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Relevant bibliographies by topics / Low-frequency variant detection

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Academic literature on the topic 'Low-frequency variant detection'

Author: Grafiati

Published: 4 June 2021

Last updated: 14 February 2022

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Journal articles on the topic "Low-frequency variant detection"

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Hermann, Bernd Timo, Sebastian Pfeil, Nicole Groenke, et al. "DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants." Genes 12, no. 4 (2021): 507. http://dx.doi.org/10.3390/genes12040507.

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Detection of genetic variants in clinically relevant genomic hot-spot regions has become a promising application of next-generation sequencing technology in precision oncology. Effective personalized diagnostics requires the detection of variants with often very low frequencies. This can be achieved by targeted, short-read sequencing that provides high sequencing depths. However, rare genetic variants can contain crucial information for early cancer detection and subsequent treatment success, an inevitable level of background noise usually limits the accuracy of low frequency variant calling a

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Ura, Hiroki, Sumihito Togi, and Yo Niida. "Dual Deep Sequencing Improves the Accuracy of Low-Frequency Somatic Mutation Detection in Cancer Gene Panel Testing." International Journal of Molecular Sciences 21, no. 10 (2020): 3530. http://dx.doi.org/10.3390/ijms21103530.

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Cancer gene panel testing requires accurate detection of somatic mosaic mutations, as the test sample consists of a mixture of cancer cells and normal cells; each minor clone in the tumor also has different somatic mutations. Several studies have shown that the different types of software used for variant calling for next generation sequencing (NGS) can detect low-frequency somatic mutations. However, the accuracy of these somatic variant callers is unknown. We performed cancer gene panel testing in duplicate experiments using three different high-fidelity DNA polymerases in pre-capture amplif

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Weng, Li, Lin Wang, Xiao Chen, et al. "Detecting ultra low-frequency variants and gene fusions in lung cancer patients using an amplicon-based Firefly NGS method." Journal of Clinical Oncology 35, no. 15_suppl (2017): e23062-e23062. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e23062.

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e23062 Background: The analysis of EGFR, KRAS, and BRAF mutations and Alk fusion is critical for guiding targeted therapy selection, detecting drug resistance, and monitoring residual disease in patients with NSCLC. Designing next-generation sequencing (NGS) assays for detecting low-frequency variants, however, is an ongoing challenge. The limited availability of cfDNA combined with the breadth of coverage necessary to create meaningful, clinically-actionable results requires a solution with multiplex capacity which, in turn, requires greater technological sensitivity and specificity. Here we

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Sater, Vincent, Pierre-Julien Viailly, Thierry Lecroq, et al. "UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries." Bioinformatics 36, no. 9 (2020): 2718–24. http://dx.doi.org/10.1093/bioinformatics/btaa053.

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Abstract Motivation Next-generation sequencing has become the go-to standard method for the detection of single-nucleotide variants in tumor cells. The use of such technologies requires a PCR amplification step and a sequencing step, steps in which artifacts are introduced at very low frequencies. These artifacts are often confused with true low-frequency variants that can be found in tumor cells and cell-free DNA. The recent use of unique molecular identifiers (UMI) in targeted sequencing protocols has offered a trustworthy approach to filter out artefactual variants and accurately call low-f

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JARVI, S. I., M. E. FARIAS, D. A. LAPOINTE, M. BELCAID, and C. T. ATKINSON. "Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands." Parasitology 140, no. 14 (2013): 1741–50. http://dx.doi.org/10.1017/s0031182013000905.

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SUMMARYNext-generation 454 sequencing techniques were used to re-examine diversity of mitochondrial cytochrome b lineages of avian malaria (Plasmodium relictum) in Hawaii. We document a minimum of 23 variant lineages of the parasite based on single nucleotide transitional changes, in addition to the previously reported single lineage (GRW4). A new, publicly available portal (Integroomer) was developed for initial parsing of 454 datasets. Mean variant prevalence and frequency was higher in low elevation Hawaii Amakihi (Hemignathus virens) with Avipoxvirus-like lesions (P = 0·001), suggesting th

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Chien, Richard, Dumitru Brinza, Jian Gu, et al. "Comprehensive detection of ctDNA variants at 0.1% allelic frequency using a broad targeted NGS panel for liquid biopsy research." Journal of Clinical Oncology 35, no. 15_suppl (2017): e23065-e23065. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e23065.

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e23065 Background: Advances in non-invasive tumor biomarker research have shown that tumor cells release fragments of DNA called circulating tumor DNA (ctDNA) into peripheral blood. Somatic mutations representing the tumors could be successfully detected from isolated ctDNA, providing new potential for tumor sample assessment in addition to traditional tissue biopsy methods. However, the low amount of ctDNA in the blood, which can be less than 1% allelic frequency, presents significant challenges for reliable variant detection with NGS assays. Improvement of sequencing accuracy at low allelic

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Watson, Simon J., Matthijs R. A. Welkers, Daniel P. Depledge, et al. "Viral population analysis and minority-variant detection using short read next-generation sequencing." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1614 (2013): 20120205. http://dx.doi.org/10.1098/rstb.2012.0205.

