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Relevant bibliographies by topics / Genotypability, targeted resequencing, variant calling

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Journal articles
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Academic literature on the topic 'Genotypability, targeted resequencing, variant calling'

Author: Grafiati

Published: 11 March 2023

Last updated: 31 July 2025

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Journal articles on the topic "Genotypability, targeted resequencing, variant calling"

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Chen, Li. "Concurrent targeted resequencing for translocations and mutations in tumor samples." Journal of Clinical Oncology 37, no. 15_suppl (2019): e14597-e14597. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e14597.

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e14597 Background: Genetic variations are diverse, and proper nucleic acid templates should be analyzed for optimal outcomes. Previous NGS assays separately treat DNA and/or RNA, and are costly and produce limited information. Here we present a concurrent assay simultaneously converting both RNA and DNA templates in a single-tube format to streamline variant detection process. Methods: We developed a high-throughput targeted resequencing assay utilizing both DNA and RNA templates for mutation and fusion detection, and applied to a cohort of over 1000 lung tumor samples. Total nucleic acids fro

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Tozaki, Teruaki, Aoi Ohnuma, Kotono Nakamura, et al. "Detection of Indiscriminate Genetic Manipulation in Thoroughbred Racehorses by Targeted Resequencing for Gene-Doping Control." Genes 13, no. 9 (2022): 1589. http://dx.doi.org/10.3390/genes13091589.

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The creation of genetically modified horses is prohibited in horse racing as it falls under the banner of gene doping. In this study, we developed a test to detect gene editing based on amplicon sequencing using next-generation sequencing (NGS). We designed 1012 amplicons to target 52 genes (481 exons) and 147 single-nucleotide variants (SNVs). NGS analyses showed that 97.7% of the targeted exons were sequenced to sufficient coverage (depth > 50) for calling variants. The targets of artificial editing were defined as homozygous alternative (HomoALT) and compound heterozygous alternative (AL

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Royo, Carolina, Pablo Carbonell-Bejerano, Rafael Torres-Pérez, et al. "Is aromatic terpenoid composition of grapes in Northwestern Iberian wine cultivars related to variation in VviDXS1 gene?" Journal of Berry Research 11, no. 2 (2021): 187–200. http://dx.doi.org/10.3233/jbr-200609.

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BACKGROUND: Monoterpenes and C13-norisoprenoids are key terpenoid compounds for wine aroma. The enzyme encoded by VviDXS1 participates in terpenoid biosynthesis in grapevine fruits and gain-of-function mutations in this gene lead to characteristic muscat aroma. OBJECTIVE: To assess for VviDXS1 contribution to aroma variation in Northwestern Iberian wine cultivars, we resequenced this gene in 111 cultivars and compared grape juice terpenic composition in 12 of them. METHODS: VviDXS1 was capture-targeted for resequencing with Illumina paired-end reads, SAMtools was used for variant calling and g

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Das, Reena, Manu Jamwal, Prashant Sharma, et al. "Genetic Spectrum of Inherited/Congenital Hemolytic Anemias in Indian Patients." Blood 138, Supplement 1 (2021): 4151. http://dx.doi.org/10.1182/blood-2021-154452.

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Abstract Introduction Hemolytic anemias are a group of disorders caused by the premature destruction of red blood cells with reticulocytosis. Common causes of inherited/congenital hemolysis are hemoglobinopathies and thalassemia syndromes, red blood cell membrane, and enzyme disorders. Most of the common causes (thalassemia, glucose-6-phosphate dehydrogenase (G6PD) deficiency, hereditary spherocytosis, etc.) are diagnosed based on laboratory testing; however, for remaining causes laboratory tests are either inaccessible or cumbersome. We follow a stepwise diagnostic pipeline and red cell morph

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Herold, Sylvia, Thoralf Stange, Matthias Kuhn, et al. "Targeted Resequencing of MLL-PTD Positive AML Patients Reveals a High Prevalence of Co-Ocurring Mutations in Epigenetic Regulator Genes." Blood 124, no. 21 (2014): 1035. http://dx.doi.org/10.1182/blood.v124.21.1035.1035.

