{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/113916"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/113916","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Sensitive detection of complex and repetitive structural variation with long read sequencing data","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-04-06 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-04-06 without embargo terms","abstract_has_math":false,"creators":["Stephens, Zachary"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Electrical & Computer Engr","degree_department":null,"school":null,"contributors":["Iyer, Ravishankar K","Hwu, Wen-mei","Robinson, Gene E","Sinha, Saurabh","Kocher, Jean-Pierre","Shomorony, Ilan"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-04-29T21:34:53Z","date_published":"2022-04-29T21:34:53Z","updated_at":"2026-07-22T22:24:53Z","subjects":["Engineering"],"languages":["en","eng"],"rights":["Copyright 2021 Zachary Stephens"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/113916","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Iyer, Ravishankar K","Hwu, Wen-mei","Robinson, Gene E","Sinha, Saurabh","Kocher, Jean-Pierre","Shomorony, Ilan"]},{"key":"dc:creator","label":"Author","values":["Stephens, Zachary"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-04-29T21:34:53Z","2021-12","2021-12-03"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Electrical & Computer Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Engineering"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2021 Zachary Stephens"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/113916"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-04-06 without embargo terms","The student, Zachary Stephens, accepted the attached license on 2021-12-03 at 11:08.","The student, Zachary Stephens, submitted this Dissertation for approval on 2021-12-03 at 11:15.","This Dissertation was approved for publication on 2021-12-03 at 16:27.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17383 on 2022-04-06 at 17:11:01","Made available in DSpace on 2022-04-29T21:34:53Z (GMT). No. of bitstreams: 3 STEPHENS-DISSERTATION-2021.pdf: 8988320 bytes, checksum: 2c88e38867c4e97cfaaca01850945839 (MD5) LICENSE.txt: 4213 bytes, checksum: fcb1756e67b48c7663d987552c85cc60 (MD5) PROQUEST_LICENSE.txt: 4559 bytes, checksum: 9904e853b67867141a5607d2b8eafba3 (MD5) Previous issue date: 2021-12-03","DNA sequencing has become a ubiquitous part of individualized medicine, playing central roles in the discovery, diagnosis, and treatment of disease. As sequencing technologies mature and become more affordable, it is expected that patient genotyping will soon become a standard practice of care across the world. The most common kind of genetic variation are single nucleotide variants (SNVs), followed by small insertions and deletions, however, roughly half of all sequence differences that differentiate individuals are in the form of larger, less frequent events called structural variants (SVs). While a large variety of analytical methods have been developed to detect SVs, they remain the most poorly characterized. SVs are challenging to detect with high sensitivity in part due to the limited ability of short read sequencing data to span large events or to identify breakpoint coordinates with high confidence. The aim of this dissertation was to develop computational methods for detecting SVs and cxSVs which are applicable to clinical use cases. That is, developing specialized methods for characterizing types of SVs that are relevant to clinical genotyping but unaddressed or insufficiently described by existing tools. Additionally it is crucial that these methods are computationally efficient, as to support the rapidly growing amounts of sequence data generated from individualized medicine."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Sensitive detection of complex and repetitive structural variation with long read sequencing data"]}]}],"canonical_facts":{"dc:contributor":["Iyer, Ravishankar K","Hwu, Wen-mei","Robinson, Gene E","Sinha, Saurabh","Kocher, Jean-Pierre","Shomorony, Ilan"],"dc:creator":["Stephens, Zachary"],"dc:date":["2022-04-29T21:34:53Z","2021-12","2021-12-03"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. 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As sequencing technologies mature and become more affordable, it is expected that patient genotyping will soon become a standard practice of care across the world. The most common kind of genetic variation are single nucleotide variants (SNVs), followed by small insertions and deletions, however, roughly half of all sequence differences that differentiate individuals are in the form of larger, less frequent events called structural variants (SVs). While a large variety of analytical methods have been developed to detect SVs, they remain the most poorly characterized. SVs are challenging to detect with high sensitivity in part due to the limited ability of short read sequencing data to span large events or to identify breakpoint coordinates with high confidence. The aim of this dissertation was to develop computational methods for detecting SVs and cxSVs which are applicable to clinical use cases. 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