FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2213884683> ?p ?o ?g. }

• W2213884683 abstract "Objectives and Rationale: Structural variants (SV) including large copy number aberrations (CNV), translocations, inversions, and large insertions and deletions (INDEL) play a critical role in tumorigenesis and progression. In fact, we now know that tumors can be categorized according to the size of mutations harbored. In several cancers, including ovarian and breast cancer, the large structural mutations, rather than single site mutations, play a dominate role in tumor etiology. Therefore, it9s critical to implement reliable algorithm for the detection of structural variants in DNA sequencing data. Mate-pair sequencing is a protocol specifically implemented for detection of the whole-genome level structural variants. It requires less sequencing depth therefor is cost effective, and enables the detection of CNVs, translocations, and inversions simultaneously. However, so far there has been no reliable bioinformatics pipeline for the analyses of the mate-pair sequencing data. Methods: Our novel algorithm, the SnowShoes-SV, is an exhaustive search algorithm designed specifically for mate-pair DNA sequencing data analyses. It calls the SVs based on disconcordant read pairs. The false SVs are filtered according to the following criteria: (i) the number of the supporting read pairs; (ii) the lack of reads from control data that implicate SV at the same region; (iii) the mappability and uniqueness of the region based on data from the ENCODE project; (iv) consistencies of the mapping orientations of the supporting read pairs; (v) the similar sizes between sequencing library and the two end read clusters. Results: Using a set of samples previously genotyped by aCGH, the SnowShoes-SV successfully detected all known CNVs and other SVs. It also identified copy number neutral translocations and inversions previously not identified by aCGH. In addition, the algorithm nominated novel SVs which are to be validated by PCR. Conclusions: SnowShoes-SV is a highly sensitive and specific algorithm for SV detection from the mate-pair DNA sequencing data. Citation Format: Yan W Asmann, Chen Wang, Brian M Necela, Xianfeng Chen, Jean-Pierre A Kocher, Matthew J Maurer, Thomas M Habermann, Susan L Slager, Andrew L Feldman, Anne J Novak, James R Cerhan, Edith A Perez, E Aubrey Thompson. An exhaustive algorithm for detecting copy number aberrations and large structural variants in whole-genome mate-pair sequencing data [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-07-03." @default.
• W2213884683 created "2016-06-24" @default.
• W2213884683 creator A5013038112 @default.
• W2213884683 creator A5022178171 @default.
• W2213884683 creator A5025688165 @default.
• W2213884683 creator A5026692399 @default.
• W2213884683 creator A5031537463 @default.
• W2213884683 creator A5036583707 @default.
• W2213884683 creator A5038191637 @default.
• W2213884683 creator A5047509474 @default.
• W2213884683 creator A5065306642 @default.
• W2213884683 creator A5067100969 @default.
• W2213884683 creator A5071782757 @default.
• W2213884683 creator A5076621021 @default.
• W2213884683 creator A5090406453 @default.
• W2213884683 date "2015-04-30" @default.
• W2213884683 modified "2023-09-28" @default.
• W2213884683 title "Abstract P6-07-03: An exhaustive algorithm for detecting copy number aberrations and large structural variants in whole-genome mate-pair sequencing data" @default.
• W2213884683 doi "https://doi.org/10.1158/1538-7445.sabcs14-p6-07-03" @default.
• W2213884683 hasPublicationYear "2015" @default.
• W2213884683 type Work @default.
• W2213884683 sameAs 2213884683 @default.
• W2213884683 citedByCount "0" @default.
• W2213884683 crossrefType "proceedings-article" @default.
• W2213884683 hasAuthorship W2213884683A5013038112 @default.
• W2213884683 hasAuthorship W2213884683A5022178171 @default.
• W2213884683 hasAuthorship W2213884683A5025688165 @default.
• W2213884683 hasAuthorship W2213884683A5026692399 @default.
• W2213884683 hasAuthorship W2213884683A5031537463 @default.
• W2213884683 hasAuthorship W2213884683A5036583707 @default.
• W2213884683 hasAuthorship W2213884683A5038191637 @default.
• W2213884683 hasAuthorship W2213884683A5047509474 @default.
• W2213884683 hasAuthorship W2213884683A5065306642 @default.
• W2213884683 hasAuthorship W2213884683A5067100969 @default.
• W2213884683 hasAuthorship W2213884683A5071782757 @default.
• W2213884683 hasAuthorship W2213884683A5076621021 @default.
• W2213884683 hasAuthorship W2213884683A5090406453 @default.
• W2213884683 hasConcept C104317684 @default.
• W2213884683 hasConcept C11413529 @default.
• W2213884683 hasConcept C119054055 @default.
• W2213884683 hasConcept C120821319 @default.
• W2213884683 hasConcept C135763542 @default.
• W2213884683 hasConcept C141231307 @default.
• W2213884683 hasConcept C151020129 @default.
• W2213884683 hasConcept C153209595 @default.
• W2213884683 hasConcept C41008148 @default.
• W2213884683 hasConcept C51679486 @default.
• W2213884683 hasConcept C54355233 @default.
• W2213884683 hasConcept C552990157 @default.
• W2213884683 hasConcept C70721500 @default.
• W2213884683 hasConcept C86803240 @default.
• W2213884683 hasConceptScore W2213884683C104317684 @default.
• W2213884683 hasConceptScore W2213884683C11413529 @default.
• W2213884683 hasConceptScore W2213884683C119054055 @default.
• W2213884683 hasConceptScore W2213884683C120821319 @default.
• W2213884683 hasConceptScore W2213884683C135763542 @default.
• W2213884683 hasConceptScore W2213884683C141231307 @default.
• W2213884683 hasConceptScore W2213884683C151020129 @default.
• W2213884683 hasConceptScore W2213884683C153209595 @default.
• W2213884683 hasConceptScore W2213884683C41008148 @default.
• W2213884683 hasConceptScore W2213884683C51679486 @default.
• W2213884683 hasConceptScore W2213884683C54355233 @default.
• W2213884683 hasConceptScore W2213884683C552990157 @default.
• W2213884683 hasConceptScore W2213884683C70721500 @default.
• W2213884683 hasConceptScore W2213884683C86803240 @default.
• W2213884683 hasLocation W22138846831 @default.
• W2213884683 hasOpenAccess W2213884683 @default.
• W2213884683 hasPrimaryLocation W22138846831 @default.
• W2213884683 hasRelatedWork W15252283 @default.
• W2213884683 hasRelatedWork W19712847 @default.
• W2213884683 hasRelatedWork W26902028 @default.
• W2213884683 hasRelatedWork W280975 @default.
• W2213884683 hasRelatedWork W31698777 @default.
• W2213884683 hasRelatedWork W32785519 @default.
• W2213884683 hasRelatedWork W35060346 @default.
• W2213884683 hasRelatedWork W35565104 @default.
• W2213884683 hasRelatedWork W4270845 @default.
• W2213884683 hasRelatedWork W9476816 @default.
• W2213884683 isParatext "false" @default.
• W2213884683 isRetracted "false" @default.
• W2213884683 magId "2213884683" @default.
• W2213884683 workType "article" @default.