The Experts below are selected from a list of 3300 Experts worldwide ranked by ideXlab platform
David Sidransky - One of the best experts on this subject based on the ideXlab platform.
-
quantitative methylation specific polymerase chain reaction gene patterns in Urine Sediment distinguish prostate cancer patients from control subjects
Journal of Clinical Oncology, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Rui Henrique, Eli Rosenbaum, Wim Van Criekinge, William H Westra, David SidranskyAbstract:Purpose Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of prostate cancers and is a promising marker for cancer detection. We sought to develop a test for prostate cancer based on a quantitative methylation-specific polymerase chain reaction (QMSP) of multiple genes in Urine Sediment DNA. Patients and Methods We tested Urine Sediment DNA for aberrant methylation of nine gene promoters (p16INK4a, p14ARF, MGMT, GSTP1, RARβ2, CDH1 [E-cadherin], TIMP3, Rassf1A, and APC) from 52 patients with prostate cancer and 21 matched primary tumors by quantitative fluorogenic real-time polymerase chain reaction. We also analyzed Urine Sediments from 91 age-matched individuals without any history of genitourinary malignancy as controls. Results Promoter hypermethylation of at least one of the genes studied was detected in Urine samples from all 52 prostate cancer patients. Urine samples from the 91 controls without evidence of genitourinary ...
-
methylation pattern of multiple genes in Urine Sediment dna from bladder cancer cases and controls by high throughput quantitative methylation specific pcr qmsp
Cancer Research, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Eli Rosenbaum, Wim Van Criekinge, William H Westra, Aditi Chatterjee, Mark P Schoenberg, David SidranskyAbstract:3150 Background: The early diagnosis of bladder cancer and the early detection of recurrence are central to effective treatment, as prognosis is directly related to the stage of disease. Promoter hypermethylation is now recognized as an important and common epigenetic pathway of gene inactivation. Because bladder cancer cells and DNA are shed into the Urine, we sought to test the value of a quantitative methylation assay in Urine Sediment for the detection of bladder cancer. Methods: We examined primary tumor and matched Urine DNA for aberrant methylation of nine gene promoters ( APC, ARF, CDH1, GSTP1, MGMT, p16, RAR-β2, Rassf1A and TIMP3 ) from 15 patients with bladder cancer by quantitative fluorogenic real-time PCR. We then tested an additional 160 Urine Sediment DNA samples (Total 175 Urine) from bladder cancer patients of different stages and grades. 94 age-matched patients without any evidence of genitourinary cancer were used as a control. Result: In cases with matched tumor, the promoter methylation pattern found in Urine matched the pattern in the primary tumors. 121 of 175(69%) patients with bladder cancer displayed methylation in at least one of four genes ( p16, ARF, MGMT and GSTP1 ), whereas all controls were negative for methylation at the established cut off (100% specificity). When we considered any one of these latter four genes and/or RAR-β2 methylation, the sensitivity and specificity were 82% and 97% respectively (positive likelihood ratio 24.19 and negative likelihood ratio 0.19). Using established cut off values for all the nine genes, 85% sensitivity and 96% specificity was achieved with a positive and negative likelihood ratio of 18.97 and 0.16 respectively. MGMT, ARF , and TIMP3 methylation in Urine correlated with primary tumor invasion and metastasis (p= ≤ 0.05, by logistic regression). The risk of death was statistically significantly higher in patients with TIMP3 methylation (hazard ratio [HR] =1.97, 95% confidence interval [CI] =1.14 to 3.4; p= 0.01) than in patients without TIMP3 methylation in Urine. Conclusion: Testing a small panel of genes with the QMSP (Quantitative Methylation Specific PCR) assay in Urine Sediment DNA represents a powerful noninvasive approach for the detection of bladder cancer on a high throughput-automated platform. Methylation patterns in Urine may also help predict the natural history of detected disease. Larger cohorts with longitudinal follow up will be required in future studies to define the impact of this technology on detection, prognosis and disease monitoring.
