Academic literature on the topic 'Targeted gene panels'
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Journal articles on the topic "Targeted gene panels"
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Kanygina, A. V., E. I. Sharova, R. I. Sultanov, Y. A. Schelygin, Y. V. Doludin, E. S. Kostryukova, and E. V. Generozov. "Targeted gene sequencing panels: applicability for neoantigen profiling of colon and rectal adenocarcinoma." Biomeditsinskaya Khimiya 64, no. 6 (2018): 517–24. http://dx.doi.org/10.18097/pbmc20186406517.
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Cancer immunotherapy represents a promising and rapidly developing approach for the treatment of oncological diseases. Among the methods of personalized adjuvant immunotherapy, neoantigenic peptide-based drugs have demonstrated substantial efficiency. These drugs are designed to target mutant proteins arising from somatic alterations in the genome of tumor cells and thus stimulate immune response against tumor tissues. The methods of individual screening for potentially immunogenic mutations are mostly based on next-generation exome sequencing of tumor samples, which is a complex and costly procedure for clinical application. Targeted gene sequencing panels limited to a certain set of genes represent a reasonable alternative to WES. Targeted sequencing is also more efficient when there is a low amount of the sample DNA available. We have estimated the potential efficiency of targeted oncological panels in terms of somatic neoantigen profiling in colorectal cancer (colon and rectal adenocarcinoma). The clinical practice of identification of frequent somatic variants does not provide enough data for designing an efficient personalized drug when applied to low and medium mutated cancers such as colorectal cancer. Our analysis of 11 commercially available panels containing different number of genes has shown that neither the larger size of a panel nor its initial customization for colorectal cancer provides a significantly better estimation of an individual somatic mutation profile. The optimal approach is to use the general-purpose medium-sized cancer panels (2300-11200 amplicons and/or 150-600 genes). These panels allow to detect a sufficient number of immunogenic epitopes (>3) per patient for over 30-50% of patients.
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Romanov, Dmitriy, and Nikolai Skoblikow. "Linkage Disequilibrium in Targeted Sequencing." Mathematical Biology and Bioinformatics 17, no. 2 (November 22, 2022): 325–37. http://dx.doi.org/10.17537/2022.17.325.
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We propose an approach for optimizing the development of gene diagnostic panels, which is based on the construction of non-equilibrium linkage maps. In the process of gene selection we essentially use genome-wide association analysis (GWAS). Whole-genome analysis of associations makes it possible to reveal the relationship of genomic variants with the studied phenotype. However, the nucleotide variants that showed the highest degree of association can only be statistically associated with the phenotype, not being the true cause of the phenotype. In this case, they may be in the block of linked inheritance with nucleotide variants that really affect the manifestation of the phenotype. The construction of maps of non-equilibrium linkage of nucleotides makes it possible to optimally determine the boundaries of linkage blocks, in which the desired variants fall. The aim of this study was to optimize the demarcation of genomic loci to create targeted panels aimed at predicting susceptibility to SARS-CoV-2 and the severity of COVID-19. The proposed method for selecting loci for a target panel, taking into account nonequilibrium linkage, makes it possible to use the phenomenon of nonequilibrium linkage in order to maximally cover the regions involved in the development of the phenotype, while simultaneously minimizing the length of these regions, and, at the same time, the cost of sequencing.
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Santani, Avni, Jill Murrell, Birgit Funke, Zhenming Yu, Madhuri Hegde, Rong Mao, Andrea Ferreira-Gonzalez, Karl V. Voelkerding, and Karen E. Weck. "Development and Validation of Targeted Next-Generation Sequencing Panels for Detection of Germline Variants in Inherited Diseases." Archives of Pathology & Laboratory Medicine 141, no. 6 (March 21, 2017): 787–97. http://dx.doi.org/10.5858/arpa.2016-0517-ra.
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Context.— The number of targeted next-generation sequencing (NGS) panels for genetic diseases offered by clinical laboratories is rapidly increasing. Before an NGS-based test is implemented in a clinical laboratory, appropriate validation studies are needed to determine the performance characteristics of the test. Objective.— To provide examples of assay design and validation of targeted NGS gene panels for the detection of germline variants associated with inherited disorders. Data Sources.— The approaches used by 2 clinical laboratories for the development and validation of targeted NGS gene panels are described. Important design and validation considerations are examined. Conclusions.— Clinical laboratories must validate performance specifications of each test prior to implementation. Test design specifications and validation data are provided, outlining important steps in validation of targeted NGS panels by clinical diagnostic laboratories.
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Bhattacharya, Arjun, Alina M. Hamilton, Melissa A. Troester, and Michael I. Love. "DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing." Nucleic Acids Research 49, no. 8 (February 1, 2021): e48-e48. http://dx.doi.org/10.1093/nar/gkab031.
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Abstract Targeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we present DeCompress, a semi-reference-free deconvolution method for targeted panels. DeCompress leverages a reference RNA-seq or microarray dataset from similar tissue to expand the feature space of targeted panels using compressed sensing. Ensemble reference-free deconvolution is performed on this artificially expanded dataset to estimate cell-type proportions and gene signatures. In simulated mixtures, four public cell line mixtures, and a targeted panel (1199 samples; 406 genes) from the Carolina Breast Cancer Study, DeCompress recapitulates cell-type proportions with less error than reference-free methods and finds biologically relevant compartments. We integrate compartment estimates into cis-eQTL mapping in breast cancer, identifying a tumor-specific cis-eQTL for CCR3 (C–C Motif Chemokine Receptor 3) at a risk locus. DeCompress improves upon reference-free methods without requiring expression profiles from pure cell populations, with applications in genomic analyses and clinical settings.
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Adeboyeje, Gboyega, Eleanor O. Caplan, Yihua Xu, Monica Chase, Sheetal Sheth, Brandon T. Suehs, and Nicole Myer. "Abstract 4111: Trends in the use of broad genomic sequencing-directed therapy among Medicare patients with newly diagnosed advanced cancer in the United States from 2018-2020: A retrospective analysis from the SEQUENCE study." Cancer Research 82, no. 12_Supplement (June 15, 2022): 4111. http://dx.doi.org/10.1158/1538-7445.am2022-4111.
