Detection of urothelial carcinoma using plasma cell-free methylated DNA.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 5046-5046
Author(s):  
Pier Vitale Nuzzo ◽  
Sandor Spisak ◽  
Jacob E Berchuck ◽  
Sylvan Baca ◽  
Keegan Korthauer ◽  
...  
Keyword(s):  
Urothelial Carcinoma ◽  
High Throughput Sequencing ◽  
High Sensitivity ◽  
P Value ◽  
Plasma Samples ◽  
Methylated Dna ◽  
Non Invasive ◽  
Muscle Invasive ◽  
And Control ◽  
Control Samples

5046 Background: Methylation profiling of circulating cell-free DNA (cfDNA) is a promising approach for non-invasive tumor detection due to the presence of tissue-specific epigenetic signatures that are detectable in cfDNA. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMedDIP-seq) is a sensitive, low-input, cost-effective, bisulfite-free approach to profiling cfDNA methylomes, capable of detecting and classifying various tumor types. We tested the feasibility of cfMeDIP-seq to detect urothelial carcinoma (UC) in plasma samples. Methods: We performed cfMeDIP-seq on plasma samples from 43 patients (pts): 18 metastatic UC (UC) pts, 12 pre-cystectomy non-metastatic UC pts, and 13 cancer-free controls. Six (50%) of pre-cystectomy cases were non-muscle invasive UC. cfDNA was immunoprecipitated and enriched using an antibody targeting 5-methylcytosine and PCR-amplified to create a sequence-ready library. The top differentially methylated regions (DMRs) between UC and control samples were used to train a regularized binomial generalized linear model using 80% of the samples as a training set. The 20% of withheld test samples were then assigned a probability of being UC or control. This process was repeated 100 times. Results: The average amount (standard deviation) of cfDNA isolated from 1 ml of UC plasma samples was 29.2 (27.4) ng/µL and 8.02 (3.58) ng/µL in cancer-free controls. We identified 9,826 DMRs in plasma samples at an adjusted p-value of < 0.01, which partitioned UC and control samples. Iterative training and classification of held out samples using the top 300 DMRs resulted in a mean AUROC of 0.987. Conclusions: cfMeDIP-seq is an interesting new approach for non-invasive detection of UC. cfMeDIP-seq demonstrates high sensitivity to detect UC across all stages of UC, including non-muscle invasive disease.

Is Immediate Radical Cystectomy Necessary for All Patients with Non-Muscle-Invasive Micropapillary Bladder Cancer?

2015 ◽  
Vol 96 (1) ◽  
pp. 32-38 ◽  
Author(s):  
Benjamin L. Jackson ◽  
Aza Mohammed ◽  
Nick Mayer ◽  
John Dormer ◽  
T.R. Leyshon Griffiths
Keyword(s):  
Urothelial Carcinoma ◽  
Prognostic Indicator ◽  
Lymph Node Involvement ◽  
Morphological Marker ◽  
Free Survival ◽  
Non Invasive ◽  
Node Involvement ◽  
Resection Specimen ◽  
Muscle Invasive

Introduction: We aim to review the outcomes of micropapillary urothelial carcinoma (MPUC) of the bladder from a single institution. The hypothesis is that non-muscle-invasive (NMI) MPUC may have a heterogeneous prognosis, and detailed pathological analysis may identify patients that could be managed without immediate cystectomy. Patients and Methods: This is a retrospective analysis of patients presenting with MPUC in a primary transurethral resection specimen (n = 40). The pattern of micropapillary (MP) differentiation [surface/non-invasive (sMP) or invasive (iMP)], extent of MP differentiation and lymphovascular invasion (LVI) were correlated with overall survival (OS), recurrence-free survival and upstaging at re-resection. Results: Sixteen of 40 patients died after a median follow-up of 37 months. Tumour stage was strongly predictive of OS (p < 0.0001). LVI was associated with increased mortality (hazard ratio 12.4, 95% CI: 3.5-44.5, p = 0.0001), higher pathological stage (p = 0.001), lymph node involvement (p = 0.001) and iMP differentiation (p = 0.006). In NMI patients not undergoing cystectomy (n = 17), NMI-sMP compared with NMI-iMP differentiation was associated with an improved OS when compared with iMP (63 vs. 47 months, p = 0.05). Conclusions: MPUC is an aggressive variant of urothelial carcinoma (UC). Similar to conventional UC, LVI associated with MPUC is an adverse prognostic indicator. iMP is a morphological marker for LVI. Histopathological reports should distinguish between sMP and iMP differentiation.

