Screening for TP53 mutations in osteosarcomas using constant denaturant gel electrophoresis (CDGE)

Smith‐Sørensen, Birgitte; Gebhardt, Mark C.; Kloen, Peter; McIntyre, Jim; Aguilar, Fernando; Cerutti, Peter; Børresen, Anne Lise

doi:10.1002/humu.1380020407

Cited by 37 publications

(11 citation statements)

References 43 publications

(50 reference statements)

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“…These similarities in taxonomic affinity, but differences in gel position, indicate that DGGE was able to detect genetic differences that may relate to species-or strain-level variation that would normally be impossible to identify using traditional methods. It is possible that in our evaluation of the DGGE sequences we have missed some of the sequence information that could account for the difference in gel position, because the length of sequence that we were able to recover from the bands varied (from 105 to 237 bases out of approximately 250 total bases) and even a single base difference can result in the distinct separation of two bands by DGGE (30).…”

Section: Dgge Analysismentioning

confidence: 99%

Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis

Gast

Dennett

Caron

2004

Appl Environ Microbiol

136

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The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a cultureindependent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different microhabitats (seawater, meltwater or slush on sea-ice floes, and ice) of the Ross Sea, Antarctica. Samples of the same type (e.g., water) shared more of the same bands than samples of different types (e.g., ice versus water), despite being collected from different sites. These findings imply that samples from the same environment have a similar protistan species composition and that the type of microenvironment significantly influences the protistan species composition of these Antarctic assemblages. It should be noted that a large number of bands among the samples within each microhabitat were distinct, indicating the potential presence of significant genetic diversity within each microenvironment. Sequence analysis of selected DGGE bands revealed sequences that represent diatoms, dinoflagellates, ciliates, flagellates, and several unidentified eukaryotes.Phototrophic and heterotrophic protists are ubiquitous in extreme cold-water environments, where they are central to the production and utilization of energy and the cycling of elements. Understanding the structure and diversity of these communities is of fundamental importance to biological oceanography and to understanding the activities and evolution of life on our planet. Traditional microscopic approaches for documenting the diversity and population structure of protistan assemblages in the coastal regions around Antarctica have contributed greatly to our current understanding of species biogeography, microbial food web structure, and biogeochemical processes in these waters (see reviews in references 6 and 9). This work has been most instructive for species generally greater than 20 m in size and possessing unambiguous morphological features, such as frustules, loricae, or skeletons (e.g., diatoms, tintinnid ciliates, and choanoflagellates). Although valuable, these approaches have been unable to characterize the diversity of a significant number of species that are morphologically less distinctive, nor to determine whether genetically related organisms are present over large spatial and temporal scales. This inability is due in part to the tremendous size range and morphological diversity among protists that necessitate the use of a variety of disparate approaches to identify and count them in natural communities (4,10)

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Section: Dgge Analysismentioning

confidence: 99%

Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis

Gast

Dennett

Caron

2004

Appl Environ Microbiol

136

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“…Not surprisingly, it was reported that p53 is deleted or mutated in the majority of cancers. Experiments involving p53 knockout mice have shown that the occurrence of tumors increases with the loss of p53 function [26,27]. In some cases inactivation of p53 involves small changes such as point mutations [28][29][30].…”

Section: Exploitation Of Protein Profiling In Leukemia Researchmentioning

confidence: 99%

The importance of protein profiling in the diagnosis and treatment of hematologic malignancies