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Abstract Introduction/Purpose: Recent advances have led to approval of multiple new targeted drugs across a variety of indications based on genomic markers. In part due to the increasing number of therapeutically actionable genomic markers in many cancers, whether a strategy of upfront broad next-generation sequencing (NGS) could potentially improve selection of patients for targeted drugs compared to narrow/single gene panels remains uncertain. We examined recent trends in the proportions of patients receiving sequencing-directed therapy following the use of broad NGS panel testing among newly diagnosed patients with advanced cancer in the United States (US). Methods: Using a retrospective cohort study design to analyze administrative claims data on patients (65-89 years) enrolled in a national US payer Medicare Advantage plans from 2018 through 2020, we identified patients with select incident advanced/metastatic cancer diagnoses (lung, colorectal [CRC], breast, ovarian) based on previously validated algorithms. We defined 2 cohorts by the occurrence of broad NGS (51+ genes) versus narrow (≤50 genes) sequencing within 182 days of diagnosis using a previously validated algorithm based on laboratory tax identification numbers, current procedural terminology codes, and diagnosis codes. We described the rates of sequencing-directed therapy (defined as receipt of an FDA-approved genomically targeted drug) within 90 days of testing by broad NGS versus narrow panels across tumor types and subgroups defined by race (White versus Black) and annual income (<$50,000 versus ≥$50,000) data. Results: We identified 32,130 patients with incident advanced cancer during the study period. Overall (broad plus narrow panels) testing rates varied by cancer type (lung, 40.1%; CRC 28.6%; breast 53.9%; ovarian 41.7%). Compared to narrow gene panels, a higher proportion of patients with lung and ovarian cancer sequenced with broad NGS panels initiated an FDA-approved genomically targeted drug within 90 days of testing (lung: 8.6% versus 7.5%; ovarian: 9.2% versus 5.5%). For CRC and breast cancer, narrow gene panels matched a higher proportion of patients with targeted drug within 90 days of testing versus broad NGS panel testing (CRC: 5.1 versus 4.5%; breast: 41.7% versus 35.7%). Conclusions: A higher proportion of patients initiated a genomically-targeted drug after broad NGS panel testing compared with narrow gene panels in lung and ovarian cancer. As the number of actionable genomic markers in advanced cancers increase, it will be important to ensure that this technology is adopted to improve upon the existing standard of care and that aligns with values important to patients. Citation Format: Gboyega Adeboyeje, Eleanor O. Caplan, Yihua Xu, Monica Chase, Sheetal Sheth, Brandon T. Suehs, Nicole Myer. Trends in the use of broad genomic sequencing-directed therapy among Medicare patients with newly diagnosed advanced cancer in the United States from 2018-2020: A retrospective analysis from the SEQUENCE study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4111.
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Bevins, Nicholas, Shulei Sun, Zied Gaieb, John A. Thorson, and Sarah S. Murray. "Comparison of commonly used solid tumor targeted gene sequencing panels for estimating tumor mutation burden shows analytical and prognostic concordance within the cancer genome atlas cohort." Journal for ImmunoTherapy of Cancer 8, no. 1 (March 2020): e000613. http://dx.doi.org/10.1136/jitc-2020-000613.
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BackgroundTumor mutation burden (TMB) is a biomarker frequently reported by clinical laboratories, which is derived by quantifying of the number of single nucleotide or indel variants (mutations) identified by next-generation sequencing of tumors. TMB values can inform prognosis or predict the response of a patient’s tumor to immune checkpoint inhibitor therapy. Methods for the calculation of TMB are not standardized between laboratories, with significant variables being the gene content of the panels sequenced and the inclusion or exclusion of synonymous variants in the calculations. The impact of these methodological differences has not been investigated and the concordance of reported TMB values between laboratories is unknown.MethodsSequence variant lists from more than 9000 tumors of various types were downloaded from The Cancer Genome Atlas. Variant lists were filtered to include only appropriate variant types (ie, non-synonymous only or synonymous and non-synonymous variants) within the genes found in five commonly used targeted solid tumor gene panels as well as an in-house gene panel. Calculated TMB was paired with corresponding overall survival (OS) data of each patient.ResultsRegression analysis indicates high concordance of TMB as derived from the examined panels. TMB derived from panels was consistently and significantly lower than that derived from a whole exome. TMB, as derived from whole exome or the examined panels, showed a significant correlation with OS in the examined data.ConclusionsTMB derived from the examined gene panels was analytically equivalent between panels, but not between panels and whole-exome sequencing. Correlation between TMB and OS is significant if TMB method-specific cut-offs are used. These results suggest that TMB values, as derived from the gene panels examined, are analytically and prognostically equivalent.
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Gierman, Hinco J., Nikhil Pai, Casey Catasus, Alvin Tam, Monica Labrador, Joseph Donaldson, Mallika Singaraju, et al. "A retrospective three-year analysis using real-world data on uptake of broad-based NextGen sequencing panels in community oncology practices." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): e13668-e13668. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13668.
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e13668 Background: There are over 100 FDA approved targeted therapies across 15 cancer types, offering improved outcomes over existing therapies. However, many of these require genetic testing, for example, advanced non-small cell lung cancer (aNSCLC) patients have over 15 targeted therapies requiring a DNA-based test. Doing multiple tests can exhaust sample, while increasing cost and turn-around time. NGS panels, often with hundreds of genes, can address some of these issues. Here we asked across aNSCLC patients if the use of NGS panels has increased over the last 3 years in community oncology practices. Methods: The Integra Connect database, which includes electronic medical record (EMR) and claims data on over 1,000,000 US cancer patients, was queried across five community oncology practices to identify aNSCLC patients (stage IIIB or IV) treated between January 2017 and January 2020. Manual chart review abstracted tumor type, stage, treatment, and testing. Patients tested for all 7 NCCN recommended genes (EGFR, ALK, ROS1, BRAF, MET, RET, ERBB2) were grouped as “NGS Panel”, patients with less genes as “Single Gene/Small Panel”, and patients with no evidence of testing as “No Test”. A Chi-Square test was used to compare actionable results between patients with NGS panels versus small panels. Results: 1,007 aNSCLC patients were analyzed and showed a doubling of the use of broad-based NGS testing from 13% in 2017 to 26% in 2019 across over 100 oncologists (table). 23% of patients had actionable results when tested on broad-based panels versus 17% using single gene or small panels (p = .048). Targeted therapies were used in 17% of broad-based tested patients, versus 15% in patients tested for single genes or small panels. Conclusions: We see an uptake of broad-based NGS testing in community oncology, which can lead to more actionable results and better utilization of targeted therapies for those patients. However, this seems to be caused by providers shifting from small panels to large panels, rather than an overall increase in testing, as we do not see the percentage of untested patients decrease. [Table: see text]
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Bansal, Nidhanjali, Hye-Won Song, Silin Sa, Woodrow E. Lomas, Gisele V. Baracho, Ian Taylor, Stephanie Widmann, and Stefanie Mortimer. "Single cell whole transcriptome analysis of disease cells to generate a targeted RNA-sequencing gene panel for the simultaneous analysis of targeted mRNA and protein." Journal of Immunology 202, no. 1_Supplement (May 1, 2019): 131.35. http://dx.doi.org/10.4049/jimmunol.202.supp.131.35.
