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Array-based comparative genomic hybridization as a tool for analyzing the leukaemia genome

Array-based comparative genomic hybridization as a tool for analyzing the leukaemia genome
Array-based comparative genomic hybridization as a tool for analyzing the leukaemia genome
Comparative genomic hybridization (CGH) is arguably the most significant technical development in the molecular cytogenetics era, and has contributed considerably to our further understanding of the cancer genome. In essence, DNA from a cancer specimen (test DNA) labeled with the fluorescence reporter molecule (or fluorochrome) is hybridized to a target genome in the presence of a differentially labeled control DNA (reference DNA). The two DNA populations compete for hybridization sites on normal metaphase chromosomes, so that the resulting fluorescence ratio is a reflection of the copy number change in the test sample. The copy number changes are mapped to their position on the chromosome template. Over recent years, the chromosomal template has been largely superseded by microarray formats (aCGH), in which changes in copy number can be mapped to the genome sequence at a high resolution. This advance allows the genome to be studied at an unbridled resolution and at a high-throughput, whilst posing several technical, statistical and interpretive challenges. It is the aim of this chapter to introduce the fundamental concepts of aCGH and to provide an overview of the steps involved in a successful aCGH processing. The materials required for BAC and oligonucleotide aCGH are included, with detailed methods and a range of refinements to improve the success rate and quality of aCGH data
9781588299895
538
151-178
Humana Press
Strefford, Jon C.
3782b392-f080-42bf-bdca-8aa5d6ca532f
Parker, Helen
33e0cd81-d45f-49bc-9539-09345d79d895
Wai, Chi
So, Eric
Strefford, Jon C.
3782b392-f080-42bf-bdca-8aa5d6ca532f
Parker, Helen
33e0cd81-d45f-49bc-9539-09345d79d895
Wai, Chi
So, Eric

Strefford, Jon C. and Parker, Helen (2009) Array-based comparative genomic hybridization as a tool for analyzing the leukaemia genome. In, Wai, Chi and So, Eric (eds.) Leukemia - Methods and Protocols. (Spinger Protocols - Methods in Molecular Biology, 538) New York, USA. Humana Press, pp. 151-178. (doi:10.1007/978-1-59745-418-6_8).

Record type: Book Section

Abstract

Comparative genomic hybridization (CGH) is arguably the most significant technical development in the molecular cytogenetics era, and has contributed considerably to our further understanding of the cancer genome. In essence, DNA from a cancer specimen (test DNA) labeled with the fluorescence reporter molecule (or fluorochrome) is hybridized to a target genome in the presence of a differentially labeled control DNA (reference DNA). The two DNA populations compete for hybridization sites on normal metaphase chromosomes, so that the resulting fluorescence ratio is a reflection of the copy number change in the test sample. The copy number changes are mapped to their position on the chromosome template. Over recent years, the chromosomal template has been largely superseded by microarray formats (aCGH), in which changes in copy number can be mapped to the genome sequence at a high resolution. This advance allows the genome to be studied at an unbridled resolution and at a high-throughput, whilst posing several technical, statistical and interpretive challenges. It is the aim of this chapter to introduce the fundamental concepts of aCGH and to provide an overview of the steps involved in a successful aCGH processing. The materials required for BAC and oligonucleotide aCGH are included, with detailed methods and a range of refinements to improve the success rate and quality of aCGH data

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Published date: 2009

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Local EPrints ID: 72668
URI: http://eprints.soton.ac.uk/id/eprint/72668
ISBN: 9781588299895
PURE UUID: 7381954f-f272-4478-a3ce-2c3beb06fd62
ORCID for Jon C. Strefford: ORCID iD orcid.org/0000-0002-0972-2881
ORCID for Helen Parker: ORCID iD orcid.org/0000-0001-8308-9781

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Date deposited: 22 Feb 2010
Last modified: 14 Mar 2024 02:49

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Contributors

Author: Helen Parker ORCID iD
Editor: Chi Wai
Editor: Eric So

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