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A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction
BACKGROUND: Changes in genomic copy number occur in many human diseases including cancer. Characterization of these changes is important for both basic understanding and diagnosis of these diseases. Microarrays have recently become the standard technique and are commercially available. However, it i...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920520/ https://www.ncbi.nlm.nih.gov/pubmed/17601344 http://dx.doi.org/10.1186/1471-2164-8-206 |
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author | Iwao-Koizumi, Kyoko Maekawa, Kazunori Nakamura, Yohko Saito, Sakae Kawamoto, Shoko Nakagawara, Akira Kato, Kikuya |
author_facet | Iwao-Koizumi, Kyoko Maekawa, Kazunori Nakamura, Yohko Saito, Sakae Kawamoto, Shoko Nakagawara, Akira Kato, Kikuya |
author_sort | Iwao-Koizumi, Kyoko |
collection | PubMed |
description | BACKGROUND: Changes in genomic copy number occur in many human diseases including cancer. Characterization of these changes is important for both basic understanding and diagnosis of these diseases. Microarrays have recently become the standard technique and are commercially available. However, it is useful to have an affordable technique to complement them. RESULTS: We describe a novel polymerase chain reaction (PCR)-based technique, termed competitive genomic PCR (CGP). The main characteristic of CGP is that different adaptors are added to the sample and control genomic DNAs after appropriate restriction enzyme digestion. These adaptor-supplemented DNAs are subjected to competitive PCR using an adaptor-primer and a locus-specific primer. The amplified products are then separated according to size differences between the adaptors. CGP eliminates the tedious steps inherent in quantitative PCR and achieves moderate throughput. Assays with different X chromosome numbers showed that it can provide accurate quantification. High-resolution analysis of neuroblastoma cell lines around the MYCN locus revealed novel junctions for amplification, which were not detected by a commercial array. CONCLUSION: CGP is a moderate throughput technique for analyzing changes in genomic copy numbers. Because CGP can measure any genomic locus using PCR primers, it is especially useful for detailed analysis of a genomic region of interest. |
format | Text |
id | pubmed-1920520 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-19205202007-07-17 A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction Iwao-Koizumi, Kyoko Maekawa, Kazunori Nakamura, Yohko Saito, Sakae Kawamoto, Shoko Nakagawara, Akira Kato, Kikuya BMC Genomics Methodology Article BACKGROUND: Changes in genomic copy number occur in many human diseases including cancer. Characterization of these changes is important for both basic understanding and diagnosis of these diseases. Microarrays have recently become the standard technique and are commercially available. However, it is useful to have an affordable technique to complement them. RESULTS: We describe a novel polymerase chain reaction (PCR)-based technique, termed competitive genomic PCR (CGP). The main characteristic of CGP is that different adaptors are added to the sample and control genomic DNAs after appropriate restriction enzyme digestion. These adaptor-supplemented DNAs are subjected to competitive PCR using an adaptor-primer and a locus-specific primer. The amplified products are then separated according to size differences between the adaptors. CGP eliminates the tedious steps inherent in quantitative PCR and achieves moderate throughput. Assays with different X chromosome numbers showed that it can provide accurate quantification. High-resolution analysis of neuroblastoma cell lines around the MYCN locus revealed novel junctions for amplification, which were not detected by a commercial array. CONCLUSION: CGP is a moderate throughput technique for analyzing changes in genomic copy numbers. Because CGP can measure any genomic locus using PCR primers, it is especially useful for detailed analysis of a genomic region of interest. BioMed Central 2007-07-02 /pmc/articles/PMC1920520/ /pubmed/17601344 http://dx.doi.org/10.1186/1471-2164-8-206 Text en Copyright © 2007 Iwao-Koizumi et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Iwao-Koizumi, Kyoko Maekawa, Kazunori Nakamura, Yohko Saito, Sakae Kawamoto, Shoko Nakagawara, Akira Kato, Kikuya A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction |
title | A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction |
title_full | A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction |
title_fullStr | A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction |
title_full_unstemmed | A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction |
title_short | A novel technique for measuring variations in DNA copy-number: competitive genomic polymerase chain reaction |
title_sort | novel technique for measuring variations in dna copy-number: competitive genomic polymerase chain reaction |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920520/ https://www.ncbi.nlm.nih.gov/pubmed/17601344 http://dx.doi.org/10.1186/1471-2164-8-206 |
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