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RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency. Here, we report

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Huang, Jiaqi, Johannes-Matthias Löhr, Magnus Nilsson, et al. "Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma." Clinical Chemistry 61, no. 11 (2015): 1408–16. http://dx.doi.org/10.1373/clinchem.2015.238543.

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Abstract BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. Variant profiling is crucial for developing personalized treatment and elucidating the etiology of this disease. METHODS Patients with PDAC undergoing surgery from 2007 to 2012 (n = 73) were followed from diagnosis until death or the end of the study. We applied an anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) method to a panel of 65 selected genes and assessed analytical performance by sequencing a quantitative multiplex DNA reference standard. In clinical PDAC samples, detection of low-lev

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Verbist, Bie M. P., Kim Thys, Joke Reumers, et al. "VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering." Bioinformatics 31, no. 1 (2014): 94–101. http://dx.doi.org/10.1093/bioinformatics/btu587.

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Underhill, Hunter, David Nix, Christian Davidson, et al. "COMP-10. THE MUTATIONAL PROFILE OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA REPRESENTS A DISTINCT SUBSET OF THE SOMATIC MUTATIONS PRESENT IN GLIOBLASTOMA SOLID TUMOR DNA." Neuro-Oncology 21, Supplement_6 (2019): vi63. http://dx.doi.org/10.1093/neuonc/noz175.253.

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Abstract Glioblastoma’s mutational landscape varies widely in the same tumor. Using conventional criteria to identify mutations from a focal tissue specimen (e.g., variant allele frequency > 5%) undersamples glioblastoma’s broad clonal diversity, which may limit detection of glioblastoma-derived circulating cell-free DNA in plasma (i.e., circulating tumor DNA; ctDNA). Here, we sought to enhance somatic variant identification in solid tumor DNA to improve detection and characterize glioblastoma-derived ctDNA. Tumor DNA and plasma cell-free DNA (collected < 24 hours prior to the surgical p

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Dissertations / Theses on the topic "Low-frequency variant detection"

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Craig, Daniel John. "Low Frequency Airway Epithelial Cell Mutation Pattern Associated with Lung Cancer Risk." University of Toledo Health Science Campus / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=mco1556918218571742.

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He, Karen Yingyi. "DETECTING LOW FREQUENCY AND RARE VARIANTS ASSOCIATED WITH BLOOD PRESSURE." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case157435735160471.

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Conference papers on the topic "Low-frequency variant detection"

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Lenhart, Justin S., Ashley Wood, Sukhinder Sandhu, et al. "Abstract 5391: Low frequency variant detection and tissue-of-origin exploration using liquid biopsies." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5391.

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Wood, Ashley, Sukhinder Sandhu, Mida Pezeshkian, et al. "Abstract 2230: Low frequency variant detection in cell free DNA by applying molecular identifiers to targeted NGS." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-2230.

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Jones, Wendell, Joshua Xu, and Binsheng Gong. "Abstract 445: A validated genomic reference material with known content applicable to panel assays requiring low frequency variant allele detection." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-445.

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Jones, Wendell, Joshua Xu, and Binsheng Gong. "Abstract 445: A validated genomic reference material with known content applicable to panel assays requiring low frequency variant allele detection." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-445.

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Lee, Lucie S., Yang Lily Liu, Kathryn Pendleton, et al. "Abstract 3533: Low-frequency variant detection in cell-free DNA by integrating double-stranded unique molecular identifiers with ultrafast amplicon-based library preparations." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3533.

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Lee, Lucie S., Yang Lily Liu, Kathryn Pendleton, et al. "Abstract 3533: Low-frequency variant detection in cell-free DNA by integrating double-stranded unique molecular identifiers with ultrafast amplicon-based library preparations." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3533.

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Alugongo, Alfayo Anyika, and Josiah Lange Munda. "A Kineto-Static Model for a Cracked Shaft Flexible Bearing System With Linear-Angular Coupled DOF in Bending." In ASME/STLE 2007 International Joint Tribology Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/ijtc2007-44435.

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In this paper, a model for vibration of a cracked rotor shaft flexible bearing system with linear-angular coupled DOF in bending is proposed. A vector approach on the change of the system’s angular momentum at a steady state has been used to derive the equation of motion leading to a linear time-variant system. By considering the forces and moments in the kinematic pairs of the shaft and bearing, an equivalent coupled 4-DOF complex spring is analytically introduced to simulate the system at a low rotating speed with the crack as an external force. Consequently, the Kineto-static response has b

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Royall, Ariel, Ushati Das Chakravarty, Katharine Dilger, et al. "Abstract 3520: Detection of low-frequency variants in highly degraded DNA and RNA samples." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3520.

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Baybayan, Primo, and Laura Nolden. "Abstract 5366: Detection of low-frequency somatic variants using single-molecule, real-time sequencing." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5366.

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Royall, Ariel, Ushati Das Chakravarty, Katharine Dilger, et al. "Abstract 3520: Detection of low-frequency variants in highly degraded DNA and RNA samples." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3520.

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