Relationship between high microRNA-200C expression and the risk of death from disease in muscle-invasive urothelial carcinoma of the bladder.

2012 ◽  
Vol 30 (5_suppl) ◽  
pp. 279-279 ◽  
Author(s):  
Neema Navai ◽  
Michael Brandon Williams ◽  
Sijin Wen ◽  
Arlene O. Siefker-Radtke ◽  
David James McConkey ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Urothelial Carcinoma ◽  
Multivariable Analysis ◽  
Surrogate Marker ◽  
Rank Test ◽  
P Value ◽  
Fisher Exact Test ◽  
Mesenchymal Transition ◽  
Risk Of Death ◽  
Muscle Invasive

279 Background: Bladder cancer represents both a common and highly morbid disease with limited tools for prognostication. Recently molecular studies have led to promising targets to inform disease behavior, including microRNAs (miRNA). miRNAs are non-coding RNAs, with widespread effects on cellular function. Our group has demonstrated that the miR200 family members play an integral role in epithelial to mesenchymal transition (EMT) via an inverse relationship with ZEB1 and a direct relationship with E-cadherin. EMT is seen as a necessary step for invasion and metastasis, however, studies have indicated a significant role for mesenchymal to epithelial transition (MET) to drive proliferation after cells have reached metastatic locations. Members of the miR200 family have been shown to induce MET and we hypothesize that miR200c, as a surrogate marker for MET, and will predict disease survival in muscle invasive urothelial carcinoma (MIUC). Methods: A clinically diverse sample set was obtained consisting of 101 unique specimens upon which real-time PCR miRNA analysis was performed. Regression tree analysis and best-fit modeling was used to establish the most discriminating relative miR200c expression level to predict disease specific survival. Fisher exact test was carried out to compare clinical variables, Kaplan-Meier estimate of survival distribution based on miR200c expression and univariate log-rank test was used to compare survival distributions between groups. Multivariate analysis was done via the proportional hazards model. A p-value of <0.05 was considered significant for all statistical analyses. Results: Patients with high miRNA200c had significantly more deaths (69 vs. 47%). In multivariable analysis of patients with MIUC miR200c expression was associated with the highest risk of death (RR 2.7). Lymph node involvement (RR 2.0) and age > 65yrs (RR 2.4) were also strong predictors of survival. High miR200c had lower median survival for all patients (59 vs 16 months; p = 0.039) and those with MIUC (41 vs 8 months; p = 0.0004). Conclusions: High miR200c expression is associated with a higher risk of death from bladder cancer in patients with muscle invasive disease.

Cell-free tumor DNA and TERT promoter mutations in bladder cancer.

2017 ◽  
Vol 35 (6_suppl) ◽  
pp. 353-353 ◽  
Author(s):  
Franklin W. Huang ◽  
Mikael L. Rinne ◽  
Kevin T. Lundgren ◽  
Stephanie Anne Mullane ◽  
Irene Moreno ◽  
...  
Keyword(s):  
Urothelial Carcinoma ◽  
Metastatic Disease ◽  
Tert Promoter Mutation ◽  
Plasma Samples ◽  
Promoter Mutation ◽  
Library Construction ◽  
Non Invasive ◽  
Tert Promoter ◽  
Tert Promoter Mutations ◽  
Promoter Mutations

