Bladder cancer (BC) is the ninth most common cancer worldwide, with urothelial carcinoma accounting for approximately 90% of all cases and presenting predominantly as non‐muscle‐invasive disease. Due to its high recurrence rate and the need for long‐term surveillance, BC is associated with the highest lifetime treatment costs per patient among all cancers, making its effective management a significant clinical and economic challenge. The most frequently identified variants in the TERT gene promoter are c.‐124C>T (C228T) and c.‐146C>T (C250T), located within a region characterized by high guanine–cytosine (GC) content, which makes amplification challenging. We aimed to validate the AbsoluteQ Digital PCR assay for the detection of urine‐based TERT promoter variants for the diagnosis of urothelial bladder cancer and to assess its diagnostic performance in comparison with standard methods. Urine samples were collected from patients with histopathologically confirmed bladder cancer (n = 58) and compared with a control group (n = 55). The C228T and C250T variants were tested using the AbsoluteQ Digital PCR assay. Sensitivity, specificity, and predictive values were calculated to evaluate the performance of the assessed method. The AbsoluteQ Digital PCR demonstrated superior diagnostic performance compared to conventional Sanger sequencing for detecting TERT promoter variants, achieving a sensitivity of 89.65% (95% CI: 78.16–95.72) and a specificity of 100% (95% CI: 91.87–100), with no false positives observed. Given its robustness and clinical relevance, AbsoluteQ Digital PCR is emerging as a promising tool for non‐invasive molecular diagnostics targeting TERT promoter variants.

Background: Molecular diagnostics has become a critical component of precision oncology in solid tumors, including colorectal cancer, yet the use of formalin-fixed, paraffin-embedded (FFPE) tissue often suffers from DNA degradation that compromises sequencing quality. This study aimed to evaluate the feasibility and effectiveness of using fresh, intraoperatively collected tumor tissue for next-generation sequencing-based molecular diagnostics in colorectal cancer. Methods: Tissue samples from 24 patients undergoing colorectal tumor resection were obtained based on macroscopic evaluation and tested with a custom gene panel. Sequencing metrics, mutation profiles, and correlations with clinical and pathological features were analyzed. Results: All samples yielded high-quality sequencing data. Oncogenic or likely oncogenic variants were detected in 21 out of 24 samples (87.5%), predominantly affecting genes frequently involved in colorectal cancer carcinogenesis, including APC, TP53, and KRAS. In three cases, no typical mutations were found despite visual confirmation of tumor tissue during surgery, which may be attributed to insufficient tumor cellularity or molecular alterations beyond the panel's scope. Conclusions: The results support the use of fresh tissue as a high-quality source for molecular diagnostics, capable of reducing turnaround time and avoiding formalin-induced artifacts. However, the findings also highlight the diagnostic risk of relying solely on macroscopic tumor assessment without histological confirmation. Overall, fresh tissue-based testing represents a promising yet currently investigational approach that can enhance molecular diagnostics in colorectal cancer.

The upcoming wave of personalized medicine, driven by genomic diagnostics and artificial intelligence, demands clearly defined pre-laboratory and laboratory procedures to ensure the acquisition of DNA and RNA of sufficient quantity and quality. In prostate cancer oncogenetics, diagnostic and prognostic assessments increasingly rely on personalized approaches, including Comprehensive Genomic Profiling (CGP). In this pilot study, we aimed to establish optimal pre-analytical and analytical conditions for selected genetic diagnostic methods using tissue samples acquired through multiparametric MRI-guided biopsy. Tissue specimens from thirteen patients were processed for DNA isolation, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). Comparative analyses were performed on DNA derived from both fresh and formalin-fixed, paraffin-embedded (FFPE) samples. Sequencing quality metrics demonstrated markedly superior performance in fresh tissue compared to FFPE. These results highlight the importance of standardized tissue collection and processing protocols to enable reliable molecular diagnostics in prostate cancer. Our findings support the feasibility of integrating high-quality genomic testing into routine biopsy workflows and emphasize the need for further large-scale validation.

Androgen insensitivity syndrome (AIS) is an X-linked genetic disorder caused by mutations in the androgen receptor gene (AR), leading to impaired androgen signaling and resulting in varying degrees of undermasculinization in individuals with a 46,XY karyotype. This study aimed to expand the molecular landscape of AIS by identifying and characterizing pathogenic variants in the AR gene via next-generation sequencing (NGS). Molecular diagnostics revealed eight distinct variants within the AR gene, two of which had not been previously described. These include the following novel variants: c.3G>A, and c.1344_1345insTA. This study broadens the spectrum of known AR gene mutations associated with AIS and highlights the critical role of molecular diagnostics in the accurate classification of variants. These findings will aid in enhancing the clinical management and genetic counseling of individuals affected by AIS.

