Ruler Arrays Reveal Haploid Genomic Structural Variation
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 i...
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| Formáid: | Alt |
| Teanga: | en_US |
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Public Library of Science
2012
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| Rochtain ar líne: | http://hdl.handle.net/1721.1/74619 https://orcid.org/0000-0003-3704-2899 https://orcid.org/0000-0003-1709-4034 |
| _version_ | 1826202160884350976 |
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| author | Gifford, David K. Rolfe, Philip Alexander Fink, Gerald R. Bernstein, Douglas A. Grisafi, Paula |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Gifford, David K. Rolfe, Philip Alexander Fink, Gerald R. Bernstein, Douglas A. Grisafi, Paula |
| author_sort | Gifford, David K. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T12:03:10Z |
| format | Article |
| id | mit-1721.1/74619 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:03:10Z |
| publishDate | 2012 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/746192022-10-01T07:50:38Z Ruler Arrays Reveal Haploid Genomic Structural Variation Gifford, David K. Rolfe, Philip Alexander Fink, Gerald R. Bernstein, Douglas A. Grisafi, Paula 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. 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) 2012-11-09T19:19:12Z 2012-11-09T19:19:12Z 2012-08 2012-02 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/74619 Rolfe, P. Alexander et al. “Ruler Arrays Reveal Haploid Genomic Structural Variation.” Ed. Gualtiero Colombo. PLoS ONE 7.8 (2012). https://orcid.org/0000-0003-3704-2899 https://orcid.org/0000-0003-1709-4034 en_US http://dx.doi.org/10.1371/journal.pone.0043210 PLoS ONE Creative Commons Attribution http://creativecommons.org/licenses/by/2.5/ application/pdf Public Library of Science PLoS |
| spellingShingle | Gifford, David K. Rolfe, Philip Alexander Fink, Gerald R. Bernstein, Douglas A. Grisafi, Paula Ruler Arrays Reveal Haploid Genomic Structural Variation |
| title | Ruler Arrays Reveal Haploid Genomic Structural Variation |
| title_full | Ruler Arrays Reveal Haploid Genomic Structural Variation |
| title_fullStr | Ruler Arrays Reveal Haploid Genomic Structural Variation |
| title_full_unstemmed | Ruler Arrays Reveal Haploid Genomic Structural Variation |
| title_short | Ruler Arrays Reveal Haploid Genomic Structural Variation |
| title_sort | ruler arrays reveal haploid genomic structural variation |
| url | http://hdl.handle.net/1721.1/74619 https://orcid.org/0000-0003-3704-2899 https://orcid.org/0000-0003-1709-4034 |
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