scholarly journals Epigenetic Markers for Molecular Detection of Prostate Cancer

2007 ◽  
Vol 23 (1-2) ◽  
pp. 31-41 ◽  
Author(s):  
Vera L. Costa ◽  
Rui Henrique ◽  
Carmen Jerónimo
Keyword(s):  
Prostate Cancer ◽  
Sensitivity And Specificity ◽  
Prostate Cancer Risk ◽  
High Sensitivity ◽  
Promoter Hypermethylation ◽  
Clinical Samples ◽  
Screening Methods ◽  
Tissue Samples ◽  
Age Related ◽  
Small Set

Prostate cancer is a highly prevalent malignancy, which is clinically silent but curable while organ-confined. Because available screening methods show poor sensitivity and specificity, the development of new molecular markers is warranted. Epigenetic alterations, mainly promoter hypermethylation of cancer-related genes, are common events in prostate cancer and might be used as cancer biomarkers. Moreover, the development of quantitative, high-throughput techniques to assess promoter methylation enabled the simultaneous screening of multiple clinical samples. From the numerous cancer-related genes hypermethylated in prostate cancer only a few proved to be strong candidates to become routine biomarkers. This small set of genes includesGSTP1,APC,RARβ2,Cyclin D2,MDR1, andPTGS2. Single and/or multigene analyses demonstrated the feasibility of detecting early prostate cancer, with high sensitivity and specificity, in body fluids (serum, plasma, urine, and ejaculates) and tissue samples. In addition, quantitative hypermethylation of several genes has been associated with clinicopathologic features of tumor aggressiveness, and also reported as independent prognostic factor for relapse. The identification of age-related methylation at specific loci and the differential frequency of methylation among ethnical groups, also provided interesting data linking methylation and prostate cancer risk. Although large trials are needed to validate these findings, the clinical use of these markers might be envisaged for the near future.

scholarly journals EGFR mutation testing in lung cancer: a review of available methods and their use for analysis of tumour tissue and cytology samples

2012 ◽  
Vol 66 (2) ◽  
pp. 79-89 ◽  
Author(s):  
Gillian Ellison ◽  
Guanshan Zhu ◽  
Alexandros Moulis ◽  
Simon Dearden ◽  
Georgina Speake ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Kinase Inhibitors ◽  
Direct Sequencing ◽  
Mutation Testing ◽  
Tumour Tissue ◽  
Clinical Samples ◽  
Screening Methods ◽  
Testing Methods ◽  
Tissue Samples ◽  
Direct Dna Sequencing

AimsActivating mutations in the gene encoding epidermal growth factor receptor (EGFR) can confer sensitivity to EGFR tyrosine kinase inhibitors such as gefitinib in patients with advanced non-small-cell lung cancer. Testing for mutations in EGFR is therefore an important step in the treatment-decision pathway. We reviewed reported methods for EGFR mutation testing in patients with lung cancer, initially focusing on studies involving standard tumour tissue samples. We also evaluated data on the use of cytology samples in order to determine their suitability for EGFR mutation analysis.MethodsWe searched the MEDLINE database for studies reporting on EGFR mutation testing methods in patients with lung cancer.ResultsVarious methods have been investigated as potential alternatives to the historical standard for EGFR mutation testing, direct DNA sequencing. Many of these are targeted methods that specifically detect the most common EGFR mutations. The development of targeted mutation testing methods and commercially available test kits has enabled sensitive, rapid and robust analysis of clinical samples. The use of screening methods, subsequent to sample micro dissection, has also ensured that identification of more rare, uncommon mutations is now feasible. Cytology samples including fine needle aspirate and pleural effusion can be used successfully to determine EGFR mutation status provided that sensitive testing methods are employed.ConclusionsSeveral different testing methods offer a more sensitive alternative to direct sequencing for the detection of common EGFR mutations. Evidence published to date suggests cytology samples are viable alternatives for mutation testing when tumour tissue samples are not available.

scholarly journals Two long non-coding RNAs, CAT179 and CAT 1796, differentiate between benign prostate hyperplasia and prostate cancer

