grade bladder cancer, MIBC and NMIBC were 0.94, 0.89, 0.97 and 0.93, respectively. Conclusions: Urinary levels of a biomarker panel enabled the accurate discrimination of bladder cancer patients and controls. The multiplex Oncuria™ test can achieve the efficient and accurate detection and monitoring of bladder cancer in a non-invasive patient setting.

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Non-invasive detection of bladder cancer through the analysis of driver gene mutations and aneuploidy

10.1101/203976 ◽

2017 ◽

Cited By ~ 3

Author(s):

Simeon Springer ◽

Maria Del Carmen Rodriguez Pena ◽

Lu Li ◽

Christopher Douville ◽

Yuxuan Wang ◽

...

Keyword(s):

At Risk ◽

Bladder Cancer ◽

Gene Mutations ◽

Urine Samples ◽

Driver Gene ◽

Low Grade ◽

Invasive Approach ◽

Non Invasive ◽

Patients At Risk ◽

Copy Number Changes

AbstractCurrent non-invasive approaches for bladder cancer (BC) detection are suboptimal. We report the development of non-invasive molecular test for BC using DNA recovered from cells shed into urine. This “UroSEEK” test incorporates assays for mutations in 11 genes and copy number changes on 39 chromosome arms. We first evaluated 570 urine samples from patients at risk for BC (microscopic hematuria or dysuria). UroSEEK was positive in 83% of patients that developed BC, but in only 7% of patients who did not develop BC. Combined with cytology, 95% of patients that developed BC were positive. We then evaluated 322 urine samples from patients soon after their BCs had been surgically resected. UroSEEK detected abnormalities in 66% of the urine samples from these patients, sometimes up to 4 years prior to clinical evidence of residual neoplasia, while cytology was positive in only 25% of such urine samples. The advantages of UroSEEK over cytology were particularly evident in low-grade tumors, wherein cytology detected none while UroSEEK detected 67% of 49 cases. These results establish the foundation for a new, non-invasive approach to the detection of BC in patients at risk for initial or recurrent disease.

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Use of next-generation deep sequencing to improve FGFR3 mutation detection in the urine of patients with bladder cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.5_suppl.289 ◽

2012 ◽

Vol 30 (5_suppl) ◽

pp. 289-289

Author(s):

John M. Millholland ◽

Shuqiang Li ◽

Cecilia A. Fernandez ◽

Anthony P. Shuber

Keyword(s):

Bladder Cancer ◽

Deep Sequencing ◽

Mutation Detection ◽

Amplicon Sequencing ◽

Urine Samples ◽

Next Generation ◽

High Background ◽

Non Invasive ◽

Fgfr3 Mutation ◽

Fgfr3 Mutations

289 Background: FGFR3 mutations have been identified in ∼60-70% of low-stage, non-invasive tumors. Our group and others have developed assays to detect FGFR3 mutations in the urine of bladder cancer patients. However, urine-based assays have been limited by the technical ability to detect rare events in a dilute medium where there is a high background of normal DNA. In these assays, FGFR3 mutations are generally found in ∼30% of the urine samples, which is < 50% concordance with the expected detection in tissue. We have now developed an ultra-deep amplicon sequencing technique that increases FGFR3 mutation detection in urine to ∼67%, near the expected detection if every mutation found in tissue could be detected in urine. Methods: Amplicons were designed against FGFR3 exons 7, 10, and 15 using PCR primers containing the adapter sequences for unidirectional sequencing. Taqman probes were used to determine if sufficient DNA was present in each sample. Primary amplification was performed from DNA isolated from 4 ml of urine. The resulting PCR products were used as template for emulsion PCR and these were then sequenced using the Roche 454 GS Junior. Samples were analyzed for total DNA reads per sample and number of mutant sequencing reads to determine percent mutation. Results: Urine samples from 29 patients with stage Ta bladder cancer were analyzed by both our previously described qPCR method and the new ultra-deep sequencing approach. Of the 29 samples, 2 did not have sufficient DNA for analysis by sequencing. Using ultra-deep amplicon sequencing, 18 out of 27 (66.7%) were positive for FGFR3 mutations, while only 3 out of 27 (11.1%) were positive for mutations by qPCR. The urine samples from the 15 newly identified mutations using deep sequencing contained FGFR3 mutations as low as 0.05%. The sensitivity achieved using deep sequencing approximates the FGFR3 mutations observed in tissue. Conclusions: We have developed a highly sensitive non-invasive urine based assay that can detect FGFR3 mutant DNA when present at < 1% of the sample and suggests > 90% concordance with the expected mutations in Ta tumor tissues. To our knowledge, this is the first practical application of next generation sequencing technology for diagnostic use.