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Abstract Single cell RNA-sequencing (scRNA-seq) is a powerful tool for understanding the sample heterogeneity of individual cells. Many methods rely on whole transcriptome analysis (WTA) to get a snapshot of the entire cellular landscape. Although WTA analysis can be used to discover novel biomarkers, this technique can be expensive. To enable scaling of experiments, WTA data can be mined to design targeted gene panels. To showcase this, we used single cell sequencing to examine thousands of B cells isolated from the bone marrow and peripheral blood of chronic lymphocytic leukemia (CLL) and healthy donors. B cells that had been sorted using the BD FACSMelody™ cell sorter were multiplexed using the BD™ Human Single-Cell Multiplexing Kit and pooled before being processed on the BD Rhapsody™ system, thereby minimizing batch effects. The resulting data was mined to design a panel of differentially expressed genes between CLL and healthy B cells that could be used for subsequent CLL phenotyping. By combining this panel with the BD Rhapsody™ Immune Response Panel (together comprising ~500 mRNAs), along with 36 DNA-barcoded BD™ AbSeq antibodies, we were able to simultaneously analyze mRNA and protein targets from a new subset of CLL and healthy B cells for additional high-resolution analysis. This study showcases the power of using WTA data to design specific gene panels that can be used alone or in combination with existing targeted panels for routine and cost-effective transcriptional profiling at a single cell level. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo, FACSMelody, and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.
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Wilson, Parker C., Latisha Love-Gregory, Meagan Corliss, Samantha McNulty, Jonathan W. Heusel, and Joseph P. Gaut. "Beyond Panel-Based Testing: Exome Analysis Increases Sensitivity for Diagnosis of Genetic Kidney Disease." Kidney360 1, no. 8 (May 13, 2020): 772–80. http://dx.doi.org/10.34067/kid.0001342020.
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BackgroundNext-generation sequencing (NGS) is a useful tool for evaluating patients with suspected genetic kidney disease. Clinical practice relies on the use of targeted gene panels that are ordered based on patient presentation. We compare the diagnostic yield of clinical panel-based testing to exome analysis.MethodsIn total, 324 consecutive patients underwent physician-ordered, panel-based NGS testing between December 2014 and October 2018. Gene panels were available for four clinical phenotypes, including atypical hemolytic uremic syndrome (n=224), nephrotic syndrome (n=56), cystic kidney disease (n=26), and Alport syndrome (n=13). Variants were analyzed and clinical reports were signed out by a pathologist or clinical geneticist at the time of testing. Subsequently, all patients underwent retrospective exome analysis to detect additional clinically significant variants in kidney disease genes that were not analyzed as part of the initial clinical gene panel. Resulting variants were classified according to the American College of Medical Genetics and Genomics 2015 guidelines.ResultsIn the initial physician-ordered gene panels, we identified clinically significant pathogenic or likely pathogenic variants in 13% of patients (n=42/324). CFHR3-CFHR1 homozygous deletion was detected in an additional 13 patients with aHUS without a pathogenic or likely pathogenic variant. Diagnostic yield of the initial physician-ordered gene panel was 20% and varied between groups. Retrospective exome analysis identified 18 patients with a previously unknown pathogenic or likely pathogenic variant in a kidney disease gene and eight patients with a high-risk APOL1 genotype. Overall, retrospective exome analysis increased the diagnostic yield of panel-based testing from 20% to 30%.ConclusionsThese results highlight the importance of a broad and collaborative approach between the clinical laboratory and their physician clients that employs additional analysis when a targeted panel of kidney disease–causing genes does not return a clinically meaningful result.
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Barbosa-Gouveia, Sofia, María E. Vázquez-Mosquera, Emiliano González-Vioque, José V. Álvarez, Roi Chans, Francisco Laranjeira, Esmeralda Martins, Ana Cristina Ferreira, Alejandro Avila-Alvarez, and María L. Couce. "Utility of Gene Panels for the Diagnosis of Inborn Errors of Metabolism in a Metabolic Reference Center." Genes 12, no. 8 (August 19, 2021): 1262. http://dx.doi.org/10.3390/genes12081262.
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Next-generation sequencing (NGS) technologies have been proposed as a first-line test for the diagnosis of inborn errors of metabolism (IEM), a group of genetically heterogeneous disorders with overlapping or nonspecific phenotypes. Over a 3-year period, we prospectively analyzed 311 pediatric patients with a suspected IEM using four targeted gene panels. The rate of positive diagnosis was 61.86% for intermediary metabolism defects, 32.84% for complex molecular defects, 19% for hypoglycemic/hyperglycemic events, and 17% for mitochondrial diseases, and a conclusive molecular diagnosis was established in 2–4 weeks. Forty-one patients for whom negative results were obtained with the mitochondrial diseases panel underwent subsequent analyses using the NeuroSeq panel, which groups all genes from the individual panels together with genes associated with neurological disorders (1870 genes in total). This achieved a diagnostic rate of 32%. We next evaluated the utility of a tool, Phenomizer, for differential diagnosis, and established a correlation between phenotype and molecular findings in 39.3% of patients. Finally, we evaluated the mutational architecture of the genes analyzed by determining z-scores, loss-of-function observed/expected upper bound fraction (LOEUF), and haploinsufficiency (HI) scores. In summary, targeted gene panels for specific groups of IEMs enabled rapid and effective diagnosis, which is critical for the therapeutic management of IEM patients.
Dissertations / Theses on the topic "Targeted gene panels"
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GROSSI, ALICE. "Development of a diagnostic protocol, mutation search, and genotype-phenotype correlation in haematological and immunological diseases by targeted resequencing using three different gene panels." Doctoral thesis, Università degli studi di Genova, 2019. http://hdl.handle.net/11567/945312.
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Introduction: Next Generation Sequencing (NGS) has driven the rapid increase in the number of recognizable inborn errors of immune system development and/or function often hampered by the wide heterogeneity of the many genetically diverse but phenotypically overlapping diseases. NGS has also led to the discovery of new genes implicated in well-defined biological pathways, revisiting frequencies and broadening their phenotypic spectrum.
