FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4245490610> ?p ?o ?g. }

• W4245490610 endingPage "3526" @default.
• W4245490610 startingPage "3526" @default.
• W4245490610 abstract "Abstract Accurate analysis of quantitative NGS data is critical for low frequency variant detection, identification of differentially expressed transcripts, and correct diagnosis and patient care in a clinical NGS setting. Two major factors affecting sequencing accuracy are 1) PCR duplication arising from amplification of library molecules; and 2) errors introduced during library preparation and actual sequencing on the flow cell. Standard practice for identification and removal of PCR duplicates relies on aligning reads to the same genomic coordinates. However, this approach can not differentiate between PCR duplicates and reads originating from unique molecules with identical ends. The most effective method for error correction is Duplex Sequencing, which utilizes UMIs to tag both strands of each individual DNA duplex followed by building consensus sequences. Unfortunately, this approach is labor intensive and cost-prohibitive for complex genomes and large target panels. Therefore, a simple and reliable approach for duplicate removal and error correction would greatly facilitate the wider adoption of NGS technology for diagnostics and clinical applications. In this study, we incorporate UMIs into UDI systems and assess the effect on the accuracy of quantitative sequencing assays. We first study the effectiveness of various computational methods to account for UMIs and remove base-calling errors introduced during sequencing. We then analyze the utility of UMIs for 1) unique and low abundance transcript identification and accurate transcript quantification; and 2) error correction in low frequency variant detection in genomic sequencing from both high quality cell line DNA and low quality FFPE DNA. In addition, we demonstrate that combining unique dual sample indexing with UMI molecular barcoding further improves data analysis accuracy, especially on patterned flow cells. Our approach involves a simple new UMI-containing UDI adaptor design that can also be applied to other sequencing methods and platforms. Citation Format: Pingfang Liu, Keerthana Krishnan, Camille X. Devoe, Bradley W. Langhorst, Eileen Dimalanta, Theodore B. Davis. Incorporation of unique molecular identifiers (UMIs) into unique dual sample indexing (UDI) improves the accuracy of quantitative next generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3526." @default.
• W4245490610 created "2022-05-12" @default.
• W4245490610 creator A5011185767 @default.
• W4245490610 creator A5012180636 @default.
• W4245490610 creator A5018311228 @default.
• W4245490610 creator A5038504526 @default.
• W4245490610 creator A5038563448 @default.
• W4245490610 creator A5065981160 @default.
• W4245490610 date "2019-07-01" @default.
• W4245490610 modified "2023-09-22" @default.
• W4245490610 title "Abstract 3526: Incorporation of unique molecular identifiers (UMIs) into unique dual sample indexing (UDI) improves the accuracy of quantitative next generation sequencing" @default.
• W4245490610 doi "https://doi.org/10.1158/1538-7445.am2019-3526" @default.
• W4245490610 hasPublicationYear "2019" @default.
• W4245490610 type Work @default.
• W4245490610 citedByCount "0" @default.
• W4245490610 crossrefType "journal-article" @default.
• W4245490610 hasAuthorship W4245490610A5011185767 @default.
• W4245490610 hasAuthorship W4245490610A5012180636 @default.
• W4245490610 hasAuthorship W4245490610A5018311228 @default.
• W4245490610 hasAuthorship W4245490610A5038504526 @default.
• W4245490610 hasAuthorship W4245490610A5038563448 @default.
• W4245490610 hasAuthorship W4245490610A5065981160 @default.
• W4245490610 hasConcept C116834253 @default.
• W4245490610 hasConcept C124101348 @default.
• W4245490610 hasConcept C154504017 @default.
• W4245490610 hasConcept C199360897 @default.
• W4245490610 hasConcept C41008148 @default.
• W4245490610 hasConcept C51679486 @default.
• W4245490610 hasConcept C54355233 @default.
• W4245490610 hasConcept C552990157 @default.
• W4245490610 hasConcept C59822182 @default.
• W4245490610 hasConcept C70721500 @default.
• W4245490610 hasConcept C86803240 @default.
• W4245490610 hasConcept C99611785 @default.
• W4245490610 hasConceptScore W4245490610C116834253 @default.
• W4245490610 hasConceptScore W4245490610C124101348 @default.
• W4245490610 hasConceptScore W4245490610C154504017 @default.
• W4245490610 hasConceptScore W4245490610C199360897 @default.
• W4245490610 hasConceptScore W4245490610C41008148 @default.
• W4245490610 hasConceptScore W4245490610C51679486 @default.
• W4245490610 hasConceptScore W4245490610C54355233 @default.
• W4245490610 hasConceptScore W4245490610C552990157 @default.
• W4245490610 hasConceptScore W4245490610C59822182 @default.
• W4245490610 hasConceptScore W4245490610C70721500 @default.
• W4245490610 hasConceptScore W4245490610C86803240 @default.
• W4245490610 hasConceptScore W4245490610C99611785 @default.
• W4245490610 hasIssue "13_Supplement" @default.
• W4245490610 hasLocation W42454906101 @default.
• W4245490610 hasOpenAccess W4245490610 @default.
• W4245490610 hasPrimaryLocation W42454906101 @default.
• W4245490610 hasRelatedWork W1882848237 @default.
• W4245490610 hasRelatedWork W2032715459 @default.
• W4245490610 hasRelatedWork W2316776327 @default.
• W4245490610 hasRelatedWork W2328387788 @default.
• W4245490610 hasRelatedWork W2390777183 @default.
• W4245490610 hasRelatedWork W2911510094 @default.
• W4245490610 hasRelatedWork W4211043580 @default.
• W4245490610 hasRelatedWork W4247174507 @default.
• W4245490610 hasRelatedWork W4252772812 @default.
• W4245490610 hasRelatedWork W4384829521 @default.
• W4245490610 hasVolume "79" @default.
• W4245490610 isParatext "false" @default.
• W4245490610 isRetracted "false" @default.
• W4245490610 workType "article" @default.