2021 ◽  
pp. 33-33
Author(s):  
Nasim Ebrahimi ◽  
Farzane Amirmahani ◽  
Maryam Akbari ◽  
Azin Ghahfarokhi ◽  
Bahareh Hajihashemi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Biology ◽  
Benign Prostate Hyperplasia ◽  
High Sensitivity ◽  
Clinical Samples ◽  
Quantitative Real Time Pcr ◽  
Roc Curve Analysis ◽  
Prostate Hyperplasia ◽  
Non Coding Rnas ◽  
Benign Prostate

Several long non-coding RNAs (lncRNAs) have recently emerged as potential biomarkers in cancer biology. In the present study, we examined the expression of four lncRNAs (CAT179, CAT1796, PRCAT47, and CAT1066) to evaluate their ability to discriminate prostate tumors from benign prostate hyperplasia (BPH). Expression of these four lncRNAs was examined in 20 prostate cancer and 20 benign prostate hyperplasia (BPH) samples, as well as in urine samples (11 BPH, and 11 cancer). Total RNA was extracted for cDNA syntheses. The expression of the candidate lncRNAs was evaluated by quantitative real-time PCR (qRT-PCR). The lncRNAs CAT1796 and CAT179 were both upregulated in prostate cancer compared to BPH clinical samples (P<0.05). ROC curve analysis showed that CAT1796 had high sensitivity and specificity for diagnosis of prostate cancer (AUC=0.8151[95%CI 0.65-0.97]), suggesting that CAT1796 lncRNA could be a prostate cancer biomarker.

scholarly journals Real-time RT-PCR diagnostics of virus causing COVID-19

2020 ◽  
Vol 13 (1) ◽  
pp. 52-63 ◽  
Author(s):  
E. V. Goncharova ◽  
A. E. Donnikov ◽  
V. V. Kadochnikova ◽  
S. A. Morozova ◽  
M. N. Boldyreva ◽  
...  
Keyword(s):  
Real Time ◽  
Sensitivity And Specificity ◽  
High Sensitivity ◽  
Medical Product ◽  
World Health ◽  
Differential Diagnostics ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Study Results ◽  
Pcr Diagnostics

Aim: the study was aimed to develop a reagent kit for the real-time RT-PCR diagnostics of virus causing COVID-19.Materials and Methods. Three target sites were chosen in the genome SARS-CoV-2. The testing included 220 samples, 48 artificially created positive samples (made from patients’ biomaterial) and 172 clinical samples (scrapes from nasal and pharyngeal cavities, bronchoalveolar lavage, expectoration, endotracheal/nasopharyngeal aspirate, feces, post-mortem material), obtained from two medical centers. Preliminary, the obtained biomaterial was analyzed with a reagent kit of comparison. The evaluation was performed with a confidential interval CI 95%. The calculation of CI for the sensitivity and specificity was made based on the distribution of χ2.Results. The authors developed a technology of novel coronavirus infection (COVID-19) real-time RT-PCR diagnostics for the application in practical healthcare and proposed the variants of testing at all the stages (preanalytical, analytical, and post-analytical, including automated results processing). The proposed reagent kit meets the requirements of the World Health Organization and the Ministry of Healthcare of the Russian Federation. The study results demonstrated high sensitivity and specificity. The sensitivity was 100% (95% CI) 95.6–100%; the specificity was 100% (95% CI) 96.7–100%.Conclusion. The proposed reagent kit was registered in the RF as a medical product; the registration certificate No. RZN 2020/9948 dated 01.04.2020. The application of the reagent kit in network laboratories will provide patients with access to testing for the virus causing COVID-19 and contribute to quick differential diagnostics, improvement of pandemic control, and accurate statistics on the spread of the virus. 

Whole-genome sequence-guided PCR for the rapid identification of thePseudomonas aeruginosa ST175 high-risk clone directly from clinical samples

2020 ◽  
Author(s):  
Gabriel Cabot ◽  
Paula Lara-Esbrí ◽  
Xavier Mulet ◽  
Antonio Oliver
Keyword(s):  
High Risk ◽  
Sensitivity And Specificity ◽  
Genome Sequence ◽  
Treatment Strategies ◽  
High Sensitivity ◽  
Whole Genome Sequence ◽  
Clinical Samples ◽  
Whole Genome ◽  
Pcr Assay ◽  
Pcr Targeting