Over a 46-month period, the objectives of the National Cancer Control Program (NCCP, pol. Narodowy Program Zwalczania Chorób Nowotworowych), coordinated by the Ministry of Health, were pursued by conducting genetic diagnostics on individuals at high risk of developing cancer. A total of 1097 individuals were enrolled in the study, leading to the identification of 128 cases of germline mutations. The implementation of the NCCP led to the identification of genetic mutations in 4.43% of the patients qualified for BRCA1 and BRCA2 screening tests, in 18.18% of those qualified for a comprehensive next-generation sequencing (NGS) panel in cases of breast and ovarian cancer, and in 17.36% of cases of colorectal and endometrial cancer. The research conducted allowed us to establish individualized preventive and therapeutic approaches for mutation carriers. However, the results prove that liberalizing the inclusion criteria for high-throughput diagnostics and the use of broad gene panels could significantly increase the percentage of detected carriers. This publication serves as a summary and discussion of the results obtained from the implementation of the NCCP as well as of the role of genetic consulting in personalized medicine.

Bladder cancer is one of the most common cancers in global statistics. One of the issues associated with this disease is the high incidence of cases with delayed diagnosis and what factors correlate with worse treatment outcomes. A possible reason for this may be the rather limited availability of non-invasive diagnostic tools. This short communication presents a case of a 68 year old male patient after an ineffective therapy, carried on for several years with symptoms commonly associated with prostate overgrowth that masked a carcinoma in situ of the urinary bladder. Implementation of several diagnostic techniques, including urine sediment cytology, immunocytochemistry, the fluorescence in situ hybridisation technique, the Bladder EpiCheck test and whole-genome sequencing, enabled the establishment of a correct diagnosis, implementation of appropriate treatment and provision of patient-friendly monitoring. The described case emphasises the usefulness of cell-based and liquid-based urine tests in bladder cancer diagnostic procedures.

We treated Candida albicans cells with a sublethal dose of nonequilibrium (cold) atmospheric-pressure He plasma and studied alterations in the genome of this fungus as well as changes in the phenotypic traits, such as assimilation of carbon from carbohydrates, hydrolytic enzyme activity, and drug susceptibility. There is a general problem if we use cold plasma to kill microorganism cells and some of them survive the process—whether the genotypic and phenotypic features of the cells are significantly altered in this case, and, if so, whether these changes are environmentally hazardous. Our molecular genetic studies have identified six single nucleotide variants, six insertions, and five deletions, which are most likely significant changes after plasma treatment. It was also found that out of 19 tested hydrolytic enzymes, 10 revealed activity, of which nine temporarily decreased their activity and one (naphthol-AS-BI- phosphohydrolase) permanently increased activity as a result of the plasma treatment. In turn, carbon assimilation and drug susceptibility were not affected by plasma. Based on the performed studies, it can be concluded that the observed changes in C. albicans cells that survived the plasma action are not of significant importance to the environment, especially for the drug resistance and pathogenicity of this fungus.

ABSTRACT INTRODUCTION. The human papilloma virus (HPV) belongs to double-stranded, DNA circular viruses which infect the epithelial cells. The highest incidence of HPV is identified in malignant processes which affect the uterine cervix, as well as vulvar, penile, rectal and pharyngeal regions. GOAL OF STUDY. An attempt to find correlations between HPV incidence rates in urine sediment cells and in desquamated epithelial cells of the uterine cervix in a group of patients with frequent, recurrent cystitis. MATERIALS AND METHODS. HPV presence was studied, both in urine sediment cells and in uterine cervix epithelial cells of 77 patients. RESULTS. An analysis of urinary sediments brought a total of twenty (25.97%) positive and 57 (74.03%) negative results. In turn, an evaluation of uterine cervix material samples revealed 17 (22.08%) positive and 60 (77.92%) negative results. CONCLUSIONS. The study enabled a comparison between HPV prevalence rates in urine sediment cells and in uterine cervix epithelial cells of an examined patient. The performed observations are likely to trigger a further analysis of the studied issue; however, the obtained results provide arguments for different natural histories of the infection processes. STRESZCZENIE WSTĘP. W przypadku raka urotelialnego jednym z potencjalnych czynników rakotwórczych jest wirus brodawczaka ludzkiego (HPV). Ludzki wirus brodawczaka należy do dwuniciowych wirusów DNA infekujących komórki nabłonka. Największa częstość występowania HPV stwierdzono w złośliwych procesach, które mają wpływ na szyjkę macicy, a także na okolice sromu, prącia, odbytnicy oraz gardła. CEL PRACY. Celem podjętych badań była próba znalezienia korelacji między częstością występowania HPV w komórkach osadu moczu a złuszczonymi komórkami nabłonka szyjki macicy w grupie pacjentów z częstym, nawracającym zapaleniem pęcherza. MATERIAŁ I METODY. Obecność wirusa HPV badano zarówno w komórkach osadu moczu, jak również w komórkach nabłonka szyjki macicy u 77 pacjentów. WYNIKI. Analiza osadów moczowych dała łącznie dwadzieścia (25,97%) pozytywnych i 57 (74,03%) negatywnych wyników. Z kolei ocena próbek pochodzących z macicy wykazała 17 dodatnich wyników (22,08%) i 60 (77,92%) negatywnych wyników. WNIOSKI. Przeprowadzone badanie umożliwiło porównanie częstości występowania wirusa HPV w komórkach osadu moczu oraz w komórkach nabłonka szyjki macicy u badanego pacjenta. Przeprowadzone obserwacje prawdopodobnie spowodują dalszą analizę badanego zagadnienia; jednak uzyskane wyniki dostarczają argumentów dla różnych naturalnych procesów infekowania.

