Construction and application of a zebrafish array comparative genomic hybridization platform.
The zebrafish is emerging as a prominent model system for studying the genetics of human development and disease. Genetic alterations that underlie each mutant model can exist in the form of single base changes, balanced chromosomal rearrangements, or genetic imbalances. To detect genetic imbalances in an unbiased genome-wide fashion, array comparative genomic hybridization (CGH) can be used. We have developed a 5-Mb resolution array CGH platform specifically for the zebrafish. This platform contains 286 bacterial artificial chromosome (BAC) clones, enriched for orthologous sequences of human oncogenes and tumor suppressor genes. Each BAC clone has been end-sequenced and cytogenetically assigned to a specific location within the zebrafish genome, allowing for ease of integration of array CGH data with the current version of the genome assembly. This platform has been applied to three zebrafish cancer models. Significant genomic imbalances were detected in each model, identifying different regions that may potentially play a role in tumorigenesis. Hence, this platform should be a useful resource for genetic dissection of additional zebrafish developmental and disease models as well as a benchmark for future array CGH platform development.
Freeman
Jennifer L
JL
Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
Ceol
Craig
C
Feng
Hui
H
Langenau
David M
DM
Belair
Cassandra
C
Stern
Howard M
HM
Song
Anhua
A
Paw
Barry H
BH
Look
A Thomas
AT
Zhou
Yi
Y
Zon
Leonard I
LI
Lee
Charles
C
D000818:Animals; D030801:Animals, Genetically Modified; D022202:Chromosomes, Artificial, Bacterial; D055028:Comparative Genomic Hybridization / Q000379:methods*; D004195:Disease Models, Animal; D016147:Genes, Tumor Suppressor; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008545:Melanoma / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009857:Oncogenes; D054218:Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics; D015203:Reproducibility of Results; D012208:Rhabdomyosarcoma / Q000235:genetics; D015027:Zebrafish / Q000235:genetics* / Q000378:metabolism