353 Background: Currently, there are no FDA-approved blood biomarkers for the prognosis or prediction of outcomes in urothelial carcinoma (UC). The telomerase reverse transcriptase ( TERT) promoter is recurrently mutated at high frequency in UC (50%). These mutations have been correlated with tumor recurrence and survival. Tumor cell-free DNA (cfDNA) with somatic genomic alterations can be found in the plasma of cancer patients and has the potential for use as a non-invasive cancer biomarker. Detection of TERT promoter mutations in cfDNA might be used as a prognostic tool to monitor disease outcome in UC patients. We set out to detect tumor cfDNA and TERT promoter mutations in cfDNA from patients with UC at different stages. Methods: UC patients receiving chemotherapy in the neoadjuvant, first or second-line metastatic setting had blood collected either before or during therapy. cfDNA was isolated from ~1ml plasma samples using the QIAmp (Qiagen) kit. Samples underwent ultra-low pass whole genome sequencing (ULP-WGS) to determine whether tumor cfDNA could be detected in these samples. TERT promoter mutations were detected using a sensitive qPCR assay. Results: 40 plasma samples from a total of 32 patients with urothelial carcinoma were analyzed. Sufficient amounts of plasma cfDNA were obtained for library construction and ULP-WGS in 11 patients. 6 of these 11 patients were determined to be positive for detectable tumor cfDNA and of these, all were metastatic and 50% (3/6) were positive for a TERT promoter mutation. In total, 8 out of 40 samples (20%) were positive for a TERT promoter mutation, including samples from two patients where total cfDNA yield was insufficient for library construction. A total of ~20% of patients with metastatic disease were positive for TERT promoter mutations in cfDNA. The low percentage of samples having sufficient cfDNA most likely reflects the low volume of plasma used. Conclusions: TERT promoter mutations were identified in cfDNA of UC patients. ULP-WGS showed tumor cfDNA in patients with a high tumor burden and metastatic disease. TERTpromoter mutations in cfDNA could potentially be used as a non-invasive method for detection of disease. These results have implications for the use of cfDNA in the evaluation of advanced UC.

Super-MSI: CfDNA-based pan-cancer microsatellite instability detection.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e13672-e13672
Author(s):  
Xiaomeng Sun ◽  
Xiaohong Xu ◽  
Rongbo Lin ◽  
Guodong Zhao
Keyword(s):  
Microsatellite Instability ◽  
Microsatellite Loci ◽  
Molecular Subtype ◽  
White Blood Cells ◽  
High Sensitivity ◽  
P Value ◽  
Plasma Samples ◽  
Candidate Locus ◽  
Tissue Samples ◽  
Pan Cancer

e13672 Background: Microsatellite instability (MSI) is a molecular subtype found in many cancers, which is often associated with the benefits of immunotherapy. However, the application of traditional testing strategies (such as PCR or IHC) is largely limited due to their dependencies on sufficient tumor tissues. Here, we introduced Super-MSI, a cfDNA-based pan-cancer MSI detection method using next-generation sequencing (NGS). Methods: 5500 detectable microsatellite loci from 250 white blood cells (WBCs) and 29 PCR-validated MSI-H tissue samples were sequenced and characterized, while the former represented for MSS pattern, and the later, for MSI-H. 91 microsatellite loci with the most variable motif repeat numbers between patterns were filtered and the Super-MSI method was established. Plasma samples were collected from 608 patients with known MSI status assessed by PCR (593 MSS and 15 MSI-H) to validate the method. All samples were sequenced with a 642-gene panel, and initial microsatellite reads count distributions were profiled by MSIsensor. Results: We characterized each microsatellite locus by REF alleles (MSI-H:WBC ratio less than 1) and ALT alleles (MSI-H:WBC ratio more than 20), then defined the sum of ALT alleles frequency in WBC group as the baseline for each candidate locus. For plasma samples with unknown MSI status, hypergeometric distribution and FDR calibration were employed to assess the difference of ALT alleles frequency between the WBC baseline and plasma samples. Locus with FDR adjusted p-value less than 0.05 was defined as an unstable locus based on prior knowledge, and negative log-transformed FDR-p was defined as MSscore for the locus. The plasma sample with both unstable microsatellite proportion larger than 20% and total MSscore larger than 270 was defined as MSI-H, and contrariwise, MSS. For all evaluable samples in the validation cohort, Super-MSI showed high sensitivity and specificity of 60% (9/15) and 100% (593/593) for an overall accuracy of 99.0% (602/608), superior to its kind bMSISEA (83.5%, 106/127) and Guardant360 (98.4%, 934/949). Within LOD of 0.5% maxAF (approximately 1% ctDNA fraction), Super-MSI was able to detect 81.8% (9/11) of MSI-H samples, demonstrating high concordance with tissue-based PCR tests. Conclusions: Super-MSI can genotype pan-cancer patients with blood cfDNA samples and give highly accurate MSI evaluation with 81.8% sensitivity and 100% specificity above 1% ctDNA fraction.