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Applications of Raman spectroscopy to the urinary bladder for cancer diagnostics

Photonics and Lasers in Medicine ◽

10.1515/plm-2014-0004 ◽

2014 ◽

Vol 3 (3) ◽

Cited By ~ 16

Author(s):

Laura T. Kerr ◽

Katarina Domijan ◽

Ivor Cullen ◽

Bryan M. Hennelly

Keyword(s):

Raman Spectroscopy ◽

Bladder Cancer ◽

Urinary Bladder ◽

Real Time ◽

Cancer Progression ◽

Cancer Diagnostics ◽

Non Invasive ◽

Clinical Methods

AbstractBiomolecular changes associated with cancer progression can be identified using Raman spectroscopy, allowing for this technique to be utilized as a non-invasive tool for the diagnosis of bladder cancer. Applications of Raman spectroscopy for diagnostics in real-time have consistently produced higher sensitivities and specificities than current clinical methods. This technique can be applied

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625 A non-invasive urine-based epigenetic urinary biomarker panel for the detection of bladder cancer and the discrimination of high-grade and low-grade disease

European Urology Supplements ◽

10.1016/s1569-9056(14)60615-1 ◽

2014 ◽

Vol 13 (1) ◽

pp. e625

Author(s):

T. Hermanns ◽

E. Olkhov-Mitsel ◽

A. Savio ◽

B. Bhindi ◽

D. Zdravic ◽

...

Keyword(s):

Bladder Cancer ◽

Low Grade ◽

High Grade ◽

Urinary Biomarker ◽

Biomarker Panel ◽

Non Invasive

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Using microRNA profiling in urine samples to develop a non-invasive test for bladder cancer

International Journal of Cancer ◽

10.1002/ijc.28274 ◽

2013 ◽

pp. n/a-n/a ◽

Cited By ~ 11

Author(s):

Lourdes Mengual ◽

Juan José Lozano ◽

Mercedes Ingelmo-Torres ◽

Cristina Gazquez ◽

María José Ribal ◽

...

Keyword(s):

Bladder Cancer ◽

Urine Samples ◽

Non Invasive ◽

Invasive Test ◽

Microrna Profiling

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Detection of low-frequency FGFR3 mutations in the urine of patients with bladder cancer using next-generation deep sequencing.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.30_suppl.59 ◽

2012 ◽

Vol 30 (30_suppl) ◽

pp. 59-59

Author(s):

John M. Millholland ◽

Shuqiang Li ◽

Cecilia A. Fernandez ◽

Anthony P. Shuber

Keyword(s):

