title: Microarray-based ultra-high resolution discovery of genomic deletion mutations.
abstract: BACKGROUND
  Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low.
  
  
  RESULTS
  Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size.
  
  
  CONCLUSIONS
  Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Belfield
authors.forename: Carly
authors.initials: C
authors.lastname: Brown
authors.forename: Xiangchao
authors.initials: X
authors.lastname: Gan
authors.forename: Caifu
authors.initials: C
authors.lastname: Jiang
authors.forename: Dilair
authors.initials: D
authors.lastname: Baban
authors.forename: Aziz
authors.initials: A
authors.lastname: Mithani
authors.forename: Richard
authors.initials: R
authors.lastname: Mott
authors.forename: Jiannis
authors.initials: J
authors.lastname: Ragoussis
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. nicholas.harberd@plants.ox.ac.uk.
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Harberd
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000032:analysis / Q000378:metabolism; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis; D017384:Sequence Deletion / Q000235:genetics*
chemical_list: D018744:DNA, Plant