Nanoanalysis of plasma volatile organic compounds using novel DNA-decorated carbon nanotube vapor sensors to noninvasively distinguish ovarian and pancreatic cancer from benign and control samples.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 5544-5544
Author(s):  
A. T. Charlie Johnson ◽  
Christopher Kehayias ◽  
Erica L. Carpenter ◽  
Jody Piltz-Seymour ◽  
Janos Laszlo Tanyi ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Pancreatic Cancer ◽  
Carbon Nanotube ◽  
Cancer Patients ◽  
Organic Compounds ◽  
Plasma Samples ◽  
Volatile Organic ◽  
Vapor Sensors ◽  
And Control ◽  
Control Samples

5544 Background: All cells release volatile organic compounds (VOCs) which emanate from body fluids. Our previous preliminary proof of concept study demonstrated that VOCs released from tissue and plasma from ovarian cancer patients are distinct from those released from samples of patients with benign tumors and controls. We seek to create a sensitive and specific, high-throughput screening test for cancer based on analysis of VOCs using novel nanosensors, first targeting cancers with limited clinical screening modalities. In this study we use these sensors to distinguish vapor characteristics in plasma samples from patients with ovarian and pancreatic cancer from benign specimens and controls. Methods: VOCs emanating from.5 mL of thawed, previously banked plasma samples from 93 total individuals were analyzed using a 10-channel nanoelectronic olfaction (“e-nose”) system based on single-stranded DNA-decorated single-walled carbon nanotube (DNA-NT) vapor sensors. Analysis was performed on samples from 20 patients with ovarian cancer, 20 with benign ovarian tumors and 20 age-matched women as well as 13 patients with pancreatic cancer, 10 patients with benign pancreatic disease, and 10 age- and sex-matched controls. All ovarian cancer patients and comparators were non-smokers, while 1 pancreatic patient and 1 corresponding control were current smokers. The sample set included cancer patients with both early- and late-stage disease. All cancer specimens were obtained proximal to initial diagnosis and prior to initiation of therapy. With a test time of approximately 20 minutes per sample, the array output for each individual sample creates a vector in a 10-dimensional sensor space. The ability of the nanosensor array to discriminate between malignant, benign, and healthy groups was investigated using linear discriminant analysis (LDA), support vector machine (SVM), k-nearest neighbors (KNN), and random forest classification algorithms. Each algorithm was trained and tested according to leave-one-out and repeated stratified k-fold cross-validation methods. Results: Compared to their corresponding benign and control specimens, the DNA-NT sensor array was able to discriminate the VOCs from ovarian cancer with 95% accuracy and pancreatic cancer with 90% accuracy. Plasma samples from patients with early-stage ovarian and pancreatic cancers were correctly identified by the algorithms. Conclusions: Nano-enabled DNA coated vapor sensors were able to distinguish the VOC pattern between cancer, benign and control samples in both ovarian and pancreatic cancer. We provide strong evidence that ovarian and pancreatic cancer alters the VOC pattern emanating from plasma. Our results provide optimism that a diagnostic approach based on vapor detection of ovarian and pancreatic cancer is achievable.

scholarly journals Evaluation of Rap1GAP and Epac1 Gene Expression in Endometriosis

2022 ◽  
Author(s):  
Mehran Dehghanian ◽  
Ghafour Yarahmadi ◽  
Reyhaneh Sadat Sandoghsaz ◽  
Farimah Shamsi ◽  
Ali Khodadadian ◽  
...  
Keyword(s):  
P Value ◽  
Nucleotide Exchange ◽  
Normal Endometrium ◽  
System Disease ◽  
Guanine Nucleotide Exchange ◽  
Nucleotide Exchange Factors ◽  
Ras Family ◽  
And Migration ◽  
And Control ◽  
Control Samples

