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Methods

Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization

¹ Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; ² Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6 Canada; ³ Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; ⁴ Department of Genome Sciences, University of Washington, Seattle, Washington 98195-7730, USA; ⁵ NimbleGen Systems Inc., Madison, Wisconsin 53711, USA

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.

E-mail moerman{at}zoology.ubc.ca; fax (604) 822-2416.

[Supplemental material is available online at www.genome.org. All data reported in this manuscript is available at GEO through accession number GSE6294.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5690307

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