FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2499125003> ?p ?o ?g. }

• W2499125003 abstract "Cancer is a genetic disease, caused by a variety of alterations to a cell9s genome. One specific type of alteration associated with cancer is point mutations, and Next-generation sequencing (NGS) is a key tool to identify those mutations. Unlike inherited mutations, cancer mutations can be found at very low frequencies, mainly because of tumor heterogeneity and their dilution in the germline background. Cell-free DNA (cfDNA) derived from blood plasma, is a promising material for cancer research and diagnosis, and can be readily obtained via non-invasive procedures. However, the amount of tumor DNA and, hence, the amount of rare allele in the cfDNA are typically very low. Sensitive methods are therefore needed for the detection of somatic, cancer-associated mutations in cfDNA isolated from liquid biopsies to support both discovery and clinical decision making in oncology. To overcome these challenges, we developed at Rubicon Genomics an NGS library preparation kit, namely ThruPLEX® Plasma-seq, optimized specifically for cfDNA at input levels from less than 1 ng to 30 ng. We designed experiments to determine the lower limit of SNV detection under these assay conditions. Six individual ThruPLEX® Plasma-seq libraries generated from 10 ng cfDNA were enriched with the Agilent SureSelect XT2 reagents and ClearSeq Comprehensive Cancer panel (151 genes). After sequencing to >500X coverage, SNP calling was performed using Agilent SureCall software to identify the SNPs specific to each sample. In a second step, the cfDNA isolated from two of these plasma samples with known SNP differences were mixed to generate various spike-in frequencies (10%, 5%, 2% and 0.5%) prior to preparing libraries and enrichment. This is to simulate low allele frequency, and to determine the sensitivity of ThruPLEX® Plasma-seq under the outlined assay conditions. Our results showed that it was possible to detect specific alleles down to an actual 0.6% with the theoretical 0.5% spike-in ratio. The percent of on­target bases was over 45%. The sensitivity (SNPs detected/total SNPs analyzed) of our test was above 97% for 10%, 5%, and 2% frequencies and 70% for 0.5%. This is a demonstration of ThruPLEX® Plasma-seq to produce libraries with high enough complexity to detect low frequency alleles from limited amounts of cfDNA from plasma. Citation Format: Kamran Shazand, Jing Ning, Anthony Popkie, Egon Ranghini, John Paul Jerome. High efficiency detection of low frequency alleles in cell-free DNA. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3621." @default.
• W2499125003 created "2016-08-23" @default.
• W2499125003 creator A5024179620 @default.
• W2499125003 creator A5039534118 @default.
• W2499125003 creator A5060527084 @default.
• W2499125003 creator A5060986600 @default.
• W2499125003 creator A5085085773 @default.
• W2499125003 date "2016-07-15" @default.
• W2499125003 modified "2023-09-26" @default.
• W2499125003 title "Abstract 3621: High efficiency detection of low frequency alleles in cell-free DNA" @default.
• W2499125003 doi "https://doi.org/10.1158/1538-7445.am2016-3621" @default.
• W2499125003 hasPublicationYear "2016" @default.
• W2499125003 type Work @default.
• W2499125003 sameAs 2499125003 @default.
• W2499125003 citedByCount "1" @default.
• W2499125003 countsByYear W24991250032017 @default.
• W2499125003 crossrefType "proceedings-article" @default.
• W2499125003 hasAuthorship W2499125003A5024179620 @default.
• W2499125003 hasAuthorship W2499125003A5039534118 @default.
• W2499125003 hasAuthorship W2499125003A5060527084 @default.
• W2499125003 hasAuthorship W2499125003A5060986600 @default.
• W2499125003 hasAuthorship W2499125003A5085085773 @default.
• W2499125003 hasConcept C104317684 @default.
• W2499125003 hasConcept C109825262 @default.
• W2499125003 hasConcept C121608353 @default.
• W2499125003 hasConcept C122060243 @default.
• W2499125003 hasConcept C134305767 @default.