Abstract Objective: Endometriosis is a female reproductive system disease in which endometrial tissue are found in other women organs. Various factors are effective in the development of endometriosis and due to the interaction of genetics and environmental factors, this disease is a multifactorial disease. MAPK/ERK and PI3K/Akt/mTOR pathways are activated by growth factors and steroid hormones and known as two important pathways involved in the processes of growth, proliferation and survival of endometriosis cells. Raps, monomeric GTPase of Ras family, are able to activate these pathways independently of Ras. The goal of our study was to evaluated the expression level of Rap1GAP and Epac1 gene, as two important RapGAPs (GTPase-activating proteins) and RapGEFs (guanine nucleotide exchange factors) respectively, in endometriosis tissues and normal endometrium tissues.Materials and Methods: In this study, 15 samples of women without signs of endometriosis were taken as control samples, 15 ectopic and 15 eutopic samples were taken from women with endometriosis using laparoscopic surgery. The expression of Epac1 and Rap1GAP genes was investigated by Real-time PCR technique and results were analysis by One-Way ANOVA test.Results: Epac1 upregulated significantly in ectopic tissues compared to eutopic and control tissues (Their P-value were <0.0001). Rap1GAP expression was lower in ectopic tissues compared to control samples (P-value was 0.003) and eutopic tissues (P-value was 0.001).Conclusion: Based on these results, it may be concluded that changes in the expression of the Rap1GAP and Epca1 genes may play role in the pathways involved in the pathogenesis, displacement, and migration of endometriosis cells.

scholarly journals Hubungan Usia Ibu Dan Paritas Dengan Kejadian Abortus Di RSUD Dr. H. Moch Ansari Saleh Banjarmasin

2019 ◽  
pp. 241-250
Author(s):  
Susanti Suhartati ◽  
Laurensia Yunita ◽  
Putri Lestari
Keyword(s):  
At Risk ◽  
Sampling Technique ◽  
Total Sample ◽  
Case Control ◽  
P Value ◽  
Chi Square ◽  
Control Approach ◽  
Abortion Incidence ◽  
And Control ◽  
Control Samples

Latar belakang: Salah satu penyebab kematian ibu adalah perdarahan, dimana salah satu penyebab perdarahan pada awal kehamilan adalah abortus. Abortus adalah berakhirnya suatu kehamilan sebelum janin mencapai berat 500 gram atau umur kehamilan kurang dari 22 minggu atau hasil konsepsi belum mampu untuk hidup di luar kandungan.Tujuan: Mengetahui hubungan usia ibu dan paritas dengan kejadian abortus di RSUD Dr. H. Moch Ansari Saleh Banjarmasin.Metode: Penelitian ini menggunakan survey analitik dengan pendekatan case control. Populasi dalam penelitian ini adalah seluruh ibu hamil yang mengalami abortus dan ibu hamil yang bersalin normal dengan mengambil sampel kasus dan sampel control  menggunakan perbandingan 1:1 dan total sampel kasus dan kontrol yang digunakan adalah 314 orang. Teknik pengambilan sampel total sampling. Data dianalisis menggunakan uji Chi-Square.Hasil: Hasil penelitian di RSUD Dr. H. Moch Ansari Saleh Banjarmasin menunjukkan, hubungan usia dengan kejadian abortus p value=0,042 dan OR=1,631 dan paritas dengan kejadian abortus p value=0,008 dan OR=1,975Simpulan: Ada hubungan antara usia dengan kejadian abortus, usia beresiko memiliki resiko 1,6 kali lebih tinggi mengalami kejadian abortus. Ada hubungan antara paritas dengan kejadian abortus, paritas beresiko memiliki resiko 1,9 kali lebih tinggi mengalami kejadian abortus. Kata kunci: Abortus, Paritas, Usia Ibu ABSTRACTBackground: One of the causes of maternal death is bleeding, where one of the causes of bleeding in early pregnancy is abortion. Abortion is the end of a pregnancy before the fetus reaches a weight of 500 grams or gestational age of fewer than 22 weeks or the conception has not been able to live out of the womb.Objective: Knowing the relationship between maternal age factor, abortion history, and parity with abortion incidence in RSUD Dr. H. Moch Ansari Saleh Banjarmasin.Method: his research uses analytical survey with a case-control approach. The population in this study were all mothers who had an abortion by taking samples of case and control samples using a ratio of 1: 1 and the total sample and control samples used were 314 people. Total sampling technique. Data were analyzed using the Chi-Square test.Results: Results of research in RSUD Dr. H. Moch Ansari Saleh Banjarmasin shows, the age relationship with the incidence of abortion p value=0,042 and OR=1,631, and parity with abortus p value=0,008 and OR=1,975Summary: There was a correlation between age and abortion, age was at risk 1.6 times higher experienced abortion. There was a relationship between abortion history and abortion, There was a relationship between parity and the incidence of abortion, parity at risk of 1.9 times higher risk of abortion. Keywords: Abortion, Mother Age, Parity  

