Ruler arrays reveal haploid genomic structural variation
| Autor: | Gerald R. Fink, Paula Grisafi, P. Alexander Rolfe, Douglas A. Bernstein, David K. Gifford |
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| Přispěvatelé: | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Gifford, David K., Rolfe, Philip Alexander, Fink, Gerald R. |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Microarrays
Array Processing Genomic Structural Variation Structure Prediction lcsh:Medicine Genomics Yeast and Fungal Models Computational biology DNA-Directed DNA Polymerase Saccharomyces cerevisiae Biology Haploidy Genome Polymorphism Single Nucleotide Structural variation Fungal Proteins 03 medical and health sciences Model Organisms Engineering Indel lcsh:Science 030304 developmental biology Oligonucleotide Array Sequence Analysis Probability Genetics 0303 health sciences Fungal protein Comparative Genomic Hybridization Multidisciplinary Models Statistical Models Genetic 030305 genetics & heredity lcsh:R Computational Biology Signal Processing Structural Genomics lcsh:Q DNA microarray Comparative genomic hybridization Research Article |
| Zdroj: | PLoS ONE, Vol 7, Iss 8, p e43210 (2012) PLoS ONE PLoS |
| ISSN: | 1932-6203 |
| Popis: | 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. United States. National Institutes of Health (Grant R01GM069676) |
| Databáze: | OpenAIRE |
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