title: A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization.
abstract: Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because 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 unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Yeun-Jun
authors.initials: YJ
authors.lastname: Chung
authors.forename: Jos
authors.initials: J
authors.lastname: Jonkers
authors.forename: Hannah
authors.initials: H
authors.lastname: Kitson
authors.forename: Heike
authors.initials: H
authors.lastname: Fiegler
authors.forename: Sean
authors.initials: S
authors.lastname: Humphray
authors.forename: Carol
authors.initials: C
authors.lastname: Scott
authors.forename: Sarah
authors.initials: S
authors.lastname: Hunt
authors.forename: Yuejin
authors.initials: Y
authors.lastname: Yu
authors.forename: Ichiko
authors.initials: I
authors.lastname: Nishijima
authors.forename: Arno
authors.initials: A
authors.lastname: Velds
authors.forename: Henne
authors.initials: H
authors.lastname: Holstege
authors.forename: Nigel
authors.initials: N
authors.lastname: Carter
authors.forename: Allan
authors.initials: A
authors.lastname: Bradley
mesh_terms: D000818:Animals; D002460:Cell Line; D045744:Cell Line, Tumor; D043171:Chromosomal Instability / Q000235:genetics; D002872:Chromosome Deletion; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D004247:DNA / Q000032:analysis*; D017931:DNA Primers / Q000235:genetics; D005260:Female; D005347:Fibroblasts / Q000737:chemistry / Q000378:metabolism; D005784:Gene Amplification / Q000235:genetics; D018628:Gene Dosage; D016678:Genome; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D012737:Sex Factors; D013234:Stem Cells / Q000737:chemistry / Q000378:metabolism
chemical_list: D017931:DNA Primers; D004247:DNA