Cell-free circulating DNA as a promising marker of colorectal cancer detection and progression

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 11059-11059
Author(s):  
S. Pucciarelli ◽  
M. Enzo ◽  
M. Agostini ◽  
S. Pizzini ◽  
P. Del Bianco ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Healthy Subjects ◽  
P Value ◽  
Circulating Dna ◽  
Plasma Samples ◽  
Alu Repeats ◽  
Non Invasive ◽  
Total Dna ◽  
Free Circulating Dna ◽  
Normal Controls

11059 Background: Since the pathologic stage is the most powerful prognostic factor for colorectal cancer (CRC), there is a strong need of non-invasive methods for early detection. Cell-free circulating DNA (cfDNA) released from cancer cells varies in size. It has been suggested that cfDNA (ALU repeats of 115 bp, representative of total DNA; ALU repeats of 247 DNA, representative of tumor DNA) may be associated with presence of tumor. Aim of this study was then to investigate whether the cfDNA may have a role as marker of CRC detection and progression. Methods: cfDNA was extracted from plasma samples from 136 patients with primary CRC at different stages [median age 64 yrs; male/female 78/58; stages I-II, 61; stages III-IV, 75], and from 24 patients with adenomas [median age 67 yrs; male/female 17/7)] and from 55 clean-colon healthy subjects [median age 56 yrs; male/female 13/43). cfDNA was assessed by quantitative real-time PCR (qPCR) of ALU repeats with 2 sets of primers (115 and 247 bp) amplifying different lengths of DNA. The levels of cfDNA (ALU-115, ALU-247) of CRC patients (stages I-II and stages III-IV) were compared with those of healthy subjects and patients with adenoma. Results: The median concentrations of total cfDNA (ALU115) in the plasma samples from patients with stages III-IV and stages I-II CRC, adenoma and normal controls were 52,4, 11.9; 1.9, and 1.7 ng/ml, respectively (p<.0001). The corresponding figures for tumor-related cfDNA (ALU247) were 48.8, 4.7, 2.2, and 0.7 ng/ml, respectively. (p<.0001). With a cut-off of 4.86 ng/ml, total DNA (ALU115) showed a sensitivity of 78.52 (95% CI 70.6–85.1) and a specificity of 86.08 (95% CI 76.4–92.8) in distinguishing patients with CRC from non-CRC [AUC: 0.860 (95% CI 0.81–0,90), p-value=.0001]. With a cut-off of 3.04, cfDNA tumor-related (ALU247) showed a sensitivity of 77.94 (95% CI 70.0–84.6) and a specificity of 82.28 (95% CI 72.1–90.0) in distinguishing patients with CRC from non-CRC [AUC: 0.864 (95% CI 0.81–0,91), p-value=.0001]. Conclusions: Both ALU115 and ALU 247 fragments of circulating cfDNA seem promising non-invasive molecular markers of detection and progression of CRC. The findings of the current study require to be confirmed on larger cohorts of patients with CRC and colonic adenoma. No significant financial relationships to disclose.

