Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations.
In this work, we explore the use of representations in conjunction with DNA microarray technology to measure gene copy number changes in cancer. We demonstrate that arrays of DNA probes derived from low-complexity representations can be used to detect amplifications, deletions, and polymorphic differences when hybridized to representations of genomic DNA. The method is both reproducible and verifiable, and is applicable even to microscopic amounts of primary tumors. We also present a mathematical model for array performance that is useful for designing and understanding DNA microarray hybridization protocols. The future applications and challenges of this approach are discussed.
Lucito
R
R
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. lucito@cshl.org
West
J
J
Reiner
A
A
Alexander
J
J
Esposito
D
D
Mishra
B
B
Powers
S
S
Norton
L
L
Wigler
M
M
D001943:Breast Neoplasms / Q000737:chemistry / Q000235:genetics* / Q000473:pathology; D015342:DNA Probes; D018628:Gene Dosage; D020869:Gene Expression Profiling / Q000379:methods / Q000639:trends; D006801:Humans; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000639:trends*; D011110:Polymorphism, Genetic / Q000235:genetics; D015203:Reproducibility of Results; D014407:Tumor Cells, Cultured
D015342:DNA Probes