Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA
<p>Abstract</p> <p>Background</p> <p>Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Pr...
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| Format: | Article |
| Language: | English |
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BMC
2006-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/7/163 |
| _version_ | 1819033582223491072 |
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| author | Chan Alan Wu Ying Datta Parikkhit Gibbons Brian AL Armour John |
| author_facet | Chan Alan Wu Ying Datta Parikkhit Gibbons Brian AL Armour John |
| author_sort | Chan Alan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length.</p> <p>Results</p> <p>In this study we showed that microarray MAPH measurement of <it>PMP22 </it>gene dosage correlates well with <it>PMP22 </it>gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A).</p> <p>Conclusion</p> <p>Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.</p> |
| first_indexed | 2024-12-21T07:20:08Z |
| format | Article |
| id | doaj.art-938606ad44dc4f0ca8f600823e496494 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T07:20:08Z |
| publishDate | 2006-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-938606ad44dc4f0ca8f600823e4964942022-12-21T19:11:48ZengBMCBMC Genomics1471-21642006-06-017116310.1186/1471-2164-7-163Microarray MAPH: accurate array-based detection of relative copy number in genomic DNAChan AlanWu YingDatta ParikkhitGibbons BrianAL Armour John<p>Abstract</p> <p>Background</p> <p>Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length.</p> <p>Results</p> <p>In this study we showed that microarray MAPH measurement of <it>PMP22 </it>gene dosage correlates well with <it>PMP22 </it>gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A).</p> <p>Conclusion</p> <p>Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.</p>http://www.biomedcentral.com/1471-2164/7/163 |
| spellingShingle | Chan Alan Wu Ying Datta Parikkhit Gibbons Brian AL Armour John Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA BMC Genomics |
| title | Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA |
| title_full | Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA |
| title_fullStr | Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA |
| title_full_unstemmed | Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA |
| title_short | Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA |
| title_sort | microarray maph accurate array based detection of relative copy number in genomic dna |
| url | http://www.biomedcentral.com/1471-2164/7/163 |
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