A Whole-Genome Mouse BAC Microarray With 1-Mb Resolution for Analysis of DNA Copy Number Changes by Array Comparative Genomic Hybridization
- Yeun-Jun Chung1,5,
- Jos Jonkers1,2,5,
- Hannah Kitson1,
- Heike Fiegler1,
- Sean Humphray1,
- Carol Scott1,
- Sarah Hunt1,
- Yuejin Yu4,
- Ichiko Nishijima4,
- Arno Velds3,
- Henne Holstege2,
- Nigel Carter1, and
- Allan Bradley1,6
- 1 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- 2 Division of Molecular Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- 3 Central Microarray Facility, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- 4 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
Abstract
Microarray-basedcomparative genomic hybridization (CGH) has become a powerful methodfor the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been usedfor mouse CGH studies, the resolving power of these analyses was limitedbecause high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwantedamplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines andprimary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.