Objectives: Identification of the genetic causes of already known and unknown immune-mediated diseases with immunedysregulation; improvement of our knowledge about clinically overlapping phenotypes through the genetic characterization of the corresponding patients; optimization of the diagnostic work-up in order to administer disease specific treatments to patients.
Methods: A total of 150 patients, selected based on a clinical history highly evocative for immune-dysregulation (peripheral and/or central cytopenia and/or lymphoprolipheration and/or autoimmunity or autoinflammation) and/or immunodeficiency were submitted to 3 custom gene panels of 146, 315 and 58 genes and sequenced through the Ion Personal Genome Machine (PGM™) System. Based on
the clinical phenotype, frequency and impact on the protein, variants were selected and validate by standard Sanger sequencing.
Results: The mutation detection rates for these panels were 15/51 (29%), and 16/69 (23%) and 2/30 (6%), respectively, for a total of 35 pathogenic variants that correlate with the respective clinical phenotypes. The patients could be classified in: ALPS/ALPS-like (97, 26 of which diagnosed), cytopenia (33, 4 diagnosed), undefined autoinfiammatory (12, 2 diagnosed) and suspected immunodeficiency (8, 1 diagnosed). Moreover, variants of unknown significance (VUS) in potentially causative genes were also found in additional 14 patients (6/30; 4/51; 4/69). A number of variants, either pathogenic, likely pathogenic, or VUS have been detected in some cases at genes unexpected on the basis of the phenotypes, among which PRKCD, PIK3CD, IL7R, NCF1, TNFRSF13C, CASP8, thus confirming wide heterogeneity in the phenotypic spectrum associated with diseases sharing haemato-immune rheumatological features. Conversely, several clinically similar cases did not reveal any relevant mutation, thus reflecting a genetic heterogeneity that is far from being disclosed yet.
Conclusion: The NGS approach has demonstrated excellent performances in the 1) evaluation of large genes and mutation detection, 2) overall timeliness of the gene panels, relying on continuous literature updates, and 3) identification of unexpected phenotypes for well-defined monogenic disease and definition of different disease clinical entities characterized by overlapping phenotypes. By contrast, due to the remarkable variability in clinical presentations, defining the appropriate list of genes for a given phenotype represents one key difficulty in the design of these panels. In the near future we will have to focus on the functional study of the many variants, especially VUS, that have emerged in a massive study like ours
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Karim, S. Q. "Development of a targeted next-generation sequencing gene panel to investigate recurrent mutations in chronic lymphocytic leukaemia." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3004906/.
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Chronic lymphocytic leukaemia (CLL) is a mono-clonal B-cell malignancy characterised by heterogeneous clinical course and response to treatment. Recent studies with whole genome or whole exome sequencing have identified novel recurrent genomic lesions, and associated them with adverse clinical outcome of this disease. Owing to their limited sensitivity, the true incidence of these mutations, subclonal complexity and evolution and their roles in disease progression and treatment resistance are still not quite clear. To gain insight into these issues, I developed a highly sensitive (with an average coverage depth being 2250x and the lowest limit of detection 1%) and robust next generation sequencing (NGS) test using HaloPlex and Ion Torrent PGM to target exons of 15 recurrently mutated genes including TP53, ATM, SF3B1, PCLO, NOTCH1, LRP1B, SAMHD1, FBXW7, BIRC3, HISTIH1E, XPO1, CHD2, MYD88, POT1 and ZFPM2 in CLL. In the initial study using this technique, samples from a cohort of 32 cases with progressive and/or therapy resistant CLL before (n = 10) or after chemotherapy (n = 22) were screened. 87.5% of the patients were found to carry at least one somatic non-synonymous mutation in the first 12 targeted genes (VAF: 2-98%). The most commonly mutated genes were SF3B1, ATM, TP53 and PCLO identified in 11, 10, 9 and 8 cases, respectively. Mutations in TP53 and its upstream regulator ATM appeared to be dominant over other concurrent gene mutations compared to other genes (P = 0.011). Combining NGS and global SNP array analyses revealed a significant association between genomic aberrations in the ATM-p53 pathway and genomic instability. Moreover, prior exposure to DNA-damaging chemotherapy was associated with the bigger numbers of mutation events and mutated genes, although the increases were borderline significant. These results suggest that ATM-p53 pathway defects contribute to the acquisition of additional genomic aberrations and that treatment with DNA-damaging chemotherapy may play a role in the induction or selection of mutations. In the subsequent longitudinal study of 33 additional samples of 23 mutated cases from the same cohort, I showed the existence of different mutational processes operative in CLL including mutations related to AID, ageing and other factors. I confirmed the significant contribution of AID-related mutations to CLL clonal evolution, implying on-going activity of this enzyme in off-target genes. In addition, I demonstrated the predominance of a linear path of clonal evolution in this cohort. Thus, 89.3% of the mutated clones/subclones identified at advanced disease stages were detectable at time of diagnosis or prior to treatment. Hence, the early detection of these mutations may potentially serve as predictive biomarkers to inform on therapeutic decisions. I also documented convergent clonal evolution with priori-selection of clones carrying deleterious mutations in 2 target genes including ATM and TP53. This observation suggests that not all the mutations in the same gene play an equal role in disease progression and/or treatment resistance. Analysis of mutation doubling time revealed that driver mutations, including those in TP53, BIRC3, NOTCH1 and SF3B1, were significantly correlated with faster evolution as indicated by the shorter doubling time of variant allele frequency. Importantly, I found that increased subclonal sizes were strongly associated with shorter treatment-free survival in patients with driver mutations. Taken together, the results from this thesis have provided strong evidence emphasising the importance and usefulness of applying the ultra-sensitive NGS test in the early detection and subsequent monitoring of these recurrent somatic mutations in CLL. A translational study based on findings in this thesis is now ongoing, with an aim to convert this test into a regional clinical service.
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Leão, Delva Pereira. "Sequenciamento de nova geração : explorando aplicações clínicas de dados de Targeted Gene Panel e Whole Exome Sequencing." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2017. http://hdl.handle.net/10183/173625.
