A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization.
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.
Chung
Yeun-Jun
YJ
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Jonkers
Jos
J
Kitson
Hannah
H
Fiegler
Heike
H
Humphray
Sean
S
Scott
Carol
C
Hunt
Sarah
S
Yu
Yuejin
Y
Nishijima
Ichiko
I
Velds
Arno
A
Holstege
Henne
H
Carter
Nigel
N
Bradley
Allan
A
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
D017931:DNA Primers; D004247:DNA