Mohammad O Hoque - One of the best experts on this subject based on the ideXlab platform.
-
tissue inhibitor of metalloproteinases 3 promoter methylation is an independent prognostic factor for bladder cancer
The Journal of Urology, 2008Co-Authors: Mohammad O Hoque, Shahnaz Begum, Eli Rosenbaum, William H Westra, Mariana Brait, Carmen Jeronimo, Marianna Zahurak, Kimberly Laskie Ostrow, Bruce J Trock, Mark P SchoenbergAbstract:Purpose: TIMP-3 (tissue inhibitor of metalloproteinases-3) is 1 of 4 members of a family of proteins that were originally classified according to their ability to inhibit matrix metalloproteinases. We analyzed TIMP-3 methylation in 175 Urine Sediment DNA samples from patients with bladder cancer with well characterized clinicopathological parameters, including patient outcome.Materials and Methods: We examined Urine Sediment DNA for aberrant methylation of 9 genes, including TIMP-3, by quantitative fluorogenic real-time polymerase chain reaction.Results: Using an optimal cutoff value by TaqMan® quantitation we found that the risk of death was statistically significantly higher in patients with higher TIMP-3 and ARF methylation (HR 1.99, 95% CI 1.12 to 3.27, p = 0.01 and HR 1.66, 95% CI 1.00 to 2.76, p = 0.05, respectively) than in patients without/lower TIMP3 and ARF methylation in Urine. A significant correlation was also seen between the risk of death and stage 3 tumor (HR 2.73, 95% CI 1.58 to 4.72, p =...
-
quantitative methylation specific polymerase chain reaction gene patterns in Urine Sediment distinguish prostate cancer patients from control subjects
Journal of Clinical Oncology, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Rui Henrique, Eli Rosenbaum, Wim Van Criekinge, William H Westra, David SidranskyAbstract:Purpose Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of prostate cancers and is a promising marker for cancer detection. We sought to develop a test for prostate cancer based on a quantitative methylation-specific polymerase chain reaction (QMSP) of multiple genes in Urine Sediment DNA. Patients and Methods We tested Urine Sediment DNA for aberrant methylation of nine gene promoters (p16INK4a, p14ARF, MGMT, GSTP1, RARβ2, CDH1 [E-cadherin], TIMP3, Rassf1A, and APC) from 52 patients with prostate cancer and 21 matched primary tumors by quantitative fluorogenic real-time polymerase chain reaction. We also analyzed Urine Sediments from 91 age-matched individuals without any history of genitourinary malignancy as controls. Results Promoter hypermethylation of at least one of the genes studied was detected in Urine samples from all 52 prostate cancer patients. Urine samples from the 91 controls without evidence of genitourinary ...
-
methylation pattern of multiple genes in Urine Sediment dna from bladder cancer cases and controls by high throughput quantitative methylation specific pcr qmsp
Cancer Research, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Eli Rosenbaum, Wim Van Criekinge, William H Westra, Aditi Chatterjee, Mark P Schoenberg, David SidranskyAbstract:3150 Background: The early diagnosis of bladder cancer and the early detection of recurrence are central to effective treatment, as prognosis is directly related to the stage of disease. Promoter hypermethylation is now recognized as an important and common epigenetic pathway of gene inactivation. Because bladder cancer cells and DNA are shed into the Urine, we sought to test the value of a quantitative methylation assay in Urine Sediment for the detection of bladder cancer. Methods: We examined primary tumor and matched Urine DNA for aberrant methylation of nine gene promoters ( APC, ARF, CDH1, GSTP1, MGMT, p16, RAR-β2, Rassf1A and TIMP3 ) from 15 patients with bladder cancer by quantitative fluorogenic real-time PCR. We then tested an additional 160 Urine Sediment DNA samples (Total 175 Urine) from bladder cancer patients of different stages and grades. 