title: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization.
abstract: We have developed array Comparative Genomic Hybridization for Caenorhabditis elegans as a means of screening for novel induced deletions in this organism. We designed three microarrays consisting of overlapping 50-mer probes to annotated exons and micro-RNAs, the first with probes to chromosomes X and II, the second with probes to chromosome II alone, and a third to the entire genome. These arrays were used to reliably detect both a large (50 kb) multigene deletion and a small (1 kb) single-gene deletion in homozygous and heterozygous samples. In one case, a deletion breakpoint was resolved to fewer than 50 bp. In an experiment designed to identify new mutations we used the X:II and II arrays to detect deletions associated with lethal mutants on chromosome II. One is an 8-kb deletion targeting the ast-1 gene on chromosome II and another is a 141-bp deletion in the gene C06A8.1. Others span large sections of the chromosome, up to >750 kb. As a further application of array Comparative Genomic Hybridization in C. elegans we used the whole-genome array to detect the extensive natural gene content variation (almost 2%) between the N2 Bristol strain and the strain CB4856, a strain isolated in Hawaii and JU258, a strain isolated in Madeira.
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Jason S
authors.initials: JS
authors.lastname: Maydan
authors.forename: Stephane
authors.initials: S
authors.lastname: Flibotte
authors.forename: Mark L
authors.initials: ML
authors.lastname: Edgley
authors.forename: Joanne
authors.initials: J
authors.lastname: Lau
authors.forename: Rebecca R
authors.initials: RR
authors.lastname: Selzer
authors.forename: Todd A
authors.initials: TA
authors.lastname: Richmond
authors.forename: Nathan J
authors.initials: NJ
authors.lastname: Pofahl
authors.forename: James H
authors.initials: JH
authors.lastname: Thomas
authors.forename: Donald G
authors.initials: DG
authors.lastname: Moerman
mesh_terms: D000818:Animals; D001266:Atlantic Islands; D017173:Caenorhabditis elegans / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005453:Fluorescence; D017353:Gene Deletion; D023281:Genomics / Q000379:methods*; D006254:Hawaii; D035683:MicroRNAs / Q000235:genetics; D046228:Microarray Analysis / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*
chemical_list: D035683:MicroRNAs