• W2499125003 hasConcept C135763542 @default.
• W2499125003 hasConcept C139275648 @default.
• W2499125003 hasConcept C152110520 @default.
• W2499125003 hasConcept C153209595 @default.
• W2499125003 hasConcept C172680121 @default.
• W2499125003 hasConcept C176944494 @default.
• W2499125003 hasConcept C180754005 @default.
• W2499125003 hasConcept C2778258057 @default.
• W2499125003 hasConcept C2779234561 @default.
• W2499125003 hasConcept C37463918 @default.
• W2499125003 hasConcept C501734568 @default.
• W2499125003 hasConcept C502942594 @default.
• W2499125003 hasConcept C51679486 @default.
• W2499125003 hasConcept C54355233 @default.
• W2499125003 hasConcept C70721500 @default.
• W2499125003 hasConcept C86803240 @default.
• W2499125003 hasConceptScore W2499125003C104317684 @default.
• W2499125003 hasConceptScore W2499125003C109825262 @default.
• W2499125003 hasConceptScore W2499125003C121608353 @default.
• W2499125003 hasConceptScore W2499125003C122060243 @default.
• W2499125003 hasConceptScore W2499125003C134305767 @default.
• W2499125003 hasConceptScore W2499125003C135763542 @default.
• W2499125003 hasConceptScore W2499125003C139275648 @default.
• W2499125003 hasConceptScore W2499125003C152110520 @default.
• W2499125003 hasConceptScore W2499125003C153209595 @default.
• W2499125003 hasConceptScore W2499125003C172680121 @default.
• W2499125003 hasConceptScore W2499125003C176944494 @default.
• W2499125003 hasConceptScore W2499125003C180754005 @default.
• W2499125003 hasConceptScore W2499125003C2778258057 @default.
• W2499125003 hasConceptScore W2499125003C2779234561 @default.
• W2499125003 hasConceptScore W2499125003C37463918 @default.
• W2499125003 hasConceptScore W2499125003C501734568 @default.
• W2499125003 hasConceptScore W2499125003C502942594 @default.
• W2499125003 hasConceptScore W2499125003C51679486 @default.
• W2499125003 hasConceptScore W2499125003C54355233 @default.
• W2499125003 hasConceptScore W2499125003C70721500 @default.
• W2499125003 hasConceptScore W2499125003C86803240 @default.
• W2499125003 hasLocation W24991250031 @default.
• W2499125003 hasOpenAccess W2499125003 @default.
• W2499125003 hasPrimaryLocation W24991250031 @default.
• W2499125003 hasRelatedWork W2007354683 @default.
• W2499125003 hasRelatedWork W2056921347 @default.
• W2499125003 hasRelatedWork W2314049137 @default.
• W2499125003 hasRelatedWork W2316911875 @default.
• W2499125003 hasRelatedWork W2319396507 @default.
• W2499125003 hasRelatedWork W2492705823 @default.
• W2499125003 hasRelatedWork W2517179206 @default.
• W2499125003 hasRelatedWork W2565972295 @default.
• W2499125003 hasRelatedWork W2740645242 @default.
• W2499125003 hasRelatedWork W2766307464 @default.
• W2499125003 hasRelatedWork W2810019399 @default.
• W2499125003 hasRelatedWork W2810161687 @default.
• W2499125003 hasRelatedWork W2949756802 @default.
• W2499125003 hasRelatedWork W2956122548 @default.
• W2499125003 hasRelatedWork W2967120295 @default.
• W2499125003 hasRelatedWork W2981981106 @default.
• W2499125003 hasRelatedWork W3010827720 @default.
• W2499125003 hasRelatedWork W3083052685 @default.
• W2499125003 hasRelatedWork W3181559172 @default.
• W2499125003 hasRelatedWork W3182246477 @default.
• W2499125003 isParatext "false" @default.
• W2499125003 isRetracted "false" @default.
• W2499125003 magId "2499125003" @default.
• W2499125003 workType "article" @default.