Human and mouse oligonucleotide-based array CGH

Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array comparative genomic hybridization (CGH). This oligo array CGH platform yields repro...

Full description

Bibliographic Details
Main Authors:	van den IJssel, Paul, Tijssen, Marianne, Chin, Suet-Feung, Eijk, Paul, Carvalho, Beatriz, Hopmans, Erik, Holstege, Henne, Bangarusamy, Dhinoth Kumar, Jonkers, Jos, Meijer, Gerrit A., Caldas, Carlos, Ylstra, Bauke
Format:	Online
Language:	English
Published:	Oxford University Press 2005
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1316119/

id	pubmed-1316119
recordtype	oai_dc
spelling	pubmed-13161192005-12-19 Human and mouse oligonucleotide-based array CGH van den IJssel, Paul Tijssen, Marianne Chin, Suet-Feung Eijk, Paul Carvalho, Beatriz Hopmans, Erik Holstege, Henne Bangarusamy, Dhinoth Kumar Jonkers, Jos Meijer, Gerrit A. Caldas, Carlos Ylstra, Bauke Methods Online Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array comparative genomic hybridization (CGH). This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridized using a hybstation and analysed using BlueFuse feature extraction software, with >95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA and a 90% reduction of Cot-1 DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using ‘off-the-shelf’ oligo libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results. Oxford University Press 2005 2005-12-16 /pmc/articles/PMC1316119/ /pubmed/16361265 http://dx.doi.org/10.1093/nar/gni191 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	van den IJssel, Paul Tijssen, Marianne Chin, Suet-Feung Eijk, Paul Carvalho, Beatriz Hopmans, Erik Holstege, Henne Bangarusamy, Dhinoth Kumar Jonkers, Jos Meijer, Gerrit A. Caldas, Carlos Ylstra, Bauke
spellingShingle	van den IJssel, Paul Tijssen, Marianne Chin, Suet-Feung Eijk, Paul Carvalho, Beatriz Hopmans, Erik Holstege, Henne Bangarusamy, Dhinoth Kumar Jonkers, Jos Meijer, Gerrit A. Caldas, Carlos Ylstra, Bauke Human and mouse oligonucleotide-based array CGH
author_facet	van den IJssel, Paul Tijssen, Marianne Chin, Suet-Feung Eijk, Paul Carvalho, Beatriz Hopmans, Erik Holstege, Henne Bangarusamy, Dhinoth Kumar Jonkers, Jos Meijer, Gerrit A. Caldas, Carlos Ylstra, Bauke
author_sort	van den IJssel, Paul
title	Human and mouse oligonucleotide-based array CGH
title_short	Human and mouse oligonucleotide-based array CGH
title_full	Human and mouse oligonucleotide-based array CGH
title_fullStr	Human and mouse oligonucleotide-based array CGH
title_full_unstemmed	Human and mouse oligonucleotide-based array CGH
title_sort	human and mouse oligonucleotide-based array cgh
description	Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array comparative genomic hybridization (CGH). This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridized using a hybstation and analysed using BlueFuse feature extraction software, with >95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA and a 90% reduction of Cot-1 DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using ‘off-the-shelf’ oligo libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results.
publisher	Oxford University Press
publishDate	2005
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1316119/
_version_	1611379894837575680

Human and mouse oligonucleotide-based array CGH

Similar Items