Microarray-based ultra-high resolution discovery of genomic deletion mutations.
BACKGROUND: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microa...
| Main Authors: | , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
BioMed Central
2014
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| Subjects: |
| _version_ | 1826270064486121472 |
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| author | Belfield, E Brown, C Gan, X Jiang, C Baban, D Mithani, A Mott, R Ragoussis, J Harberd, N |
| author_facet | Belfield, E Brown, C Gan, X Jiang, C Baban, D Mithani, A Mott, R Ragoussis, J Harberd, N |
| author_sort | Belfield, E |
| collection | OXFORD |
| description | BACKGROUND: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS: Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS: Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence. |
| first_indexed | 2024-03-06T21:35:00Z |
| format | Journal article |
| id | oxford-uuid:45f00528-43b3-45d8-95ce-fdedd1a4017b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T21:35:00Z |
| publishDate | 2014 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:45f00528-43b3-45d8-95ce-fdedd1a4017b2022-03-26T15:10:47ZMicroarray-based ultra-high resolution discovery of genomic deletion mutations.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:45f00528-43b3-45d8-95ce-fdedd1a4017bGenetics (life sciences)Plant SciencesEnglishSymplectic Elements at OxfordBioMed Central2014Belfield, EBrown, CGan, XJiang, CBaban, DMithani, AMott, RRagoussis, JHarberd, NBACKGROUND: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS: Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS: Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence. |
| spellingShingle | Genetics (life sciences) Plant Sciences Belfield, E Brown, C Gan, X Jiang, C Baban, D Mithani, A Mott, R Ragoussis, J Harberd, N Microarray-based ultra-high resolution discovery of genomic deletion mutations. |
| title | Microarray-based ultra-high resolution discovery of genomic deletion mutations. |
| title_full | Microarray-based ultra-high resolution discovery of genomic deletion mutations. |
| title_fullStr | Microarray-based ultra-high resolution discovery of genomic deletion mutations. |
| title_full_unstemmed | Microarray-based ultra-high resolution discovery of genomic deletion mutations. |
| title_short | Microarray-based ultra-high resolution discovery of genomic deletion mutations. |
| title_sort | microarray based ultra high resolution discovery of genomic deletion mutations |
| topic | Genetics (life sciences) Plant Sciences |
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