Rapid analysis of XRCC1 polymorphisms using real-time polymerase chain reaction.

2.50
Hdl Handle:
http://hdl.handle.net/10146/55133
Title:
Rapid analysis of XRCC1 polymorphisms using real-time polymerase chain reaction.
Authors:
Schneider, Joachim; Classen, Vera; Philipp, Monika; Helmig, Simone
Abstract:
DNA repair plays a critical role in protecting the genome from carcinogens or ionizing radiation. Three coding polymorphisms at codons 194, 280, and 399 in X-ray cross-complementing group 1 (XRCC1) DNA repair gene have been identified that may affect DNA repair and alter cancer susceptibility. In order to study their role in molecular-epidemiology studies we developed a single-step procedure for genotyping these polymorphisms using real-time polymerase chain reaction (rt-PCR) and subsequent melting curve analysis. Genotypes of 622 unrelated Caucasians without prior history of cancer were determined by real-time PCR and compared to genotypes obtained by restriction fragment length polymorphism PCR. In the population studied, the allele frequency of the XRCC1 26304 site (C-->T) of codon 194 in exon 6 was 0.065, the allele frequency of the XRCC1 27466 site (G-->A) of codon 280 in exon 9 was 0.048 and of the XRCC1 28152 site (G-->A) of codon 399 in exon 10 was 0.35. There was no disagreement between the two methods. These findings confirm the real-time fluorescence PCR method as a rapid and reliable assay for the analysis of large numbers of samples.
Citation:
Mol. Cell. Probes 20 (3-4):259-262
Journal:
Molecular and cellular probes
Issue Date:
13-Mar-2009
URI:
http://hdl.handle.net/10146/55133
DOI:
10.1016/j.mcp.2006.01.004
PubMed ID:
16542819
Additional Links:
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNC-4JHMRY2-2&_user=1843694&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000055040&_version=1&_urlVersion=0&_userid=1843694&md5=328c2a2a364e7240a11bf00a5a44abab
Type:
Article
Language:
en
Description:
biomarkers of individual susceptibility: method development & validationBiomarker (including alleles if genetic):coding polymorphisms at codons 194, 280, and 399 in X-ray cross-complementing group 1 (XRCC1) DNA repair geneEffect studied (phenotype/pathology):lung cancer riskTissue/biological material/sample size:Peripheral blood samples from 622 unrelated Caucasians (600 male, 22 female)Method of analysis: real-time polymerase chain reaction (rt-PCR)Specificity:compared with RFLP method there was no disagreement between the two methodsAccuracy:compared with RFLP method there was no disagreement between the two methodsInterlaboratory repeatability:The frequency of mutant XRCC1 alleles were similar to those reported previouslyHigh-throughput automation:Thirty-two samples can be analysed within w60 minBiomarkers of individual susceptibility: field studiesBiomarker (including alleles if genetic): coding polymorphisms at codons 194, 280, and 399 in X-ray cross-complementing group 1 (XRCC1) DNA repair geneEffect studied (phenotype/pathology):lung cancer riskTissue/biological material/sample size:Peripheral blood samples from 622 unrelated Caucasians (600 male, 22 female)Method of analysis: real-time polymerase chain reaction (rt-PCR)Study design: cross-sectionalStudy size: 622 unrelated Caucasians (600 male, 22 female)Surrogate/target tissue relationship:no differenceQuality control:restriction fragment length polymorphism PCR. KEYWORDS CLASSIFICATION: analysis;Adult;Aged;Aged,80 and over;blood;biomarkers of individual susceptibility: field studies;biomarkers of individual susceptibility: method development & validation;DNA-Binding Proteins;Female;genetics;Gene Frequency;Genotype;Germany;history;Humans;methods;Male;Middle Aged;Polymerase Chain Reaction;Polymorphism,Genetic;Proteins;method development & validation;validation;genetic;field studies.
ISSN:
0890-8508
Appears in Collections:
Articles with annotation