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A tecnologia de sequenciamento de nova geração (next-generation sequencing – NGS) e suas aplicações tem sido cada vez mais utilizada na prática médica para elucidar a base molecular de doenças Mendelianas. Embora seja uma poderosa ferramenta de pesquisa, ainda existe uma importante transição quanto à análise dos dados entre as tecnologias tradicionais de sequenciamento e o NGS. A primeira parte deste trabalho aborda aspectos analíticos envolvidos nesta mudança, com foco na plataforma Ion Torrent Personal Genome Machine. Esta é uma plataforma amplamente utilizada para sequenciar painéis de genes, já que esta aplicação requer menor rendimento de dados. Este trabalho demonstra indicadores adequados para avaliar a qualidade de corridas de sequenciamento e também uma estratégia baseada em valores de profundidade de cobertura para avaliar a performance de amplicons em diferentes cenários. Por outro lado, o NGS permitiu a realização de estudos populacionais em larga escala que estão mudando nossa compreensão sobre as variações genéticas humanas. Um desses exemplos são as mutações até então chamadas de silenciosas, que estão sendo implicadas como causadoras de doenças humanas. A segunda parte deste trabalho investiga a patogenicidade de polimorfismos de núcleotídeo único sinônimos (synonymous single nucleotide polymorphisms – sSNP) baseado em dados públicos obtidos do Exome Aggregation Consortium (ExAC) (exac.broadinstitute.org/) utilizando o software Silent Variant Analysis (SilVA) (compbio.cs.toronto.edu/silva/) e outros recursos para reunir informações adicionais sobre consequências funcionais visando fornecer um panorama dos efeitos patogênicos de sSNP em mais de 60.000 exomas humanos. Nós demonstramos que de 1,691,045 variantes sinônimas, um total de 26,034 foram classificadas como patogênicas pelo SilVA, com frequência alélica menor que 0,05. Análises funcionais in silico revelaram que as variantes sinônimas patogênicas estão envolvidas em processos biológicos importantes, como regulação celular, metabolismo e transporte. Ao expor um cenário de variações sinônimas patogênicas em exomas humanos, nós concluímos que filtrar sSNP em workflows de priorização é razoável, no entanto em situações específicas os sSNP podem ser considerados. Pesquisas futuras neste campo poderão fornecer uma imagem clara do papel de tais variações em doenças genéticas.Next-generation sequencing (NGS) technologies and its applications are increasingly used in medicine to elucidate the molecular basis of Mendelian diseases. Although it is a powerful research tool, there is still an important transition regarding data analysis between traditional sequencing techniques and NGS. The first part of this work addresses analytical aspects involved on this switch-over, focusing on the Ion Torrent Personal Genome Machine platform. This is a widely used platform for sequencing gene panels, as this application demands lower throughput of data. We present indicators suitable to evaluate quality of sequencing runs and also a strategy based on depth of coverage values to evaluate amplicon performance on different scenarios. On the other hand, NGS enabled large-scale population studies that are changing our understanding about human genetic variations. One of these examples are the so-called silent mutations, that are being implied as causative of human diseases. The second part of this work investigates the pathogenicity of synonymous single nucleotide polymorphisms (sSNP) based on public data obtained from the Exome Aggregation Consortium (ExAC) (exac.broadinstitute.org/) using the software Silent Variant Analysis (SilVA) (compbio.cs.toronto.edu/silva/) and other sources to gather additional information about affected protein domains, mRNA folding and functional consequences aiming to provide a landscape of harmfulness of sSNP on more than 60,000 human exomes. We show that from 1,691,045 synonymous variants a total of 26,034 were classified as pathogenic and by SilVA, with allele frequency lower than 0.05. In silico functional analysis revealed that pathogenic synonymous variants found are involved in important biological process, such as cellular regulation, metabolism and transport. By exposing a scenario of pathogenic synonymous variants on human exomes we conclude that filtering out sSNP on prioritization workflows is reasonable, although in some specific cases sSNP should be considered. Future research on this field will provide a clear picture of such variations on genetic diseases.
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Brajadenta, Gara Samara. "Development of a functional assay for CHD7, a protein involved in CHARGE syndrome." Thesis, Poitiers, 2019. http://www.theses.fr/2019POIT1401/document.
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Le syndrome CHARGE (CS) est une maladie génétique rare caractérisée par de nombreuses anomalies congénitales, majoritairement causées par des altérations de novo du gène CHD7. Celui-ci code pour une protéine à chromodomaines, impliquée dans le remodelage ATP-dépendant de la chromatine. La grande majorité des altérations de CHD7 consiste en allèles nuls tels que des délétions, des substitutions non-sens ou des décalages du cadre de lecture. Nous avons réalisé le premier diagnostic moléculaire d’un patient Indonésien atteint du CS, en étudiant un panel de gènes (CHD7, EFTUD2, et HOXA1) par NGS (next-generation sequencing). Nous avons identifié une nouvelle mutation non-sens hétérozygote dans l’exon 34 du gène CHD7 (c.7234G>T ou p.Glu2412Ter). Par ailleurs, il n'existe pas d’analyse fonctionnelle qui permettrait de caractériser la pathogénicité des variants de la protéine CHD7 rencontrés chez des patients. C’est pourquoi l’objectif de ce travail est de mettre au point un test fonctionnel de la protéine CHD7, sous forme sauvage ou mutée. Pour cela, nous avons généré par mutagénèse dirigée des vecteurs codant pour trois variants faux-sens de CHD7 et le variant présentant une insertion de cinq acides aminés. Ensuite, les protéines CHD7, sous forme sauvage ou variante, ont été surexprimées dans la lignée HeLa. L’expression des protéines a été mise en évidence par western blot et par immunofluorescence. Pour étudier la fonctionnalité de CHD7, nous avons quantifié par RT-qPCR les transcrits de cinq gènes (l’ADNr 45S, SOX4, SOX10, MYRF, et ID2), dont la transcription est selon le littérature régulée par CHD7. Nous avons observé que l’expression de CHD7 sauvage entraînait une diminution significative et reproductible des quantités de transcrits correspondant à tous les gènes rapporteurs. Par contre, l’expression des quatre allèles variants de CHD7 n’avait aucun impact, ce qui suggère que ces variants ne sont pas fonctionnels. Par ailleurs, nous avons appliqué notre test biologique dans des cellules de la lignée SH-SY5Y, pour lesquelles nous avons introduit une mutation faux-sens dans le génome en utilisant la technique CRISPR/Cas9. Lorsque ce variant était exprimé, les niveaux de transcription des cinq gènes rapporteurs n’étaient pas significativement différents de ceux observés dans les cellules où les deux allèles de CHD7 avaient été invalidés. Par conséquent, les variants étudiés peuvent être répertoriés comme résultant de mutations causales du CSCHARGE syndrome (CS) is a rare genetic disease characterized by numerous congenital abnormalities, mainly caused by de novo alterations of the CHD7 gene. It encodes a chromodomain protein, involved in the ATP-dependent remodeling of chromatin. The vast majority of CHD7 alterations consists in null alleles like deletions, non-sense substitutions or frameshift-causing variations. We report the first molecular diagnosis of an Indonesian CS patient by a targeted NGS (next-generation sequencing) gene panel (CHD7, EFTUD2, and HOXA1). We identified a novel heterozygous nonsense mutation in exon 34 of CHD7 (c.7234G>T or p.Glu2412Ter). Functional analyses to confirm the pathogenicity of CHD7 variants are lacking and urgently needed. Therefore, the aim of this study was to establish a functional test for wild-type (WT) or variants of CHD7 protein found in CS patients. Using an expression vector encoding CHD7, three variants harboring an amino acid substitution and one variant with a five-amino acid insertion were generated via site-directed mutagenesis. Then CHD7 proteins, either wild-type (WT) or variants, were overexpressed in HeLa cell line. Protein expression was highlighted by western blot and immunofluorescence. We then used real-time RT-PCR to study CHD7 functionality by evaluating the transcript amounts of five genes whose expression is regulated by CHD7 according to the literature. These reporter genes are 45S rDNA, SOX4, SOX10, ID2, and MYRF. We observed that, upon WT-CHD7 expression, the reporter gene transcriptions were downregulated, whereas the four variant alleles of CHD7 had no impact. This suggests that these alleles are not polymorphisms because the variant proteins appeared non-functional. Furthermore, we applied our biological assay in SH-SY5Y cell line in which endogenous CHD7 gene was mutated using the CRISPR/Cas9 technique. Then, we observed that when a CHD7 missense variant was expressed, the transcription levels of the five reporter genes were non-significantly different, compared with the cells in which both CHD7 alleles were knocked-out. Therefore, the studied variants can be considered as disease-causing of CS
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Cioppi, Francesca. "Genetic diagnostic yield of rare endocrine diseases through Next-Generation Sequencing: our-7-year experience based on targeted gene panels." Doctoral thesis, 2022. http://hdl.handle.net/2158/1263211.
