scholarly journals Estimation of total bacteria by real-time PCR in patients with periodontal disease

2016 ◽  
Vol 144 (1-2) ◽  
pp. 10-14 ◽  
Author(s):  
Gavrilo Brajovic ◽  
Branka Popovic ◽  
Miljan Puletic ◽  
Marija Kostic ◽  
Jelena Milasin
Keyword(s):  
Periodontal Disease ◽  
Real Time ◽  
Copy Number ◽  
Quantitative Estimation ◽  
Periodontal Diseases ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Additional Tool ◽  
Significant Difference ◽  
Total Bacteria

Introduction. Periodontal diseases are associated with the presence of elevated levels of bacteria within the gingival crevice. Objective. The aim of this study was to evaluate a total amount of bacteria in subgingival plaque samples in patients with a periodontal disease. Methods. A quantitative evaluation of total bacteria amount using quantitative real-time polymerase chain reaction (qRT-PCR) was performed on 20 samples of patients with ulceronecrotic periodontitis and on 10 samples of healthy subjects. The estimation of total bacterial amount was based on gene copy number for 16S rRNA that was determined by comparing to Ct values / gene copy number of the standard curve. Results. A statistically significant difference between average gene copy number of total bacteria in periodontal patients (2.55.107) and healthy control (2.37.106) was found (p=0.01). Also, a trend of higher numbers of the gene copy in deeper periodontal lesions (>7 mm) was confirmed by a positive value of coefficient of correlation (r=0.073). Conclusion. The quantitative estimation of total bacteria based on gene copy number could be an important additional tool in diagnosing periodontitis.

TaqMan real-time PCR quantification strategy of CYP2D6 gene copy number for the LightCycler 2.0

2009 ◽  
Vol 403 (1-2) ◽  
pp. 207-211 ◽  
Author(s):  
Duc L. Nguyen ◽  
Julia Staeker ◽  
Barbara Laika ◽  
Werner Steimer
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Cyp2d6 Gene

scholarly journals 27P Quantitative Analysis by Real-Time Pcr for ESR1 Gene Copy Number in Serum in Breast Cancer Samples

2012 ◽  
Vol 23 ◽  
pp. ii22
Author(s):  
J. Martinez-Galan ◽  
B. Torres-Torres ◽  
J.R. Delgado ◽  
M.I. Núñez ◽  
S. Ríos
Keyword(s):  
Breast Cancer ◽  
Quantitative Analysis ◽  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Esr1 Gene

A Simple Multiplex Real-Time PCR Methodology for the SMN1 Gene Copy Number Quantification

2009 ◽  
Vol 13 (1) ◽  
pp. 37-42 ◽  
Author(s):  
Nadia Passon ◽  
Federico Pozzo ◽  
Cristiano Molinis ◽  
Elisa Bregant ◽  
Cinzia Gellera ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Smn1 Gene

Insulin-like growth factor 1 (IGF-1R) protein expression (PE) and gene copy number (GCN) for discrimination of response and outcome to figitumumab in NSCLC.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 7597-7597 ◽  
Author(s):  
Murry W. Wynes ◽  
Simon Ekman ◽  
Bernadette Reyna Asuncion ◽  
Rafal Dziadziuszko ◽  
Bonnie S. Glisson ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Phase Iii ◽  
Gene Copy ◽  
Clinical Activity ◽  
Two Phase ◽  
Significant Difference ◽  
Score Method ◽  
Average Copy ◽  
Tumor Types

7597 Background: Early clinical data suggested figitumumab (F), an anti-IGF-1R antibody, had clinical activity in several tumor types. However, two phase III studies, A4021016 carboplatin/paclitaxel (CP) +/- F in 1st line treatment or A4021018 erlotinib (E) +/- F in 2nd line therapy for patients with advanced NSCLC, were closed prematurely due to futility. Neither study used biomarker driven selection criteria. The aim of this study was to retrospectively examine the phase III specimens in order to determine if IGF-1R PE or GCN could discriminate response and/or outcome to F. Methods: IGF-1R PE was determined by immunohistochemistry (IHC) and the tumor specimens were scored using the H-score method (0-300) with separate enumeration of membranous and cytoplasmic components and then combination of these scores. GCN was evaluated by bright field silver in situ hybridization (SISH) with recording the average copy number for 50 tumor cells. Results: IHC was evaluable in 25 CP+F, 20 CP, 27 E+F and 26 E specimens whereas SISH was evaluable in 24, 17, 21 and 22 specimens, respectively. Median PE for membrane, cytoplasm and both in A4021016 were 130, 110 and 120 and in A4021018 they were 135, 140 and 140. Median GCN was 1.88 and 1.98 for A4021016 and A4021018, respectively. There were no significant differences in PE or GCN between treatment arms within each study. Neither PE nor GCN were able to discriminate between response/non-response or disease control/progression in either study. Likewise, neither study showed a significant difference in OS or PFS when using the median cut-points for either PE or GCN. Conclusions: Neither IGF1R PE or GCN were able to discriminate response or outcome in the limited quantity of specimens available from two studies that examined the IGF-1R targeted therapy figitumumab.