94 age-matched patients without any evidence of genitourinary cancer were used as a control. Result: In cases with matched tumor, the promoter methylation pattern found in Urine matched the pattern in the primary tumors. 121 of 175(69%) patients with bladder cancer displayed methylation in at least one of four genes ( p16, ARF, MGMT and GSTP1 ), whereas all controls were negative for methylation at the established cut off (100% specificity). When we considered any one of these latter four genes and/or RAR-β2 methylation, the sensitivity and specificity were 82% and 97% respectively (positive likelihood ratio 24.19 and negative likelihood ratio 0.19). Using established cut off values for all the nine genes, 85% sensitivity and 96% specificity was achieved with a positive and negative likelihood ratio of 18.97 and 0.16 respectively. MGMT, ARF , and TIMP3 methylation in Urine correlated with primary tumor invasion and metastasis (p= ≤ 0.05, by logistic regression). The risk of death was statistically significantly higher in patients with TIMP3 methylation (hazard ratio [HR] =1.97, 95% confidence interval [CI] =1.14 to 3.4; p= 0.01) than in patients without TIMP3 methylation in Urine. Conclusion: Testing a small panel of genes with the QMSP (Quantitative Methylation Specific PCR) assay in Urine Sediment DNA represents a powerful noninvasive approach for the detection of bladder cancer on a high throughput-automated platform. Methylation patterns in Urine may also help predict the natural history of detected disease. Larger cohorts with longitudinal follow up will be required in future studies to define the impact of this technology on detection, prognosis and disease monitoring.
Sean D Owens - One of the best experts on this subject based on the ideXlab platform.
-
comparison of idexx sedivue dx Urine Sediment analyzer to manual microscopy for detection of casts in canine Urine
Journal of Veterinary Internal Medicine, 2021Co-Authors: Demitria M Vasilatis, Larry D Cowgill, Giosi Farace, Sarah Peterson, Murthy V S N Yerramilli, Sean D OwensAbstract:Background Detection of urinary casts is difficult due to their intermittent presence and deterioration in Urine samples. Objective To compare the performance of the IDEXX SediVue Dx® Urine Sediment Analyzer (SediVue) with manual microscopy for the detection of urinary casts. We hypothesized that the SediVue analyzer would perform similarly to manual microscopy in cast detection. Animals Four hundred forty-three samples from 420 dogs from a hospital population. Methods This is a prospective, cross-sectional study. For SediVue analysis (software version [SW] 1.0.1.3), uncentrifuged Urine was pipetted into a disposable cartridge. Seventy images were captured and processed by an onboard algorithm. For manual microscopy, Urine was centrifuged to obtain Sediment. Any cast identified by either method was considered a positive result (>0/low-power field [LPF]). SediVue images were evaluated if casts were detected by either methodology. A revised sensitivity and specificity were calculated after image review and when using a threshold of >1 cast/LPF. Results The sensitivity of the SediVue analysis for the detection of urinary casts was 53.7% (43.85%-63.35%), and specificity was 86.0% (81.78%-89.51%). After image review, the revised sensitivity/specificity was 52.0% (42.89%-61.02%) and 90.6% (86.81%-93.54%), respectively. When using a more clinically relevant threshold of >1/LPF, the sensitivity was 52.6% (35.82%-69.02%) and specificity was 99.3% (97.85%-99.85%). Conclusions and clinical importance The SediVue provides moderate agreement to manual methodology for detection of casts in Urine.