Abstract Objectives Pseudomonas aeruginosa frequently show MDR/XDR profiles, which are associated with worldwide-disseminated high-risk clones (HRCs). We developed a PCR assay for the detection in clinical samples of ST175, an HRC that is widespread in European countries. Methods The whole-genome sequence was obtained for one ST175 isolate using a PacBio RSII sequencer. Reads from multiple isolates belonging to ST175 and the PAO1 reference strain were mapped against the ST175 genome to identify potentially specific regions. Once curated, using the BLAST database to search for the presence of those regions in any other organism, we designed a specific PCR for the detection of ST175. Results Assembly of the ST175 PacBio-sequenced genome resulted in three contigs with a total length of 7 087 985 bases, encoding 6566 coding sequences. Specific regions for ST175 genomes were detected and a PCR targeting a 318 bp fragment located within a 3177 bp ORF coding for a putative reverse transcriptase was designed. The PCR test was first evaluatedin silico against 229 XDRP. aeruginosa genomes (73 ST175) from two multicentre studies, yielding 100% sensitivity and specificity. Then, the PCR was evaluatedin vitro in 25 isolates (12 ST175) and in 120 clinical samples (30 urine samples, 30 blood cultures, 30 sputum samples and 30 rectal swabs) of which 10% contained ST175, yielding again 100% sensitivity and specificity. Conclusions The PCR assay developed, showing high sensitivity and specificity for the detection of the ST175 HRC directly from clinical samples, could become a useful tool for guiding infection control and treatment strategies in areas with a high prevalence of this clone.

Development of test kit for detection of specific IgM to SARS-CoV-2 by immune blotting in the «Line blot» format

2021 ◽  
Vol 66 (8) ◽  
pp. 472-479
Author(s):  
S. G. Mardanly ◽  
A. S. Avdonina
Keyword(s):  
Blood Serum ◽  
Sensitivity And Specificity ◽  
High Sensitivity ◽  
Confirmatory Test ◽  
Clinical Samples ◽  
Etiological Diagnosis ◽  
Healthy Donors ◽  
Test Kit ◽  
Preliminary Study

Test kit for detection of specific IgM to SARS-CoV-2 by immune blotting in the «Line blot» format has been developed. A preliminary study of diagnostic effectivity on clinical samples of blood serum from patients with COVID-19 and healthy donors showed its high sensitivity and specificity. The new test kit allows to detect IgM to all four structural antigens of SARS-CoV-2 and can be used as a confirmatory test to verify indeterminant screening results in laboratory etiological diagnosis of COVID-19.

scholarly journals Aberrant DOCK2, GRASP, HIF3A and PKFP Hypermethylation has Potential as a Prognostic Biomarker for Prostate Cancer

2019 ◽  
Vol 20 (5) ◽  
pp. 1173 ◽  
Author(s):  
Marianne Bjerre ◽  
Siri Strand ◽  
Maibritt Nørgaard ◽  
Helle Kristensen ◽  
Anne Rasmussen ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Blood Cells ◽  
Cox Regression ◽  
High Sensitivity ◽  
Cancer Tissue ◽  
Dna Hypermethylation ◽  
450K Array ◽  
Systematic Analysis ◽  
Tissue Samples ◽  
Independent Population

Prostate cancer (PCa) is a clinically heterogeneous disease and currently, accurate diagnostic and prognostic molecular biomarkers are lacking. This study aimed to identify novel DNA hypermethylation markers for PCa with future potential for blood-based testing. Accordingly, to search for genes specifically hypermethylated in PCa tissue samples and not in blood cells or other cancer tissue types, we performed a systematic analysis of genome-wide DNA methylation data (Infinium 450K array) available in the Marmal-aid database for 4072 malignant/normal tissue samples of various types. We identified eight top candidate markers (cg12799885, DOCK2, FBXO30, GRASP, HIF3A, MOB3B, PFKP, and TPM4) that were specifically hypermethylated in PCa tissue samples and hypomethylated in other benign and malignant tissue types, including in peripheral blood cells. Potential as diagnostic and prognostic biomarkers was further assessed by the quantitative methylation specific PCR (qMSP) analysis of 37 nonmalignant and 197 PCa tissue samples from an independent population. Here, all eight hypermethylated candidates showed high sensitivity (75–94%) and specificity (84–100%) for PCa. Furthermore, DOCK2, GRASP, HIF3A and PKFP hypermethylation was significantly associated with biochemical recurrence (BCR) after radical prostatectomy (RP; 197 patients), independent of the routine clinicopathological variables. DOCK2 is the most promising single candidate marker (hazard ratio (HR) (95% confidence interval (CI)): 1.96 (1.24–3.10), adjusted p = 0.016; multivariate cox regression). Further validation studies are warranted and should investigate the potential value of these hypermethylation candidate markers for blood-based testing also.

