Table 5.
Table presenting data for mutations biomarkers.
| Biomarker | Purpose | Number of Patients | Method | Diagnostic Value | Prognostic Value | Predictive Capacity | Type of Study | Reference |
|---|---|---|---|---|---|---|---|---|
| PIK3CA | diagnostic | n = 70 (LG = 27, HG = 43) | Genomic DNA extracted from fresh frozen tumours and urine cell sediments of 70 patients using phenol/chloroform method. DNA was quantified with a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). DNA amplification was performed on ProFlex PCR system (Applied Biosystems, Foster City, CA, USA). Sequencing was performed with BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA). Data analysis IBM SPSS software version 23. | BCa detection | Se. = 66.7%, Sp. = 100% | prospective | [48] | |
| AKT1 | Se. = 100%, Sp. = 100% | |||||||
| TERT | diagnostic | n = 60 (BCa (NMIBC) = 27, LG = 16, HG = 6; control group = 23; n = 10, tmr) | DNA was isolated from urine samples of 60 patients using QIAamp Circulating Nucleic Acid Kit (Qiagen GmbH, Hilden, Germany). The reference plasmids were created using pUC19 vector (cloning sites KpnI and HindIII). Forward primer and reverse primer were provided by Evrogen RU, AO. DNA isolated from liver cancer cells (originating from the HepG2 cell line; cat no. 85011430; MilliporeSigma) was used for amplification of the mutant C228T fragment. High-Fidelity DNA Polymerase (New England BioLabs Inc., Ipswich, MA, USA) was used to amplify the mutant insert. Quantification of DNA was performed using the QX200 ddPCR System (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Detection of TERT promoter and mutations was achieved using TaqMan Liquid Biopsy dPCR Assays (TERT_C228T, Assay ID Hs000000092_rm and TERT_C250T, Assay ID Hs000000093_rm; Thermo Fisher Scientific Inc.). Data analysis performed with IBM SPSS Statistics 22.0 Software (IBM Corp., Armonk, NY, USA). |
BCa detection | AUC = 0.768, Se. = 55.56%, Sp. = 100% | retrospective | [49] | |
| DNA sequencing | diagnostic | Retrospective haematuria clinic cohort = 214 (BCa = 97, non-BCa = 117) | DNA extraction was performed with Quick-DNA urine kits (D3061; Zymo Research, Irvine, CA, USA) on urine samples collected from all patients and quantified using high-sensitivity dsDNA Qubit kits (Thermo Fisher, Waltham, MA, USA). Libraries were prepare using Nonacus Cell3 Target enrichment and sequenced on a NovaSeq (Illumina, San Diego, CA, USA). | BCa detection | Se. = 87.6%, Sp. = 88.9% | retrospective | [50] | |
| Prospective haematuria clinic cohort = 215 (BCa = 68, non-BCa = 147) | Se. = 86.8%, Sp. = 81.0% | prospective | ||||||
| NMIBC surveillance cohort = 293 (BCa = 29, non-BCa = 264) | Se. = 86.2%, Sp. = 62.5% | prospective | ||||||
| Control group = 162 (normal samples = 100, confirmatory control samples = 62) | Normal samples Sp. = 89.9% Confirmatory control samples Sp. = 91.2% |
retrospective | ||||||
| GWAS (rs9642880, rs710521) | prognostic | n = 200 (BCa = 150, NMIBC = 12, MIBC = 123; control group = 50) | DNA was extracted from urine of 200 patients with Qiagen Kits (Hilden, Germany) and then measured on a Nanodrop ND-2000c (Thermo Scientific, Waltham, MA, USA). PCR was carried out using Bio-RAD T100Thermal cycler. Thermo Scientific FastDigestStyl was used to digest. Data analysis performed with Microsoft Excel 2016 and IBM SPSS Statistics for Windows, version 26 (IBM Corp., Armonk, NY, USA). | BCa progression | No data | retrospective | [51] |
Abbreviations: AUC—Area under the ROC Curve, n—number of patients participating in study, HG—high grade, LG—low grade, BCa—bladder cancer, PCR—polymerase chain reaction, PPV—positive predictive value, NPV—negative predictive value, Se.—sensitivity, Sp.—specificity, PIK3CA—Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha, AKT1—AKT Serine/Threonine Kinase 1, TERT—Telomerase Reverse Transcriptase, GWAS—Genome-wide association studies.