Methylated DNA markers for plasma detection of ovarian cancer: Discovery, validation, and clinical feasibility.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 6072-6072
Author(s):  
Jamie Nadine Bakkum-Gamez ◽  
Lisa Marinelli ◽  
David A. Ahlquist ◽  
Seth Slettedahl ◽  
Douglas W. Mahoney ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
High Sensitivity ◽  
Screening Tests ◽  
Early Event ◽  
Plasma Samples ◽  
Reduced Representation ◽  
Methylated Dna ◽  
Biological Validation ◽  
Specific Pcr ◽  
Pre Treatment

6072 Background: Effective screening tests for ovarian cancer (OC) are lacking; most cases present at advanced stage and portend poor prognosis. DNA methylation is an early event in carcinogenesis and can be detected in blood plasma samples from cancer patients. In DNA extracted from tissues, we first discovered, then validated discriminant methylated DNA marker (MDM) candidates for OC and subsequently tested independent plasma from women with and without OC. Methods: For discovery, DNA from 67 frozen tissues (18 high grade serous (HGS), 18 endometrioid, 15 clear cell (CC), 6 mucinous OCs; 10 benign fallopian tube epithelium (FT); and 19 buffy coats from cancer-free women underwent reduced representation bisulfite sequencing (RRBS) to identify MDMs associated with OC. Candidate MDM selection was based on receiver operating characteristic (ROC) discrimination, methylation fold change, and low background methylation among controls. Blinded biological validation was performed using methylated specific PCR on DNA extracted from independent FFPE tissues from OCs (36 HGS, 22 endometrioid, 21 CC, and 14 mucinous) and 29 FT. Top performing MDMs in tissue were tested using long-probe quantitative amplified signal assays in independent pre-treatment plasma samples from women newly-diagnosed with OC and population-sampled healthy women. A random forest modeling analysis was performed to generate predictive probability of disease; results were 500-fold in silico cross-validated. Results: After RRBS discovery and biological validation, 33 MDMs showed marked methylation fold changes (10 to > 1000) across all OC histologies vs FT. The top 11 MDMs ( GPRIN1, CDO1, SRC, SIM2, AGRN, FAIM2, CELF2, DSCR6, GYPC, CAPN2, BCAT1) were tested on plasma from 91 women with OC (76 (84%) HGS) and 91 without OC; the cross-validated 11-MDM panel highly discriminated OC from controls (96% (95%CI 89-99%) specificity; 79% (69-87%) sensitivity, and AUC 0.91 (0.86 - 0.96)). Among HGS, the panel correctly identified 83%, including 5/6 stage I/II, and the majority of other subtypes (Table). Conclusions: Whole methylome sequencing, stringent filtering criteria, and biological validation yielded outstanding candidate MDMs for OC that performed with promisingly high sensitivity and specificity in plasma. Larger plasma-based OC MDM testing studies, with larger numbers of non-HGS histologies are warranted. [Table: see text]

scholarly journals Saliva Exhibits High Sensitivity and Specificity for the Detection of SARS-COV-2

Diseases ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 38
Author(s):  
Ibrahim Warsi ◽  
Zohaib Khurshid ◽  
Hamda Shazam ◽  
Muhammad Farooq Umer ◽  
Eisha Imran ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
High Sensitivity ◽  
Minimal Risk ◽  
Non Invasive ◽  
Oral Fluids ◽  
Home Testing ◽  
Screening Strategies ◽  
Online Calculator ◽  
And Control ◽  
High Degree

In the wake of the COVID-19 pandemic, it is crucial to assess the application of a multitude of effective diagnostic specimens for conducting mass testing, for accurate diagnosis and to formulate strategies for its prevention and control. As one of the most versatile and amenable specimen options, saliva offers great advantages for widespread screening strategies due to its non-invasive properties, cost-effectiveness, excellent stability and minimal risk of cross-infection. This review attempts to outline the scientific rationale for detection of SARS-COV-2 in saliva specimens. By combining the data obtained from ten chosen published clinical studies, we calculated the pooled sensitivity and specificity using an online calculator. Through evidence, we established that SARS-COV-2 is detectable in saliva with a high degree of diagnostic sensitivity (87%) and specificity (98%). We also presented a review of emerging technologies approved by the FDA for detection of SARS-COV-2 in oral fluids (saliva and sputum) using polymerase chain reaction methods. Given the challenges involved in obtaining invasive specimens from the naso- and oropharynx, saliva can serve as an easy to collect diagnostic specimen for screening in the work environment, schools and for home testing. Furthermore, saliva offers the opportunity to screen early cases that can be missed by invasive sampling.

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