Şanlı-Mohamed¹,

Turan²,

Ekiz³

et al. 2011

Turk J Hematol

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Proteins are important targets in cancer research because malignancy is associated with defects in cell protein machinery. Protein profiling is an emerging independent subspecialty of proteomics that is rapidly expanding and providing unprecedented insight into biological events. Quantitative assessment of protein levels in hematologic malignancies seeks a comprehensive understanding of leukemiaassociated protein patterns for use in aiding diagnosis, follow-up treatment, and the prediction of clinical outcomes. Many recently developed high-throughput proteomic methods can be applied to protein profiling. Herein the importance of protein profiling, its exploitation in leukemia research, and its clinical usefulness in the treatment and diagnosis of various cancer types, and techniques for determining changes in protein profiling are reviewed. (Turk J Hematol 2011; 28: 1-14) Key words: Hematologic malignancies, leukemia, proteomics, protein profiling Received: November 24, 2010 Accepted: January 19, 2011 ÖzetMalignitelerde proteinlerin hücresel mekanizmalarında meydana gelen bozukluklardan dolayı, proteinler kanser araştırmaları için önemli hedeflerdir. Proteomiksin alt uzmanlık dalı olarak ortaya çıkan ve bağımsız bir alan olan protein profilleme biyolojik olaylara farklı bir bakış açısı sağlamak amacıyla hızla gelişmektedir. Hematolojik malignitelerdeki protein düzeylerinin kantitatif olarak değerlendiril-mesi, teşhise yardımcı olması, tedavinin izlenmesi ve klinik sonuçların tahmininde mükemmel bir yaklaşım olması nedeni ile lösemi ile ilgili protein modellerinin kapsamlı bir şekilde incelenmesini amaçlamaktadır. Son dönemlerde geliştirilen yüksek verimli yöntemler protein profillemede kullanıla-bilir. Bu makalede, protein profillemenin önemi, lösemi araştırmalarındaki rolü, çeşitli kanser tiplerinin tanısı ve tedavisi için klinik kullanımları ve protein profilindeki değişikliklerin belirlenmesinde kullanılan teknikler değerlendirilmiştir.

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“…All the conditions and PCR primers (shown in Figure 1) for CDGE have been described previously (B0rresen et al, 1991;Smith-S0rensen et al, 1993;Andersen et al, 1995). A specific analysis was made to identify a frequently described G to C mutation in codon 156.…”

Section: Loss Of Heterozygosity (Loh)mentioning

confidence: 99%

Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families

Zelada-Hedman

Børresen‐Dale²,

Claro³

et al. 1997

Br J Cancer

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Summary To estimate the prevalence of TP53 mutations in familial breast cancer, constant denaturant gel electrophoresis (CDGE) was used to screen exons 5-8 of the TP53 gene for germline mutations. Genomic DNA from 128 breast cancer patients belonging to 109 families with familial cancer were screened. No germline mutations were found in any of the patients. We also studied TP53 mutations in tumour DNA from 51 of the same individuals and found mutations in 14%. This is similar to what has been reported in sporadic breast cancer.Keywords: TP53; p53; mutation analysis; constant denaturant gel electrophoresis; familial breast cancer The p53 protein is a transcription factor and is frequently altered by mutation in most types of cancer. The majority of the mutations are missense mutations (Hollstein et al, 1994).Germline mutations in the TP53 gene were found to segregate in families with the Li-Fraumeni syndrome resulting in a very high risk for early onset breast cancer, sarcoma, leukaemia, brain tumours and other tumours (Malkin, 1994; Wang et al, 1995). It has also been shown that not all families with the classical criteria for Li-Fraumeni segregate a mutation in p53, while some other families with non-classical Li-Fraumeni syndrome do (Birch et al, 1994). Germline mutations have also been found in families with breast and ovarian cancer (Prosser et al, 1992;Jolly et al, 1994). However, germline mutations have not been found to segregate frequently in breast cancer families or patients with early onset or bilateral disease (Prosser et al, 1991;Sidransky et al, 1992;B0rresen et al, 1992;Lidereau and Soussi, 1992).One study, which compared the frequency of somatic TP53 mutations in sporadic breast carcinomas with tumours from patients with a family history, showed that, while sporadic TP53 mutations occurred in 13% of the sporadic tumours, the frequency in the familial cases was 58% (Glebov et al, 1994).We have used constant denaturant gel electrophoresis (CDGE) to screen for germline mutations in exons 5-8 of the TP53 gene in members from 109 breast cancer families. This study also involved searching for mutations in 51 of the tumours from our patients with familial breast cancer. MATERIALS AND METHODS PatientsA total of 128 patients from 109 families with familial cancer, predominantly breast cancer, were identified. The families were selected as described (Lindblom et al, 1992a Correspondence to: A Lindblom number of breast cancer and other cancer diagnoses, the families were categorized as follows: 45 families were defined as breast cancer families and 25 families were defined as cancer families using the following criteria. Breast cancer family -at least three first-or second-degree relatives with breast cancer. Cancer family -the index patient with breast cancer plus at least three first-or second-degree relatives with cancer. The remaining 39 families had a family history of two first-degree relatives with breast cancer. Tumour tissue was available from 51 of these patients.

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Screening for TP53 mutations in osteosarcomas using constant denaturant gel electrophoresis (CDGE)

Cited by 37 publications

References 43 publications

Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis

Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis

The importance of protein profiling in the diagnosis and treatment of hematologic malignancies

Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families

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