title: Ruler arrays reveal haploid genomic structural variation.
abstract: Despite the known relevance of genomic structural variants to pathogen behavior, cancer, development, and evolution, certain repeat based structural variants may evade detection by existing high-throughput techniques. Here, we present ruler arrays, a technique to detect genomic structural variants including insertions and deletions (indels), duplications, and translocations. A ruler array exploits DNA polymerase's processivity to detect physical distances between defined genomic sequences regardless of the intervening sequence. The method combines a sample preparation protocol, tiling genomic microarrays, and a new computational analysis. The analysis of ruler array data from two genomic samples enables the identification of structural variation between the samples. In an empirical test between two closely related haploid strains of yeast ruler arrays detected 78% of the structural variants larger than 100 bp.
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: P Alexander
authors.initials: PA
authors.lastname: Rolfe
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Bernstein
authors.forename: Paula
authors.initials: P
authors.lastname: Grisafi
authors.forename: Gerald R
authors.initials: GR
authors.lastname: Fink
authors.forename: David K
authors.initials: DK
authors.lastname: Gifford
mesh_terms: D055028:Comparative Genomic Hybridization; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics; D016678:Genome; D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods; D006238:Haploidy; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011336:Probability; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D004259:DNA-Directed DNA Polymerase