scholarly journals IS INFLAMMATION AN AGE-RELATED CAUSE OF BPH PROGRESSION

2011 ◽  
Vol 18 (1) ◽  
Author(s):  
Hendra Herman ◽  
Agus Rizal AH Hamid ◽  
Chaidir Arif Mochtar
Keyword(s):  
Prostate Cancer ◽  
Young Adult ◽  
Older Adult ◽  
Prostate Volume ◽  
Specific Antigen ◽  
Intraepithelial Neoplasia ◽  
Adult Group ◽  
Tissue Samples ◽  
Age Related ◽  
Prostate Enlargement

Objective: To find the role of inflammation in BPH progression represented by prostate enlargement compared between age group. Material & method: Tissue samples of BPH were collected from biopsy, transurethral resection or open surgery. Clinical information was collected including such as patient age, prostate volume, serum prostate specific antigen (PSA) and history of retention before procedure. Patients were divided into three groups, below 63 years old (young adult), 63 - 69 years old (older adult) and equal or above 70 years old (elderly). The samples were analyzed to define the microscopic structure of the hyperplasia (stromal or glandular) and to detect prostatic intraepithelial neoplasia, atypical stromal acinic proliferation, atypical acinar hyperplasia or prostate cancer. Prostate cancer was excluded from study samples. Grade of inflammation was determined by a pathologist depending on number of inflammatory cells. Grade of inflammation was classified in two groups, with mild inflammation or moderate-to-severe inflammation. Results: A total of 1189 patients were reviewed, 1172 were diagnosed with BPH. There were 381 patients (32,5%) with age below 63 years old (young adult), 380 (32,4%) between 63-69 years old (older adult) and 411 (35,1%) in equal or above 70 years old (elderly). In young-adult group, median of prostate volume between mild and moderate to severe inflammations was 42,56 and 45,75 (p = 0,500), for older adult group median was 45,00 and 51,00 (p = 0,038), for elderly group median was 49,00 and 51,98 (p = 0,621). Conclusion: Inflammation has a role in progression of prostate enlargement especially for the older adult group. Keywords: inflammation in BPH progression, prostate volume, age, PSA.

scholarly journals Detecting and Quantitating Low Fraction DNA Variants with Low-Depth Sequencing

2020 ◽  
Author(s):  
Ping Song ◽  
Sherry X. Chen ◽  
Yan Helen Yan ◽  
Alessandro Pinto ◽  
Lauren Y. Cheng ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
High Sensitivity ◽  
Human Cell Line ◽  
Clinical Samples ◽  
Single Nucleotide Variants ◽  
Tumor Biopsy ◽  
Single Nucleotide ◽  
Tissue Samples ◽  
Acquired Drug Resistance ◽  
Dna Variants

DNA sequence variants with low allele frequencies below 1% are difficult to detect and quantitate by sequencing, due to the intrinsic error of sequencing-by-synthesis (NGS). Unique molecular identifier barcodes can in principle help NGS detect mutations down to 0.1% variant allele frequency (VAF), but require extremely high sequencing depths of over 25,000x, rendering high sensitivity mutation detection out of reach for most research and clinical samples. Here, we present the multiplex blocker displacement amplification (mBDA) method to selectively enrich DNA variants by an average of 300-fold in highly multiplexed NGS settings. On a 80-plex human single nucleotide polymorphism panel, mBDA achieves a 0.019% VAF limit of detection for single nucleotide variants, using only 250x sequencing depth, and detects human cell line contamination down to 0.07%. Using this technology, we constructed a 16-plex melanoma NGS panel covering 145 actionable mutations across 9 genes, and applied it to 19 fresh/frozen tumor biopsy tissue samples with high tumor fractions. We found low VAF mutations (0.2% to 5%) in 37% of the samples (7/19, 95% confidence interval 19%-58%). These results suggest that tumor heterogeneity could be significantly more pervasive than previously recognized, and can contribute significantly to acquired drug resistance to targeted therapies. We also validate mBDA panels on clinical cell-free DNA samples from lung cancer patients.

Sign in / Sign up

Export Citation Format

Share Document