Dissect: detection and characterization of novel structural alterations in transcribed sequences
Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of iden...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Oxford University Press
2012
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| Online Access: | http://hdl.handle.net/1721.1/75411 https://orcid.org/0000-0003-2315-0768 |
| _version_ | 1811073121878278144 |
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| author | Yorukoglu, Deniz Hac, Faraz Swanson, Lucas Collins, Colin C. Birol, Inanc Sahinalp, S. Cenk |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Yorukoglu, Deniz Hac, Faraz Swanson, Lucas Collins, Colin C. Birol, Inanc Sahinalp, S. Cenk |
| author_sort | Yorukoglu, Deniz |
| collection | MIT |
| description | Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention.
In this article, we introduce two novel algorithmic formulations for identifying transcriptomic structural variants through aligning transcripts to the reference genome under the consideration of such variation. The first formulation is based on a nucleotide-level alignment model; a second, potentially faster formulation is based on chaining fragments shared between each transcript and the reference genome. Based on these formulations, we introduce a novel transcriptome-to-genome alignment tool, Dissect (DIScovery of Structural Alteration Event Containing Transcripts), which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.
Results: We tested Dissect on simulated transcripts altered via structural events, as well as assembled RNA-Seq contigs from human prostate cancer cell line C4-2. Our results indicate that Dissect has high sensitivity and specificity in identifying structural alteration events in simulated transcripts as well as uncovering novel structural alterations in cancer transcriptomes. |
| first_indexed | 2024-09-23T09:28:47Z |
| format | Article |
| id | mit-1721.1/75411 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:28:47Z |
| publishDate | 2012 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/754112022-09-26T11:40:17Z Dissect: detection and characterization of novel structural alterations in transcribed sequences Yorukoglu, Deniz Hac, Faraz Swanson, Lucas Collins, Colin C. Birol, Inanc Sahinalp, S. Cenk Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Yorukoglu, Deniz Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention. In this article, we introduce two novel algorithmic formulations for identifying transcriptomic structural variants through aligning transcripts to the reference genome under the consideration of such variation. The first formulation is based on a nucleotide-level alignment model; a second, potentially faster formulation is based on chaining fragments shared between each transcript and the reference genome. Based on these formulations, we introduce a novel transcriptome-to-genome alignment tool, Dissect (DIScovery of Structural Alteration Event Containing Transcripts), which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs. Results: We tested Dissect on simulated transcripts altered via structural events, as well as assembled RNA-Seq contigs from human prostate cancer cell line C4-2. Our results indicate that Dissect has high sensitivity and specificity in identifying structural alteration events in simulated transcripts as well as uncovering novel structural alterations in cancer transcriptomes. Pacific Institute for the Mathematical Sciences (Fellowship) 2012-12-12T16:37:43Z 2012-12-12T16:37:43Z 2012 Article http://purl.org/eprint/type/JournalArticle 1367-4803 1460-2059 http://hdl.handle.net/1721.1/75411 Yorukoglu, D. et al. “Dissect: Detection and Characterization of Novel Structural Alterations in Transcribed Sequences.” Bioinformatics 28.12 (2012): i179–i187. https://orcid.org/0000-0003-2315-0768 en_US http://dx.doi.org/10.1093/bioinformatics/bts214 Bioinformatics Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/3.0 application/pdf Oxford University Press Oxford |
| spellingShingle | Yorukoglu, Deniz Hac, Faraz Swanson, Lucas Collins, Colin C. Birol, Inanc Sahinalp, S. Cenk Dissect: detection and characterization of novel structural alterations in transcribed sequences |
| title | Dissect: detection and characterization of novel structural alterations in transcribed sequences |
| title_full | Dissect: detection and characterization of novel structural alterations in transcribed sequences |
| title_fullStr | Dissect: detection and characterization of novel structural alterations in transcribed sequences |
| title_full_unstemmed | Dissect: detection and characterization of novel structural alterations in transcribed sequences |
| title_short | Dissect: detection and characterization of novel structural alterations in transcribed sequences |
| title_sort | dissect detection and characterization of novel structural alterations in transcribed sequences |
| url | http://hdl.handle.net/1721.1/75411 https://orcid.org/0000-0003-2315-0768 |
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