Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH.
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.
Cardoso
Joana
J
Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
Molenaar
Lia
L
de Menezes
Renée X
RX
Rosenberg
Carla
C
Morreau
Hans
H
Möslein
Gabriela
G
Fodde
Riccardo
R
Boer
Judith M
JM
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
D004273:DNA, Neoplasm; D004247:DNA