title: Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH.
abstract: Comparative genomic hybridization by means of BAC microarrays (array CGH) allows high-resolution profiling of copy-number aberrations in tumor DNA. However, specific genetic lesions associated with small but clinically relevant tumor areas may pass undetected due to intra-tumor heterogeneity and/or the presence of contaminating normal cells. Here, we show that the combination of laser capture microdissection, phi29 DNA polymerase-mediated isothermal genomic DNA amplification, and array CGH allows genomic profiling of very limited numbers of cells. Moreover, by means of simple statistical models, we were able to bypass the exclusion of amplification distortions and variability prone areas, and to detect tumor-specific chromosomal gains and losses. We applied this new combined experimental and analytical approach to the genomic profiling of colorectal adenomatous polyps and demonstrated our ability to accurately detect single copy gains and losses affecting either whole chromosomes or small genomic regions from as little as 2 ng of DNA or 1000 microdissected cells.
authors.affiliation: Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors.forename: Joana
authors.initials: J
authors.lastname: Cardoso
authors.forename: Lia
authors.initials: L
authors.lastname: Molenaar
authors.forename: Renée X
authors.initials: RX
authors.lastname: de Menezes
authors.forename: Carla
authors.initials: C
authors.lastname: Rosenberg
authors.forename: Hans
authors.initials: H
authors.lastname: Morreau
authors.forename: Gabriela
authors.initials: G
authors.lastname: Möslein
authors.forename: Riccardo
authors.initials: R
authors.lastname: Fodde
authors.forename: Judith M
authors.initials: JM
authors.lastname: Boer
mesh_terms: D018256:Adenomatous Polyps / Q000235:genetics* / Q000473:pathology; D002460:Cell Line; D003106:Colon / Q000166:cytology; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D004247:DNA / Q000096:biosynthesis; D004273:DNA, Neoplasm / Q000032:analysis*; D005260:Female; D018628:Gene Dosage; D023281:Genomics / Q000379:methods; D006801:Humans; D007413:Intestinal Mucosa / Q000166:cytology; D007834:Lasers; D019656:Loss of Heterozygosity; D008297:Male; D042282:Microdissection / Q000379:methods; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D016133:Polymerase Chain Reaction; D011786:Quality Control; D015203:Reproducibility of Results
chemical_list: D004273:DNA, Neoplasm; D004247:DNA