BACKGROUND: Promoter hypermethylation can be a useful biomarker for early detection and prognosis of bladder cancer, monitoring response to treatment and complement classical diagnostic procedures. OBJECTIVE: The molecular test was performed on DNA from bladder cancer cells in voided urine samples, tumor tissue DNA and normal control DNAs. We aimed to assess the diagnostic potential of epigenetic changes in urine DNA from bladder cancer cases at various clinico-pathological stages of the disease. METHODS: The methylation status of 5 genes (p14ARF, p16INK4A, RASSF1A, DAPK, APC) in 113 tumor samples paired with voided urine specimens was analyzed by MSP. We compared the results of methylation analysis with UroVysion test. RESULTS: The methylation profile in tumor/urine DNA was significantly correlated (p ≤ 0,05) with tumor grade in p14ARF, RASSF1a, APC/p14ARF, APC genes, respectively and with stage in p14ARF, RASSF1a/p14ARF genes, respectively. The results of UroVysion test were in correlation with hypermethylation both in tumor and urine DNA in p14ARF, RASSF1a and APC genes (p = 0,008; 0,02 and 0,04, respectively). CONCLUSIONS: Promoter hypermethylation of tumor suppressor genes is a frequent mechanism in bladder cancer. We found promoter hypermethylation in all grades and stages of all cases examined. Methylation profile of selected suppressor genes may be a potential useful biomarker and enhance early detection of bladder cancer using a noninvasive urine test.

The aim of the study was to assess the genetic diversity of bladder cancer and determine the suitability of a proposed molecular marker panel to monitor the course of bladder cancer patients. The study involved 185 patients with diagnosed bladder cancer. The genetic diversity of the bladder cancer was evaluated by the prevalence of mutations in the TP53, HRAS, FGFR3 and WWOX genes.Mutations were detected in 62.2% of the tumor samples. The most frequently mutated genes were FGFR3 (49.7%) and TP53 (16.2%). No mutation was observed in the WWOX gene. FGFR3 mutations, contrary to TP53, correlated with lower tumor stage and grade, and the presence of multiple tumors. The risk of death was significantly higher in patients with TP53 mutant tumors (HR=3.12; 95%CI: 1.14-7.27; p=0.006) but lower in patients with FGFR3 mutations (HR=0.36; 95%CI: 0.15-0.87; p=0.002). None of the investigated genes was an independent predictor of disease-specific survival, recurrence-free survival or progression-free survival.The results confirm the existence of two alternative pathways of bladder cancer. However the presence of a high percentage of wild type variants in the higher stages of the disease suggest the existence of another pathway of molecular changes leading to the development of bladder cancer. Molecular analysis may have prognostic value and may facilitate the assignment of patients to appropriate forms of treatment - especially in the case of patients with a T1 tumor, where different mutational patterns were observed in each grade.

INTRODUCTIONThe SHOX gene has been mapped at the pseudoautosomal region 1 (PAR1) of chromosomes X (Xp22.33) and Y (Yp11.32). The loss of SHOX gene functionality is assumed to be responsible for the Leri-Weill syndrome formation and the disproportionate short stature (DSS). The SHOX gene rearrangements constitute the majority of cases of gene functionality loss. Therefore, a practical application of the method, which allows for the diagnostics of the gene rearrangements, becomes a primary issue. With such an assumption, the MLPA technique (multiplex ligation - dependent probe amplification) becomes the method of choice.MATERIAL AND METHODSDNA samples were evaluated in the study by means of the MLPA method. The DNA was isolated from peripheral blood of sixty-three (63) 46,XX patients with short stature.RESULTSOut of the examined patients, deletions within the SHOX gene were found in five (5) patients, and duplication at the PAR1 regulatory region of the SHOX gene in one (1) case.CONCLUSIONSThe obtained results confirm the opinion that the MLPA method, while enabling the diagnostics of the etiopathogenetic factor of short stature, identified in approximately 9.5% of cases, is a useful tool in the diagnostics of SHOX gene deletion and duplication. (Endokrynol Pol 2016; 67 (4): 397-402).