-
Comparison of IDEXX SediVue Dx® Urine Sediment analyzer to manual microscopy for detection of casts in canine Urine
'Wiley', 2021Co-Authors: Demitria M Vasilatis, Larry D Cowgill, Giosi Farace, Sarah Peterson, Murthy V S N Yerramilli, Sean D OwensAbstract:Abstract Background Detection of urinary casts is difficult due to their intermittent presence and deterioration in Urine samples. Objective To compare the performance of the IDEXX SediVue Dx® Urine Sediment Analyzer (SediVue) with manual microscopy for the detection of urinary casts. We hypothesized that the SediVue analyzer would perform similarly to manual microscopy in cast detection. Animals Four hundred forty‐three samples from 420 dogs from a hospital population. Methods This is a prospective, cross‐sectional study. For SediVue analysis (software version [SW] 1.0.1.3), uncentrifuged Urine was pipetted into a disposable cartridge. Seventy images were captured and processed by an onboard algorithm. For manual microscopy, Urine was centrifuged to obtain Sediment. Any cast identified by either method was considered a positive result (>0/low‐power field [LPF]). SediVue images were evaluated if casts were detected by either methodology. A revised sensitivity and specificity were calculated after image review and when using a threshold of >1 cast/LPF. Results The sensitivity of the SediVue analysis for the detection of urinary casts was 53.7% (43.85%‐63.35%), and specificity was 86.0% (81.78%‐89.51%). After image review, the revised sensitivity/specificity was 52.0% (42.89%‐61.02%) and 90.6% (86.81%‐93.54%), respectively. When using a more clinically relevant threshold of >1/LPF, the sensitivity was 52.6% (35.82%‐69.02%) and specificity was 99.3% (97.85%‐99.85%). Conclusions and Clinical Importance The SediVue provides moderate agreement to manual methodology for detection of casts in Urine
Eli Rosenbaum - One of the best experts on this subject based on the ideXlab platform.
-
tissue inhibitor of metalloproteinases 3 promoter methylation is an independent prognostic factor for bladder cancer
The Journal of Urology, 2008Co-Authors: Mohammad O Hoque, Shahnaz Begum, Eli Rosenbaum, William H Westra, Mariana Brait, Carmen Jeronimo, Marianna Zahurak, Kimberly Laskie Ostrow, Bruce J Trock, Mark P SchoenbergAbstract:Purpose: TIMP-3 (tissue inhibitor of metalloproteinases-3) is 1 of 4 members of a family of proteins that were originally classified according to their ability to inhibit matrix metalloproteinases. We analyzed TIMP-3 methylation in 175 Urine Sediment DNA samples from patients with bladder cancer with well characterized clinicopathological parameters, including patient outcome.Materials and Methods: We examined Urine Sediment DNA for aberrant methylation of 9 genes, including TIMP-3, by quantitative fluorogenic real-time polymerase chain reaction.Results: Using an optimal cutoff value by TaqMan® quantitation we found that the risk of death was statistically significantly higher in patients with higher TIMP-3 and ARF methylation (HR 1.99, 95% CI 1.12 to 3.27, p = 0.01 and HR 1.66, 95% CI 1.00 to 2.76, p = 0.05, respectively) than in patients without/lower TIMP3 and ARF methylation in Urine. A significant correlation was also seen between the risk of death and stage 3 tumor (HR 2.73, 95% CI 1.58 to 4.72, p =...
-
quantitative methylation specific polymerase chain reaction gene patterns in Urine Sediment distinguish prostate cancer patients from control subjects
Journal of Clinical Oncology, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Rui Henrique, Eli Rosenbaum, Wim Van Criekinge, William H Westra, David SidranskyAbstract:Purpose Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of prostate cancers and is a promising marker for cancer detection. We sought to develop a test for prostate cancer based on a quantitative methylation-specific polymerase chain reaction (QMSP) of multiple genes in Urine Sediment DNA. Patients and Methods We tested Urine Sediment DNA for aberrant methylation of nine gene promoters (p16INK4a, p14ARF, MGMT, GSTP1, RARβ2, CDH1 [E-cadherin], TIMP3, Rassf1A, and APC) from 52 patients with prostate cancer and 21 matched primary tumors by quantitative fluorogenic real-time polymerase chain reaction. We also analyzed Urine Sediments from 91 age-matched individuals without any history of genitourinary malignancy as controls. Results Promoter hypermethylation of at least one of the genes studied was detected in Urine samples from all 52 prostate cancer patients. Urine samples from the 91 controls without evidence of genitourinary ...
