Efficient high-resolution deletion discovery inCaenorhabditis elegansby 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.

Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae

“…Despite the unique geographical origin of these additional strains, we failed to find high divergence of any of them from global samples for these six loci (see haplotype Y for JU1088, haplotype I for JU1171, haplotype K for JU1172 and haplotype Z for JU258, in Figures 2a and 3a). Furthermore, JU258 was not strongly allied to the Hawaiian strain, CB4856 (haplotype T), relative to the N2 strain (haplotype A), as previously suggested (Haber et al, 2005;Stewart et al, 2005;Maydan et al, 2007).…”

Whole-Genome Profiling of Mutagenesis inCaenorhabditis elegans

“…With the microarray designs used in the current study, CGH has previously been capable of detecting deletions up to megabases in size and mutations as small as single-base changes (Maydan et al 2007). Only two deletion candidates were found in our mutagenized strains and these were confirmed using Sanger sequencing.…”

“…To test this hypothesis, we reanalyzed all the sequencing data sets The middle panel shows the apparent distance between the alignments of read pairs to the reference genome. The bottom panel shows the fluorescence ratio in log2 scale in a comparative genomic hybridization experiment (Maydan et al 2007). used in the current work with the BWA/Samtools combination (Li and Durbin 2009;). The new analysis program correctly identified the single-base insertion relative to the reference genome in all 12 data sets, including in both wild-type strains (our unpublished results).…”

“…Comparative genomic hybridization: The VC and DM mutant strains were processed with whole-genome comparative genomic hybridization following the procedure described in detail in Maydan et al (2007), using the N2 wild-type VC2010 strain for reference DNA. Roche NimbleGen manufactured the microarrays but the experiments and subsequent data processing were performed in the laboratory of D. G. Moerman.…”

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification inCaenorhabditis elegans

“…One such example is comparative genomic hybridization (CGH), a technique that has been extensively used in human genetics to quantify chromosomal copy number aberrations (Kallioniemi et al 1992). In C. elegans oligonucleotide CGH arrays have been used to detect deletions (Jones et al 2007;Maydan et al 2007) and to identify single-nucleotide alterations that were previously mapped (Maydan et al 2009;O'Meara et al 2009). Although WGS is by far the most efficient method for identifying singlenucleotide alteration, CGH arrays offer a useful alternative for detecting structural variations.…”