TOP1 gene copy number in stage III colorectal cancer (CRC) samples: Association to prognosis.

2012 ◽  
Vol 30 (4_suppl) ◽  
pp. 475-475
Author(s):  
Sune Boris Nygaard ◽  
Maria Unni Rømer ◽  
Ib Jarle Christensen ◽  
Signe Lykke Nielsen ◽  
David Hersi Smith ◽  
...  
Keyword(s):  
Predictive Value ◽  
Copy Number ◽  
Gene Copy Number ◽  
Tumor Location ◽  
Response To Therapy ◽  
Stage Iii ◽  
Gene Copy ◽  
Continuous Variables ◽  
Future Studies ◽  
Significant Difference

475 Background: TOP1 inhibitor treatment is frequently being used in combination therapy of metastatic CRC. This study aims to reveal whether TOP1 gene copy number associates with patient prognosis, since such a relationship may have significant implications for future studies aiming at validating the predictive value of TOP1 gene copy number. Methods: The study included TOP1 and CEN-20 FISH analyses (DAKO A/S Denmark) on FFPE tissue sections from 154 stage III CRC patients who did not receive adjuvant chemotherapy. TOP1 gene copy number, CEN-20 copy number and the TOP1/CEN-20 ratios were analyzed and correlated to overall survival (OS), to time to recurrence (TTR) of patients with CRC and to local recurrence (LR) in patients with rectal cancer (RC). Results: TOP1 copy number counts and the TOP1/CEN-20 ratios, age, gender and primary tumor location were separately added into a multivariate analysis as continuous variables. For OS and LR, TOP1 copy number was significant and the ratio was borderline significant with higher copy number associated with longer OS or longer time to LR. When the patients were dichotomized using the TOP1 median copy number, we found that patients with high TOP1 copy number in their tumor cells had a significant longer OS (HR: 0.68; 95% CI: 0.47-0.98; p = 0.04) compared to patients with low TOP1 copy number. Using the median TOP1/CEN-20 ratio to dichotomize, no significant differences were observed between patients with levels above or below the median ratio number for OS (HR: 0.76; 95% CI: 0.53-1.10; p = 0.14). TOP1 copy number divided the RC patients into two groups with a trend towards a significant difference in time to LR (HR: 0.56; 95% CI: 0.27-1.16; p = 0.11) with higher copy number. If the median ratio was used, a significant association with longer time to LR (HR: 0.43; 95% CI: 0.20-0.92; p = 0.03) was found. No significant associations between TOP1 copy number or ratio and TTR were observed. Conclusions: Increased TOP1 copy number is associated with longer OS in CRC patients and fewer LR in RC patients. Thus, future studies analyzing the association between TOP1 copy number and response to therapy in CRC patients should be planned in such a way that a prognostic and a predictive value of TOP1 can be separated.

Robust quantification of the SMN gene copy number by real-time TaqMan PCR

Neurogenetics ◽  
2007 ◽  
Vol 8 (4) ◽  
pp. 271-278 ◽  
Author(s):  
Ilsa Gómez-Curet ◽  
Karyn G. Robinson ◽  
Vicky L. Funanage ◽  
Thomas O. Crawford ◽  
Mena Scavina ◽  
...  
Keyword(s):  
Real Time ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Smn Gene ◽  
Taqman Pcr

scholarly journals Real-time PCR for the detection of precise transgene copy number in durum wheat

2011 ◽  
Vol 16 (4) ◽  
Author(s):  
Agata Gadaleta ◽  
Angelica Giancaspro ◽  
Maria Cardone ◽  
Antonio Blanco
Keyword(s):  
Durum Wheat ◽  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Gene Copy Number ◽  
Correlation Coefficients ◽  
Gene Copy ◽  
Transgene Copy Number ◽  
Locus Number ◽  
Wheat Lines

AbstractRecent results obtained in various crops indicate that real-time PCR could be a powerful tool for the detection and characterization of transgene locus structures. The determination of transgenic locus number through real-time PCR overcomes the problems linked to phenotypic segregation analysis (i.e. lack of detectable expression even when the transgenes are present) and can analyse hundreds of samples in a day, making it an efficient method for estimating gene copy number. Despite these advantages, many authors speak of “estimating” copy number by real-time PCR, and this is because the detection of a precise number of transgene depends on how well real-time PCR performs.This study was conducted to determine transgene copy number in transgenic wheat lines and to investigate potential variability in sensitivity and resolution of real-time chemistry by TaqMan probes. We have applied real-time PCR to a set of four transgenic durum wheat lines previously obtained. A total of 24 experiments (three experiments for two genes in each transgenic line) were conducted and standard curves were obtained from serial dilutions of the plasmids containing the genes of interest. The correlation coefficients ranged from 0.95 to 0.97. By using TaqMan quantitative real-time PCR we were able to detect 1 to 41 copies of transgenes per haploid genome in the DNA of homozygous T4 transformants. Although a slight variability was observed among PCR experiments, in our study we found real-time PCR to be a fast, sensitive and reliable method for the detection of transgene copy number in durum wheat, and a useful adjunct to Southern blot and FISH analyses to detect the presence of transgenic DNA in plant material.

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