Full textAbstract:
Currently, NGS-based genetic testing has become an indispensable component of the comprehensive diagnostic workup in rare endocrine diseases. For this reason, our clinical genetics laboratory has designed a custom NGS panel including all the known candidate and susceptibility genes for Congenital Hypogonadotropic Hypogonadism (CHH) and Pheochromocytoma/Paraganglioma (Pheo/PGL/HNPGL), respectively. In addition, the VHL mutational screening has been developed to diagnose the von Hippel-Lindau syndrome (VHL) in suspected cases. This study aimed to evaluate the diagnostic yield basedon genetic testing in the above-mentioned rare endocrine diseases. After the NGS sequencing, a comprehensive bioinformatic analysis of each variant was performed in order to evaluate their pathogenicity and genotype-phenotype correlations were examined. The first part of this thesis focused on CHH, which is a congenital disorder covering a widespectrum of signs/symptoms, from classical forms with absent puberty, including Kallmannsyndrome and other syndromic conditions, to milder forms with Adult-Onset Hypogonadism (AOH). To date more than 40 candidate genes have been identified in approximately 40-50% of cases with a genetic diagnosis of CHH. We have enrolled 26 affected patients, of whom 12 showed the classic forms of disease whereas 14 were AOH. The total genetic diagnostic yield of our NGS panel, including 34 candidate genes with strong/definitive clinical evidence, was 23%, with the highest diagnostic rate in classic forms (42%) and the lowest one in the AOH (7%). The majority of mutated genes are well knowncausative genes, with the exception of DMXL2, for which only a few familial cases have beendescribed so far. Interestingly, the unique case of AOH with a clear genetic diagnosis carriedan affected DMXL2 allele, which is responsible for a mild reproductive phenotype, according to the literature. Our finding contributes to elucidate the role of DMXL2 gene in the aetiology of CHH. The second part of this thesis focused on rare endocrine tumours. Among them, Pheo/PGL/HNPGL arise from neural crest cells and affect adrenal gland (Pheo) or extra-adrenal sites (PGL/HNPGL). More than 20 susceptibility genes have been reported to predispose to Pheo/PGL/HNPGL, with a diagnostic yield of approximately 30%. On the other hand, the VHL syndrome is a monogenic disorder arising from germline mutations in the VHL gene and involving multiple organs. All these conditions follow an autosomal mode of inheritance, with an incomplete and age-dependent penetrance related to the specific gene defect. We have enrolled 95 patients affected by Pheo/PGL/HNPGL and 8 suspected VHL cases. Concerning the former, our NGS panel containing 15 susceptibility genes revealed a genetic diagnostic yield of 20%, with the highest diagnostic rate in PGLs (33%) and the lowest one in Pheos (14%). The majority of mutated genes belongs to the SDHx family, in line with previous data. Interestingly, one Pheo patient carrying two germline defects in the SDHD and VHL genes received a diagnosis of VHL syndrome, thanks to the gene panel results. Regarding patients with suspected VHL, we diagnosed a “true” VHL syndrome in 25% of cases. This study highlights the power of genetic testing as a diagnostic tool with relevant implications in genetic counselling and clinical management of the mutation carriers. Based on our results, CHH patients should be well-characterized prior to genetic testing, as the presence of a disease-causing genotype is almost exclusively found in classic forms. Hence, the genotype of AOH patients seems to be different from those with CHH. In case of rare endocrine tumours, we confirmed that genetic testing is relevant for correct and early diagnosis, leading to a better prognosis and to an appropriate treatment, of both the patient and her/his family members through an active surveillance.
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Reis, Cláudia Alexandra Sousa. "Genetic hearing loss: GJB2 gene and a targeted-gene panel analysis." Master's thesis, 2020. https://hdl.handle.net/10216/128776.
Full textAbstract:
A hipoacusia neurossensorial (HNS) é a anomalia sensorial congénita mais comum, afetando aproximadamente 1 em cada 500-1000 recém-nascidos. É não sindrómica em 70% dos indivíduos, apresentando hereditariedade autossómica dominante em 15-20% dos casos, autossómica recessiva em 80%, ou ainda ligada ao cromossoma X ou mitocondrial numa minoria dos casos.
As mutações no gene GJB2 são responsáveis por mais de 50% dos casos de HNS não-sindrómica autossómica recessiva, em todo o mundo. Várias variantes deste gene têm sido descritas, sendo que a classificação quanto à patogenicidade é ainda controversa para muitas delas. O estudo da frequência das variantes nas populações (não doentes) é uma ferramenta importante para a classificação das mesmas. Por sua vez, o esclarecimento da patogenicidade das variantes assume cada vez mais um papel relevante e útil no aconselhamento genético familiar. Até à data, foi estimada a frequência na população portuguesa (não doente) de apenas duas mutações: Gly12Valfs*2 (35delG) e Met34Thr. Nesta dissertação, reportam-se as prevalências, numa amostra da população portuguesa, das variantes menos comuns do gene GJB2.