Full metadata record

DC FieldValue Language
dc.contributor.authorSchneider, Joachim-
dc.contributor.authorClassen, Vera-
dc.contributor.authorPhilipp, Monika-
dc.contributor.authorHelmig, Simone-
dc.date.accessioned2009-03-13T08:01:40Z-
dc.date.available2009-03-13T08:01:40Z-
dc.date.issued2009-03-13T08:01:40Z-
dc.identifier.citationMol. Cell. Probes 20 (3-4):259-262en
dc.identifier.issn0890-8508-
dc.identifier.pmid16542819-
dc.identifier.doi10.1016/j.mcp.2006.01.004-
dc.identifier.urihttp://hdl.handle.net/10146/55133-
dc.descriptionbiomarkers of individual susceptibility: method development & validationBiomarker (including alleles if genetic):coding polymorphisms at codons 194, 280, and 399 in X-ray cross-complementing group 1 (XRCC1) DNA repair geneEffect studied (phenotype/pathology):lung cancer riskTissue/biological material/sample size:Peripheral blood samples from 622 unrelated Caucasians (600 male, 22 female)Method of analysis: real-time polymerase chain reaction (rt-PCR)Specificity:compared with RFLP method there was no disagreement between the two methodsAccuracy:compared with RFLP method there was no disagreement between the two methodsInterlaboratory repeatability:The frequency of mutant XRCC1 alleles were similar to those reported previouslyHigh-throughput automation:Thirty-two samples can be analysed within w60 minBiomarkers of individual susceptibility: field studiesBiomarker (including alleles if genetic): coding polymorphisms at codons 194, 280, and 399 in X-ray cross-complementing group 1 (XRCC1) DNA repair geneEffect studied (phenotype/pathology):lung cancer riskTissue/biological material/sample size:Peripheral blood samples from 622 unrelated Caucasians (600 male, 22 female)Method of analysis: real-time polymerase chain reaction (rt-PCR)Study design: cross-sectionalStudy size: 622 unrelated Caucasians (600 male, 22 female)Surrogate/target tissue relationship:no differenceQuality control:restriction fragment length polymorphism PCR. KEYWORDS CLASSIFICATION: analysis;Adult;Aged;Aged,80 and over;blood;biomarkers of individual susceptibility: field studies;biomarkers of individual susceptibility: method development & validation;DNA-Binding Proteins;Female;genetics;Gene Frequency;Genotype;Germany;history;Humans;methods;Male;Middle Aged;Polymerase Chain Reaction;Polymorphism,Genetic;Proteins;method development & validation;validation;genetic;field studies.en
dc.description.abstractDNA repair plays a critical role in protecting the genome from carcinogens or ionizing radiation. Three coding polymorphisms at codons 194, 280, and 399 in X-ray cross-complementing group 1 (XRCC1) DNA repair gene have been identified that may affect DNA repair and alter cancer susceptibility. In order to study their role in molecular-epidemiology studies we developed a single-step procedure for genotyping these polymorphisms using real-time polymerase chain reaction (rt-PCR) and subsequent melting curve analysis. Genotypes of 622 unrelated Caucasians without prior history of cancer were determined by real-time PCR and compared to genotypes obtained by restriction fragment length polymorphism PCR. In the population studied, the allele frequency of the XRCC1 26304 site (C-->T) of codon 194 in exon 6 was 0.065, the allele frequency of the XRCC1 27466 site (G-->A) of codon 280 in exon 9 was 0.048 and of the XRCC1 28152 site (G-->A) of codon 399 in exon 10 was 0.35. There was no disagreement between the two methods. These findings confirm the real-time fluorescence PCR method as a rapid and reliable assay for the analysis of large numbers of samples.en
dc.language.isoenen
dc.relation.urlhttp://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNC-4JHMRY2-2&_user=1843694&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000055040&_version=1&_urlVersion=0&_userid=1843694&md5=328c2a2a364e7240a11bf00a5a44ababen
dc.subjectXRCC1 polymorphismsen
dc.subjectReal-time PCRen
dc.subject.meshAdult-
dc.subject.meshAged-
dc.subject.meshAged, 80 and over-
dc.subject.meshDNA-Binding Proteins-
dc.subject.meshFemale-
dc.subject.meshGene Frequency-
dc.subject.meshGenotype-
dc.subject.meshHumans-
dc.subject.meshMale-
dc.subject.meshMiddle Aged-
dc.subject.meshPolymerase Chain Reaction-
dc.subject.meshPolymorphism, Genetic-
dc.titleRapid analysis of XRCC1 polymorphisms using real-time polymerase chain reaction.en
dc.typeArticleen
dc.identifier.journalMolecular and cellular probesen

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