-
methylation pattern of multiple genes in Urine Sediment dna from bladder cancer cases and controls by high throughput quantitative methylation specific pcr qmsp
Cancer Research, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Eli Rosenbaum, Wim Van Criekinge, William H Westra, Aditi Chatterjee, Mark P Schoenberg, David SidranskyAbstract:3150 Background: The early diagnosis of bladder cancer and the early detection of recurrence are central to effective treatment, as prognosis is directly related to the stage of disease. Promoter hypermethylation is now recognized as an important and common epigenetic pathway of gene inactivation. Because bladder cancer cells and DNA are shed into the Urine, we sought to test the value of a quantitative methylation assay in Urine Sediment for the detection of bladder cancer. Methods: We examined primary tumor and matched Urine DNA for aberrant methylation of nine gene promoters ( APC, ARF, CDH1, GSTP1, MGMT, p16, RAR-β2, Rassf1A and TIMP3 ) from 15 patients with bladder cancer by quantitative fluorogenic real-time PCR. We then tested an additional 160 Urine Sediment DNA samples (Total 175 Urine) from bladder cancer patients of different stages and grades. 94 age-matched patients without any evidence of genitourinary cancer were used as a control. Result: In cases with matched tumor, the promoter methylation pattern found in Urine matched the pattern in the primary tumors. 121 of 175(69%) patients with bladder cancer displayed methylation in at least one of four genes ( p16, ARF, MGMT and GSTP1 ), whereas all controls were negative for methylation at the established cut off (100% specificity). When we considered any one of these latter four genes and/or RAR-β2 methylation, the sensitivity and specificity were 82% and 97% respectively (positive likelihood ratio 24.19 and negative likelihood ratio 0.19). Using established cut off values for all the nine genes, 85% sensitivity and 96% specificity was achieved with a positive and negative likelihood ratio of 18.97 and 0.16 respectively. MGMT, ARF , and TIMP3 methylation in Urine correlated with primary tumor invasion and metastasis (p= ≤ 0.05, by logistic regression). The risk of death was statistically significantly higher in patients with TIMP3 methylation (hazard ratio [HR] =1.97, 95% confidence interval [CI] =1.14 to 3.4; p= 0.01) than in patients without TIMP3 methylation in Urine. Conclusion: Testing a small panel of genes with the QMSP (Quantitative Methylation Specific PCR) assay in Urine Sediment DNA represents a powerful noninvasive approach for the detection of bladder cancer on a high throughput-automated platform. Methylation patterns in Urine may also help predict the natural history of detected disease. Larger cohorts with longitudinal follow up will be required in future studies to define the impact of this technology on detection, prognosis and disease monitoring.
William H Westra - One of the best experts on this subject based on the ideXlab platform.
-
tissue inhibitor of metalloproteinases 3 promoter methylation is an independent prognostic factor for bladder cancer
The Journal of Urology, 2008Co-Authors: Mohammad O Hoque, Shahnaz Begum, Eli Rosenbaum, William H Westra, Mariana Brait, Carmen Jeronimo, Marianna Zahurak, Kimberly Laskie Ostrow, Bruce J Trock, Mark P SchoenbergAbstract:Purpose: TIMP-3 (tissue inhibitor of metalloproteinases-3) is 1 of 4 members of a family of proteins that were originally classified according to their ability to inhibit matrix metalloproteinases. We analyzed TIMP-3 methylation in 175 Urine Sediment DNA samples from patients with bladder cancer with well characterized clinicopathological parameters, including patient outcome.Materials and Methods: We examined Urine Sediment DNA for aberrant methylation of 9 genes, including TIMP-3, by quantitative fluorogenic real-time polymerase chain reaction.Results: Using an optimal cutoff value by TaqMan® quantitation we found that the risk of death was statistically significantly higher in patients with higher TIMP-3 and ARF methylation (HR 1.99, 95% CI 1.12 to 3.27, p = 0.01 and HR 1.66, 95% CI 1.00 to 2.76, p = 0.05, respectively) than in patients without/lower TIMP3 and ARF methylation in Urine. A significant correlation was also seen between the risk of death and stage 3 tumor (HR 2.73, 95% CI 1.58 to 4.72, p =...