Embora as mutações no gene GJB2 sejam a principal causa de HNS não-sindrómica em todo o mundo, esta é uma doença geneticamente heterogénea, sendo que foram identificadas mutações em mais de 100 genes até à data. Neste contexto, estudos moleculares baseados na análise de um único gene podem ser ineficientes e mais caros. A sequenciação de nova geração permite a análise simultânea de múltiplos genes associados a uma determinada doença ou fenótipo. Esta tecnologia é já amplamente utilizada na investigação. Mais recentemente, surgiu a sua utilização como meio de diagnóstico. Como tal, torna-se necessário objetivar a sua utilidade diagnóstica quando aplicada a um contexto clínico. Nesta dissertação, avaliamos o valor da análise de um painel de genes por sequenciação de nova geração no diagnóstico das causas genéticas da hipoacusia numa amostra da população portuguesa.Sensorineural hearing (SNHL) loss is one the most common congenital sensory impairments, affecting approximately 1 in 500-1000 newborns. About 60% of early-onset hearing loss cases are due to genetic causes, of which 70% are non-syndromic. Nonsyndromic SNHL is inherited in an autosomal recessive trait in 80%, but it can also be transmitted in an autosomal dominant (15-20%), X-linked (2-3%) or mitochondrial (1%) patterns. Sequence variations at the GJB2 locus account for up to 50% of cases of nonsyndromic SNHL in several populations. Although the pathogenic role has been clearly established for several GJB2 sequence variations, it remains controversial for some less common variants. An important tool for the classification of their pathogenicity is the assessment of their frequency in a healthy population. It must be remembered that the elucidation of the pathogenic role of each variant is of paramount importance in a familial genetic counselling. To our knowledge, only two GJB2 variants have their prevalence in a Portuguese community sample estimated: Gly12Valfs*2 (35delG) and Met34Thr. In this dissertation, we report the prevalence of the less common variants of the GJB2 gene in a Portuguese sample. Despite the fact that GJB2 mutations are the main cause of nonsyndromic SNHL, more than 100 hearing loss related genes have been identified to date. The extreme genetic heterogeneity of SNHL makes genetic diagnosis based on gene-by-gene Sanger sequencing very laborious, expensive and time-consuming. As a technology of high throughput, next-generation sequencing (NGS), allows for the routine sequencing of a large number of genes per patient in a single, fast and cost-effective experiment. NGS technologies are already broadly used in the investigation setting. More recently, emerged its utilization as a diagnostic tool. Therefore, objectifying NGS diagnostic utility when applied to a clinical context is necessary. In this dissertation, we evaluate the diagnostic yield of NGS targeting a panel of several genes related to hearing loss in a Portuguese sample.
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Reis, Cláudia Alexandra Sousa. "Genetic hearing loss: GJB2 gene and a targeted-gene panel analysis." Dissertação, 2020. https://hdl.handle.net/10216/128776.
Full textAbstract:
A hipoacusia neurossensorial (HNS) é a anomalia sensorial congénita mais comum, afetando aproximadamente 1 em cada 500-1000 recém-nascidos. É não sindrómica em 70% dos indivíduos, apresentando hereditariedade autossómica dominante em 15-20% dos casos, autossómica recessiva em 80%, ou ainda ligada ao cromossoma X ou mitocondrial numa minoria dos casos.
As mutações no gene GJB2 são responsáveis por mais de 50% dos casos de HNS não-sindrómica autossómica recessiva, em todo o mundo. Várias variantes deste gene têm sido descritas, sendo que a classificação quanto à patogenicidade é ainda controversa para muitas delas. O estudo da frequência das variantes nas populações (não doentes) é uma ferramenta importante para a classificação das mesmas. Por sua vez, o esclarecimento da patogenicidade das variantes assume cada vez mais um papel relevante e útil no aconselhamento genético familiar. Até à data, foi estimada a frequência na população portuguesa (não doente) de apenas duas mutações: Gly12Valfs*2 (35delG) e Met34Thr. Nesta dissertação, reportam-se as prevalências, numa amostra da população portuguesa, das variantes menos comuns do gene GJB2.
Embora as mutações no gene GJB2 sejam a principal causa de HNS não-sindrómica em todo o mundo, esta é uma doença geneticamente heterogénea, sendo que foram identificadas mutações em mais de 100 genes até à data. Neste contexto, estudos moleculares baseados na análise de um único gene podem ser ineficientes e mais caros. A sequenciação de nova geração permite a análise simultânea de múltiplos genes associados a uma determinada doença ou fenótipo. Esta tecnologia é já amplamente utilizada na investigação. Mais recentemente, surgiu a sua utilização como meio de diagnóstico. Como tal, torna-se necessário objetivar a sua utilidade diagnóstica quando aplicada a um contexto clínico. Nesta dissertação, avaliamos o valor da análise de um painel de genes por sequenciação de nova geração no diagnóstico das causas genéticas da hipoacusia numa amostra da população portuguesa.Sensorineural hearing (SNHL) loss is one the most common congenital sensory impairments, affecting approximately 1 in 500-1000 newborns. About 60% of early-onset hearing loss cases are due to genetic causes, of which 70% are non-syndromic. Nonsyndromic SNHL is inherited in an autosomal recessive trait in 80%, but it can also be transmitted in an autosomal dominant (15-20%), X-linked (2-3%) or mitochondrial (1%) patterns. Sequence variations at the GJB2 locus account for up to 50% of cases of nonsyndromic SNHL in several populations. Although the pathogenic role has been clearly established for several GJB2 sequence variations, it remains controversial for some less common variants. An important tool for the classification of their pathogenicity is the assessment of their frequency in a healthy population. It must be remembered that the elucidation of the pathogenic role of each variant is of paramount importance in a familial genetic counselling. To our knowledge, only two GJB2 variants have their prevalence in a Portuguese community sample estimated: Gly12Valfs*2 (35delG) and Met34Thr. In this dissertation, we report the prevalence of the less common variants of the GJB2 gene in a Portuguese sample. Despite the fact that GJB2 mutations are the main cause of nonsyndromic SNHL, more than 100 hearing loss related genes have been identified to date. The extreme genetic heterogeneity of SNHL makes genetic diagnosis based on gene-by-gene Sanger sequencing very laborious, expensive and time-consuming. As a technology of high throughput, next-generation sequencing (NGS), allows for the routine sequencing of a large number of genes per patient in a single, fast and cost-effective experiment. NGS technologies are already broadly used in the investigation setting. More recently, emerged its utilization as a diagnostic tool. Therefore, objectifying NGS diagnostic utility when applied to a clinical context is necessary. In this dissertation, we evaluate the diagnostic yield of NGS targeting a panel of several genes related to hearing loss in a Portuguese sample.
