VEGAWES: variational segmentation on whole exome sequencing for copy number detection
<p dir="ltr">Copy number variations are important in the detection and progression of significant tumors and diseases. Recently, Whole Exome Sequencing is gaining popularity with copy number variations detection due to low cost and better efficiency. In this work, we developed VEGAWE...
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| مؤلفون آخرون: | , , , |
| منشور في: |
2015
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إضافة وسم
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| _version_ | 1864513505661550592 |
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| author | Samreen Anjum (19651882) |
| author2 | Sandro Morganella (683128) Fulvio D’Angelo (2432143) Antonio Iavarone (3814138) Michele Ceccarelli (184154) |
| author2_role | author author author author |
| author_facet | Samreen Anjum (19651882) Sandro Morganella (683128) Fulvio D’Angelo (2432143) Antonio Iavarone (3814138) Michele Ceccarelli (184154) |
| author_role | author |
| dc.creator.none.fl_str_mv | Samreen Anjum (19651882) Sandro Morganella (683128) Fulvio D’Angelo (2432143) Antonio Iavarone (3814138) Michele Ceccarelli (184154) |
| dc.date.none.fl_str_mv | 2015-09-29T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1186/s12859-015-0748-0 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/VEGAWES_variational_segmentation_on_whole_exome_sequencing_for_copy_number_detection/27001942 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Clinical sciences Copy number variation Whole-exome sequencing Segmentation Variational based model |
| dc.title.none.fl_str_mv | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Copy number variations are important in the detection and progression of significant tumors and diseases. Recently, Whole Exome Sequencing is gaining popularity with copy number variations detection due to low cost and better efficiency. In this work, we developed VEGAWES for accurate and robust detection of copy number variations on WES data. VEGAWES is an extension to a variational based segmentation algorithm, VEGA: Variational estimator for genomic aberrations, which has previously outperformed several algorithms on segmenting array comparative genomic hybridization data. We tested this algorithm on synthetic data and 100 Glioblastoma Multiforme primary tumor samples. The results on the real data were analyzed with segmentation obtained from Single-nucleotide polymorphism data as ground truth. We compared our results with two other segmentation algorithms and assessed the performance based on accuracy and time. In terms of both accuracy and time, VEGAWES provided better results on the synthetic data and tumor samples demonstrating its potential in robust detection of aberrant regions in the genome.</p><h2>Other Information</h2><p dir="ltr">Published in: BMC Bioinformatics<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" rel="license" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s12859-015-0748-0" target="_blank">https://dx.doi.org/10.1186/s12859-015-0748-0</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_0380bca57159913e60b31c91ee469942 |
| identifier_str_mv | 10.1186/s12859-015-0748-0 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/27001942 |
| publishDate | 2015 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | VEGAWES: variational segmentation on whole exome sequencing for copy number detectionSamreen Anjum (19651882)Sandro Morganella (683128)Fulvio D’Angelo (2432143)Antonio Iavarone (3814138)Michele Ceccarelli (184154)Biological sciencesBioinformatics and computational biologyGeneticsBiomedical and clinical sciencesClinical sciencesCopy number variationWhole-exome sequencingSegmentationVariational based model<p dir="ltr">Copy number variations are important in the detection and progression of significant tumors and diseases. Recently, Whole Exome Sequencing is gaining popularity with copy number variations detection due to low cost and better efficiency. In this work, we developed VEGAWES for accurate and robust detection of copy number variations on WES data. VEGAWES is an extension to a variational based segmentation algorithm, VEGA: Variational estimator for genomic aberrations, which has previously outperformed several algorithms on segmenting array comparative genomic hybridization data. We tested this algorithm on synthetic data and 100 Glioblastoma Multiforme primary tumor samples. The results on the real data were analyzed with segmentation obtained from Single-nucleotide polymorphism data as ground truth. We compared our results with two other segmentation algorithms and assessed the performance based on accuracy and time. In terms of both accuracy and time, VEGAWES provided better results on the synthetic data and tumor samples demonstrating its potential in robust detection of aberrant regions in the genome.</p><h2>Other Information</h2><p dir="ltr">Published in: BMC Bioinformatics<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" rel="license" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s12859-015-0748-0" target="_blank">https://dx.doi.org/10.1186/s12859-015-0748-0</a></p>2015-09-29T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1186/s12859-015-0748-0https://figshare.com/articles/journal_contribution/VEGAWES_variational_segmentation_on_whole_exome_sequencing_for_copy_number_detection/27001942CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/270019422015-09-29T03:00:00Z |
| spellingShingle | VEGAWES: variational segmentation on whole exome sequencing for copy number detection Samreen Anjum (19651882) Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Clinical sciences Copy number variation Whole-exome sequencing Segmentation Variational based model |
| status_str | publishedVersion |
| title | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| title_full | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| title_fullStr | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| title_full_unstemmed | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| title_short | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| title_sort | VEGAWES: variational segmentation on whole exome sequencing for copy number detection |
| topic | Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Clinical sciences Copy number variation Whole-exome sequencing Segmentation Variational based model |