Introduction: The SHOX gene has been mapped at the pseudoautosomal region 1 (PAR1) of chromosomes X (Xp22.33) and Y (Yp11.32). The loss of SHOX gene functionality is assumed to be responsible for the Leri-Weill syndrome formation and the disproportionate short stature (DSS). The SHOX gene rearrangements constitute the majority of cases of gene functionality loss. Therefore, a practical application of the method, which allows for the diagnostics of the gene rearrangements, becomes a primary issue. With such an assumption, the MLPA technique (multiplex ligation — dependent probe amplification) becomes the method of choice. Material and methods: DNA samples were evaluated in the study by means of the MLPA method. The DNA was isolated from peripheral blood of sixty-three (63) 46,XX patients with short stature. Results: Out of the examined patients, deletions within the SHOX gene were found in five (5) patients, and duplication at the PAR1 regulatory region of the SHOX gene in one (1) case. Conclusions: The obtained results confirm the opinion that the MLPA method, while enabling the diagnostics of the etiopathogenetic factor of short stature, identified in approximately 9.5% of cases, is a useful tool in the diagnostics of SHOX gene deletion and duplication. (Endokrynol Pol 2016; 67 (4): 397–402)

Endometrial cancer belongs to the most frequently diagnosed malignant neoplasms of female genital organs, and its incidence is steadily growing. For the timebeing, no chromosomal aberrations have been determined unequivocally, which would be specific for the particular stages of endometrial hyperplasia and neoplastic transformation development. The goal of the undertaken studies was an identification of the earliest and specific genetic changes, which could be attributed to an increased risk of neoplastic transformation in a group of patients with endometrial hyperplasia plus the characteristics of genetic changes associated with the mature form of neoplasm. The study involved forty-four (44) patients, including five (5) histopathologically unconfirmed hyperplasia, twenty-six (26) with histopathologically confirmed endometrial hyperplasia and thirteen (13) with diagnosed endometrial cancer. The applied aCGH (array Comparative Genomic Hybridisation) method enabled selection of a few chromosomal regions which indicated a higher incidence of chromosomal rearrangements than in the control group. The study included also an evaluation of the frequency of mutations of the genes specific for neoplastic transformation development, the genes at chromosomal loci, which most frequently presented with genomic imbalance. In cases without hyperplasia, changes were diagnosed, described as CNVs (Copy Number Variations), which occurred with varying prevalence in the genome of the population of healthy subjects. Significant genomic imbalance was identified in 26 (100%) patients with diagnosed hyperplasia and in 11 (84.6%) of the patients with diagnosed endometrial cancer. Also other, till now unreported changes were found, localised at characteristic regions of the genome.

The pilot study included 25 patients with symptoms of recurrent infection of the urinary tract. The results of urine sediment cytology (presence of atypical cells = cytology +), which was performed in this group (positive in 92%), were accepted as an additional criterion for inclusion to the study group. The control group was consisted of the 78 female patients, from whom we obtained DNA from cervical smears, while realizing one of the local Screening Programs and these patients reported no complaints from the genitourinary system. In the DNA samples obtained from patients of the study group, the infection of the high-risk Human Papilloma Virus (HPV=HPV+) was confirmed in 65%, the same group of patients were tested on the presence of high-risk HPV in material derived by catheterization of the urinary bladder, the result was positive (HPV +) in 32% cases. In the control group the presence of high-risk HPV DNA in samples derived from cervical smears were found in 20.6% of patients. In these group of HPV (+) patients, the DNA samples obtained from urine sediment, the methylation profile of five genes: p16INK4a, p14ARF, DAPK, RASSF1A, APC was analysed. It was based on an assessment of the presence or absence of specific U or M bands, which are the visualization of the PCR products after the electrophoresis in a polyacrylamide gel followed by staining using ethidium bromide. Two patients (DNA samples from the urine sediment: cytology + ; HPV +) demonstrated the presence of abnormal methylation profile. In the first case the result concern the p16INK4a gene, the second - the APC gene. In one case, during diagnostic transurethral bladder cystoscopy, verified by histopathological examination, the presence of squamous cell metaplasia was revealed. The second case was diagnosed with chronic cystitis. It appears that urine cytology supplemented by the DNA test for the presence of HPV and a molecular test for the presence of methylation of selected genes may provide a valuable indication for bladder cystoscopy. The study was financed by Genos NON-Public Healthcare funds.