Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA

Michael T. Barrett, Alicia Scheffer, Amir Ben-Dor, Nick Sampas, Doron Lipson, Robert Kincaid, Peter Tsang, Bo Curry, Kristin Baird, Paul S. Meltzer, Zohar Yakhini, Laurakay Bruhn, Stephen Laderman

Research output: Contribution to journalArticle

292 Scopus citations

Abstract

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 probe-design 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.

Original languageEnglish (US)
Pages (from-to)17765-17770
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume101
Issue number51
DOIs
StatePublished - Dec 21 2004

Keywords

  • Cancer
  • DNA microarrays
  • Genome

ASJC Scopus subject areas

  • General

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  • Cite this

    Barrett, M. T., Scheffer, A., Ben-Dor, A., Sampas, N., Lipson, D., Kincaid, R., Tsang, P., Curry, B., Baird, K., Meltzer, P. S., Yakhini, Z., Bruhn, L., & Laderman, S. (2004). Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proceedings of the National Academy of Sciences of the United States of America, 101(51), 17765-17770. https://doi.org/10.1073/pnas.0407979101