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Construction and application of a zebrafish array comparative genomic hybridization platform
Author(s) -
Freeman Jennifer L.,
Ceol Craig,
Feng Hui,
Langenau David M.,
Belair Cassandra,
Stern Howard M.,
Song Anhua,
Paw Barry H.,
Look A. Thomas,
Zhou Yi,
Zon Leonard I.,
Lee Charles
Publication year - 2009
Publication title -
genes, chromosomes and cancer
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.754
H-Index - 119
eISSN - 1098-2264
pISSN - 1045-2257
DOI - 10.1002/gcc.20623
Subject(s) - zebrafish , biology , comparative genomic hybridization , genome , genetics , model organism , bacterial artificial chromosome , computational biology , gene
Abstract 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. © 2008 Wiley‐Liss, Inc.