Bladder Cancer ◽

Deep Sequencing ◽

Amplicon Sequencing ◽

Urine Samples ◽

Next Generation ◽

High Background ◽

Next Generation Sequencing Technology ◽

Non Invasive ◽

Detection Frequency ◽

Fgfr3 Mutations

59 Background: FGFR3 mutations have been identified in ~60-70% of low-stage, non-invasive tumors. Our group and others have developed assays to detect FGFR3 mutations in the urine of bladder cancer patients. However, urine-based assays have been limited by the technical ability to detect rare events in a dilute medium where there is a high background of normal DNA. In these assays, FGFR3 mutations are generally found in ~30% of the urine samples, which is < 50% concordance with the expected detection in tissue. We have now developed an ultra-deep amplicon sequencing technique that increases FGFR3 mutation detection in urine to ~67%, close to the expected detection frequency if every mutation found in tissue could be detected in urine. Methods: Amplicons were designed against FGFR3 exons 7, 10, and 15 using PCR primers containing the adapter sequences for unidirectional sequencing. Primary amplification was performed from DNA isolated from 4 ml of urine. The resulting PCR products were used as template for emulsion PCR and these were then sequenced using the Roche 454 GS Junior. Samples were analyzed for total DNA reads per sample and number of mutant sequencing reads to determine percent mutation. Results: Urine samples from 43 patients with bladder cancer were analyzed by both our previously described qPCR method and the new ultra-deep sequencing approach. Using ultra-deep amplicon sequencing, 24 out of 43 (55.8%) were positive for FGFR3 mutations, while only 5 out of 43 (11.6%) were positive for mutations by qPCR. The urine samples from the 15 newly identified mutations using deep sequencing contained FGFR3 mutations as low as 0.05% mutant DNA. The sensitivity achieved using deep sequencing was 91% concordant with the FGFR3 mutations observed in tissue. Conclusions: We have developed a highly sensitive non-invasive urine based assay that can detect FGFR3 mutant DNA when present at < 1% of the sample and is > 90% concordance with the mutations found in tumor tissues. To our knowledge, this is the first practical application of next generation sequencing technology for diagnostic use.

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Non-Invasive Diagnosis of Diabetes by Volatile Organic Compounds in Urine Using FAIMS and Fox4000 Electronic Nose

Biosensors ◽

10.3390/bios8040121 ◽

2018 ◽

Vol 8 (4) ◽

pp. 121 ◽

Cited By ~ 15

Author(s):

Siavash Esfahani ◽

Alfian Wicaksono ◽

Ella Mozdiak ◽

Ramesh Arasaradnam ◽

James Covington

Keyword(s):

Volatile Organic Compounds ◽

Organic Compounds ◽

Electronic Nose ◽

Area Under The Curve ◽

Urine Samples ◽

Support Vector ◽

Sparse Logistic Regression ◽

Non Invasive ◽

Volatile Organic ◽

Sample Age

The electronic nose (eNose) is an instrument designed to mimic the human olfactory system. Usage of eNose in medical applications is more popular than ever, due to its low costs and non-invasive nature. The eNose sniffs the gases and vapours that emanate from human waste (urine, breath, and stool) for the diagnosis of variety of diseases. Diabetes mellitus type 2 (DM2) affects 8.3% of adults in the world, with 43% being underdiagnosed, resulting in 4.9 million deaths per year. In this study, we investigated the potential of urinary volatile organic compounds (VOCs) as novel non-invasive diagnostic biomarker for diabetes. In addition, we investigated the influence of sample age on the diagnostic accuracy of urinary VOCs. We analysed 140 urine samples (73 DM2, 67 healthy) with Field-Asymmetric Ion Mobility Spectrometry (FAIMS); a type of eNose; and FOX 4000 (AlphaM.O.S, Toulouse, France). Urine samples were collected at UHCW NHS Trust clinics over 4 years and stored at −80 °C within two hours of collection. Four different classifiers were used for classification, specifically Sparse Logistic Regression, Random Forest, Gaussian Process, and Support Vector on both FAIMS and FOX4000. Both eNoses showed their capability of diagnosing DM2 from controls and the effect of sample age on the discrimination. FAIMS samples were analysed for all samples aged 0–4 years (AUC: 88%, sensitivity: 87%, specificity: 82%) and then sub group samples aged less than a year (AUC (Area Under the Curve): 94%, Sensitivity: 92%, specificity: 100%). FOX4000 samples were analysed for all samples aged 0–4 years (AUC: 85%, sensitivity: 77%, specificity: 85%) and a sub group samples aged less than 18 months: (AUC: 94%, sensitivity: 90%, specificity: 89%). We demonstrated that FAIMS and FOX 4000 eNoses can discriminate DM2 from controls using urinary VOCs. In addition, we showed that urine sample age affects discriminative accuracy.

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