Comparative Genomic Hybridization Using Oligonucleotide Microarrays and Total Genomic DNA

Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing as... Ausführliche Beschreibung

1. Person: Barrett, Michael T.
Weitere Personen: Scheffer, Alicia verfasserin; Ben-Dor, Amir verfasserin; Sampas, Nick verfasserin; Lipson, Doron verfasserin; Kincaid, Robert verfasserin; Tsang, Peter verfasserin; Curry, Bo verfasserin; Baird, Kristin verfasserin; Meltzer, Paul S. verfasserin; Yakhini, Zohar verfasserin; Bruhn, Laurakay verfasserin; Laderman, Stephen verfasserin; Caruthers, Marvin H. verfasserin
Quelle: in Proceedings of the National Academy of Sciences of the United States of America Vol. 101, No. 51 (2004), p. 17765-17770
Weitere Artikel
Format: Online-Artikel
Sprache: English
Veröffentlicht: 2004
Beschreibung: Online-Ressource
Schlagworte: research-article
Cancer
DNA microarrays
Genome
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Anmerkung: Copyright: Copyright 1993/2004 The National Academy of Sciences of the United States of America
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245 1 0 |a Comparative Genomic Hybridization Using Oligonucleotide Microarrays and Total Genomic DNA  |h Elektronische Ressource 
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520 |a Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing assemblies of BAC or cDNA clones typically require maintenance, propagation, replication, and verification of large clone sets. Furthermore, it is difficult to control the specificity of the hybridization to the complex sequences that are present in each feature of such arrays. To develop a more robust and flexible platform, we created probedesign methods and assay protocols that make oligonucleotide microarrays synthesized in situ by inkjet technology compatible with array-based comparative genomic hybridization applications employing samples of total genomic DNA. Hybridization of a series of cell lines with variable numbers of X chromosomes to arrays designed for CGH measurements gave median ratios for X-chromosome probes within 6% of the theoretical values (0.5 for XY/XX, 1.0 for XX/XX, 1.4 for XXX/XX, 2.1 for XXXX/XX, and 2.6 for XXXXX/XX). Furthermore, these arrays detected and mapped regions of single-copy losses, homozygous deletions, and amplicons of various sizes in different model systems, including diploid cells with a chromosomal breakpoint that has been mapped and sequenced to a precise nucleotide and tumor cell lines with highly variable regions of gains and losses. Our results demonstrate that oligonucleotide arrays designed for CGH provide a robust and precise platform for detecting chromosomal alterations throughout a genome with high sensitivity even when using full-complexity genomic samples. 
653 |a research-article 
653 |a Cancer 
653 |a DNA microarrays 
653 |a Genome 
700 1 |a Scheffer, Alicia  |e verfasserin  |4 aut 
700 1 |a Ben-Dor, Amir  |e verfasserin  |4 aut 
700 1 |a Sampas, Nick  |e verfasserin  |4 aut 
700 1 |a Lipson, Doron  |e verfasserin  |4 aut 
700 1 |a Kincaid, Robert  |e verfasserin  |4 aut 
700 1 |a Tsang, Peter  |e verfasserin  |4 aut 
700 1 |a Curry, Bo  |e verfasserin  |4 aut 
700 1 |a Baird, Kristin  |e verfasserin  |4 aut 
700 1 |a Meltzer, Paul S.  |e verfasserin  |4 aut 
700 1 |a Yakhini, Zohar  |e verfasserin  |4 aut 
700 1 |a Bruhn, Laurakay  |e verfasserin  |4 aut 
700 1 |a Laderman, Stephen  |e verfasserin  |4 aut 
700 1 |a Caruthers, Marvin H.  |e verfasserin  |4 aut 
773 0 8 |i in  |t Proceedings of the National Academy of Sciences of the United States of America  |d Washington, DC : National Acad. of Sciences  |g Vol. 101, No. 51 (2004), p. 17765-17770  |q 101:51<17765-17770  |w (DE-601)JST069399220  |x 0027-8424 
856 4 1 |u https://www.jstor.org/stable/3374043  |3 Volltext 
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951 |a AR 
952 |d 101  |j 2004  |e 51  |h 17765-17770 

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