-
quantitative methylation specific polymerase chain reaction gene patterns in Urine Sediment distinguish prostate cancer patients from control subjects
Journal of Clinical Oncology, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Rui Henrique, Eli Rosenbaum, Wim Van Criekinge, William H Westra, David SidranskyAbstract:Purpose Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of prostate cancers and is a promising marker for cancer detection. We sought to develop a test for prostate cancer based on a quantitative methylation-specific polymerase chain reaction (QMSP) of multiple genes in Urine Sediment DNA. Patients and Methods We tested Urine Sediment DNA for aberrant methylation of nine gene promoters (p16INK4a, p14ARF, MGMT, GSTP1, RARβ2, CDH1 [E-cadherin], TIMP3, Rassf1A, and APC) from 52 patients with prostate cancer and 21 matched primary tumors by quantitative fluorogenic real-time polymerase chain reaction. We also analyzed Urine Sediments from 91 age-matched individuals without any history of genitourinary malignancy as controls. Results Promoter hypermethylation of at least one of the genes studied was detected in Urine samples from all 52 prostate cancer patients. Urine samples from the 91 controls without evidence of genitourinary ...
-
methylation pattern of multiple genes in Urine Sediment dna from bladder cancer cases and controls by high throughput quantitative methylation specific pcr qmsp
Cancer Research, 2005Co-Authors: Mohammad O Hoque, Ozlem Topaloglu, Shahnaz Begum, Eli Rosenbaum, Wim Van Criekinge, William H Westra, Aditi Chatterjee, Mark P Schoenberg, David SidranskyAbstract:3150 Background: The early diagnosis of bladder cancer and the early detection of recurrence are central to effective treatment, as prognosis is directly related to the stage of disease. Promoter hypermethylation is now recognized as an important and common epigenetic pathway of gene inactivation. Because bladder cancer cells and DNA are shed into the Urine, we sought to test the value of a quantitative methylation assay in Urine Sediment for the detection of bladder cancer. Methods: We examined primary tumor and matched Urine DNA for aberrant methylation of nine gene promoters ( APC, ARF, CDH1, GSTP1, MGMT, p16, RAR-β2, Rassf1A and TIMP3 ) from 15 patients with bladder cancer by quantitative fluorogenic real-time PCR. We then tested an additional 160 Urine Sediment DNA samples (Total 175 Urine) from bladder cancer patients of different stages and grades. 94 age-matched patients without any evidence of genitourinary cancer were used as a control. Result: In cases with matched tumor, the promoter methylation pattern found in Urine matched the pattern in the primary tumors. 121 of 175(69%) patients with bladder cancer displayed methylation in at least one of four genes ( p16, ARF, MGMT and GSTP1 ), whereas all controls were negative for methylation at the established cut off (100% specificity). When we considered any one of these latter four genes and/or RAR-β2 methylation, the sensitivity and specificity were 82% and 97% respectively (positive likelihood ratio 24.19 and negative likelihood ratio 0.19). Using established cut off values for all the nine genes, 85% sensitivity and 96% specificity was achieved with a positive and negative likelihood ratio of 18.97 and 0.16 respectively. MGMT, ARF , and TIMP3 methylation in Urine correlated with primary tumor invasion and metastasis (p= ≤ 0.05, by logistic regression). The risk of death was statistically significantly higher in patients with TIMP3 methylation (hazard ratio [HR] =1.97, 95% confidence interval [CI] =1.14 to 3.4; p= 0.01) than in patients without TIMP3 methylation in Urine. Conclusion: Testing a small panel of genes with the QMSP (Quantitative Methylation Specific PCR) assay in Urine Sediment DNA represents a powerful noninvasive approach for the detection of bladder cancer on a high throughput-automated platform. Methylation patterns in Urine may also help predict the natural history of detected disease. Larger cohorts with longitudinal follow up will be required in future studies to define the impact of this technology on detection, prognosis and disease monitoring.