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Abstract Background Partial tandem duplication mutations of the Mixed Lineage Leukemia gene (MLL-PTD) can be found in about 10% of patients with AML, especially in patients with normal karyotype AML. The mutation generates a self-fusion within the N-terminal part of MLL and has been shown to be leukemogenic in mouse models. In patients, the presence of the mutation is associated with poor prognosis. Little is known on the molecular profile of patients with MLL-PTD and on the cooperating mutations. In order to identify accompanying molecular alterations, we performed whole exome sequencing (WES

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Clifford, Ruth M., Pauline Robbe, Susanne Weller, et al. "Towards Response Prediction Using Integrated Genomics in Chronic Lymphocytic Leukaemia: Results on 250 First-Line FCR Treated Patients from UK Clinical Trials." Blood 124, no. 21 (2014): 1942. http://dx.doi.org/10.1182/blood.v124.21.1942.1942.

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Abstract Background: Major progress has been made in understanding disease biology and therapeutic options for patients with chronic lymphocytic leukaemia (CLL). Recurrent mutations have been discovered using next generation sequencing, but with the exception of TP53 disruption their potential impact on response to treatment is unknown. In order to address this question, we characterised the genomic landscape of 250 first-line chemo-immunotherapy treated CLL patients within UK clinical trials using targeted resequencing and whole-genome SNP array. Methods: We studied patients from two UK-based

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Hamblin, Angela, Adam Burns, Christopher Tham, et al. "Development and Evaluation of the Clinical Utility of a Next Generation Sequencing (NGS) Tool for Myeloid Disorders." Blood 124, no. 21 (2014): 2373. http://dx.doi.org/10.1182/blood.v124.21.2373.2373.

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Abstract Background Historically diagnosis and prognosis of myeloid disorders including acute myeloid leukemia (AML) have been determined using a combination of morphology, immunophenotype, cytogenetic and more recently single gene, if not single mutation, analysis. The introduction of NGS technology has resulted in an explosion in the quantity of mutation data available. However, the feasibility and utility of NGS technology with regards to decision-making in routine clinical practice of myeloid disorders is currently unknown. We therefore developed an advanced NGS tool for simultaneous asses

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Natarajan, Srikrupa N., Samdani Ansar, Sarangapani Sripriya, et al. "Whole-exome sequencing and molecular dynamics confirm pathogenicity of a novel SLC6A6 mutation in Leber congenital amaurosis." Egyptian Journal of Medical Human Genetics 26, no. 1 (2025). https://doi.org/10.1186/s43042-025-00659-x.

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Abstract Introduction Inherited retinal diseases (IRDs) are a clinically and genetically heterogenous group where the robust advancement of next-generation sequencing technologies has facilitated genotype-assisted diagnosis. Leber congenital amaurosis (LCA) is a severe form of inherited retinal dystrophy that causes congenital blindness or near-blindness with a global prevalence of 3 per 100,000 live births.It is characterized by a loss of vision at birth or within the first few years of life with overlapping phenotypes to many syndromic and non-syndromic IRDs. With India's rich genetic hetero

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Dissertations / Theses on the topic "Genotypability, targeted resequencing, variant calling"

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Iadarola, Barbara. "Enhanced genotypability for a more accurate variant calling in targeted resequencing." Doctoral thesis, 2020. http://hdl.handle.net/11562/1019475.

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The analysis of Next-Generation Sequencing (NGS) data for the identification of DNA genetic variants presents several bioinformatics challenges. The main requirements of the analysis are the accuracy and the reproducibility of results, as their clinical interpretation may be influenced by many variables, from the sample processing to the adopted bioinformatics algorithms. Targeted resequencing, which aim is the enrichment of genomic regions to identify genetic variants possibly associated to clinical diseases, bases the quality of its data on the depth and uniformity of coverage, for the diffe

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