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Galatolo, Daniele. "An integrated, next-generation approach to identify new genes and new pathways in hereditary ataxias." Doctoral thesis, 2020. http://hdl.handle.net/2158/1188709.
Full textAbstract:
The Hereditary ataxias (HAs) are a group of heterogenous neurological disorders associated with multiple genetic etiologies and encompassing a wide spectrum of phenotypes, where ataxia is the prominent feature. HAs are characterized by degeneration of Purkinje cell and/or spinocerebellar connections, often associated with defects in additional brain structures, and all patterns of inheritance may occur. Similar to other fields of medical genetics, Next Generation Sequencing (NGS) has entered the HA scenario widening our genetic and clinical knowledge of this condition, but routine NGS applications still miss genetic diagnosis in about two third of patients.
In this doctoral study, we applied multi-gene panels to define the molecular basis in 259 patients with a clinical diagnosis of HA and negative to tests for pathological expansion in SCA1, 2, 3, 6, 7, 8, 12, 17 and FXN. We found a positive molecular diagnosis in 25% of patients, whereas a similar number of patients had an uncertain diagnosis due to the presence of either variants of uncertain significance or lack of biological samples to determine segregation among family members. Hence despite a higher positive diagnostic rate compared to similar studies described in literature, a half of patients lacked any indication of the genetic cause of their disease. Using exome sequencing as a second-tier approach in some families, refractory to multi-gene panel analysis, did not significantly improved our diagnostic yield. On the other hand, NGS analysis in our cohort indicated that familial cases were more easily diagnosed rather than sporadic cases, and also that combining massive sequencing with detailed clinical information and family studies increases the likelihood to reach a molecular diagnosis. Among positive patients, we could expand clinical and allelic information in a subgroup of genes offering original description of new mutations and corroborating genetic findings with functional investigations that took advantage of different in vitro or in vivo platforms. In particular, through functional studies in SPG7 knock-down models of Drosophila melanogaster, we remarked that SPG7, whose mutations cause spastic paraplegia type 7, has a critical role in neurons more than in skeletal muscle. The high frequency of p.Ala510Val mutation in SPG7 observed in our cohort as well in similar studies performed elsewhere moved us to develop a humanized knock-in fruit fly model harboring that specific mutation and prepare preliminary characterizations. Similar studies in fruit fly were performed silencing AFG3L2, the gene causing SPAX5 in a child in association with an unusual, relatively milder phenotype. Furthermore, combination of skin fibroblasts and Saccharomyces cerevisiae as models was employed in the genetic characterization of new mutations in a novel recessive HARS-related phenotype whereas primary human cells, yeast and Danio rerio models were used to functionally characterize new HA-related mutations in COQ4. Finally, we could expand the clinical presentation of rare causes of HAs describing new dominant mutations in STUB1 and biallelic variants in RFN216, COQ8A, and ATP13A2.
Altogether, studies performed during this doctoral work further underlined the usefulness of NGS in HAs and highlighted how NGS technologies rely on the integrated use of family and clinical studies and different in vitro/in vivo platforms to substantiate molecular findings. The latter platform will be also a tool for future investigations to dissect pathogenesis and to improve therapies.
Book chapters on the topic "Targeted gene panels"
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Clark, Robin D., and Cynthia J. Curry. "Hypotonia." In Genetic Consultations in the Newborn, edited by Robin D. Clark and Cynthia J. Curry, 3–10. Oxford University Press, 2019. http://dx.doi.org/10.1093/med/9780199990993.003.0001.
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This chapter reviews the incidence, risk factors, genetics, recurrence risk, and epidemiology of the multiple disorders causing congenital hypotonia. The differential diagnosis of various types of hypotonic syndromes includes chromosome anomalies, metabolic myopathies, peroxisomal disorders, brain malformations, congenital lower motor neuron diseases, hypoxic ischemic encephalopathy, congenital disorders of glycosylation, and multiple congenital anomaly single gene syndromes such as Kabuki syndrome and Bohring-Opitz syndrome. Recommendations for evaluation and management include discussion of key neurologic findings in the physical exam, biochemical and other laboratory screening, targeted single gene testing, panels for clinically heterogeneous disorders and exome sequencing. The clinical consult features an infant with congenital myotonic dystrophy.
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"Targeted Hotspot Gene Panel Table." In Diagnostic Pathology: Molecular Oncology, 4–22. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-323-37678-5.50048-7.
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"Targeted Hotspot Gene Panel Using Massively Parallel Sequencing (Next Generation Sequencing)." In Diagnostic Pathology: Molecular Oncology, 4–20. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-323-37678-5.50047-5.
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Clark, Robin D., and Cynthia J. Curry. "Intrauterine Growth Restriction." In Genetic Consultations in the Newborn, edited by Robin D. Clark and Cynthia J. Curry, 11–16. Oxford University Press, 2019. http://dx.doi.org/10.1093/med/9780199990993.003.0002.
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This chapter reviews isolated and syndromic intrauterine growth restriction (IUGR) or small for gestational age infants. The differential diagnosis of intrauterine growth restriction includes placental, maternal, and fetal causes. Maternal causes of IUGR include exposure to teratogens, various maternal illnesses, and multiple gestation. Infant causes include congenital infection, chromosomal aneuploidy, and multiple syndromes including primordial dwarfism. Other causes include genomic imprinting errors (Russell Silver syndrome and IMAGe syndrome) and endocrine and metabolic causes, the lipodystrophies, and skeletal dysplasias including SHOX deficiency. The evaluation of IUGR usually includes a SNP microarray and often targeted or gene panel testing. A clinical case presentation features an infant with Majewski (microcephalic) osteodysplastic primordial dwarfism (MOPD II) .
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Holt, Jon Patrick. "Type Five and Beyond." In Exploring Comics and Graphic Novels in the Classroom, 46–63. IGI Global, 2022. http://dx.doi.org/10.4018/978-1-6684-4313-2.ch003.
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Great is the need now for structure in comics-studies pedagogy, especially for Japanese manga, given the growth of comics-studies and pop-culture programs at North American colleges. Although teaching manga can be supported using any number of English-based texts, instructors will want to explore target-culture resources, such as those by Natsume, Yomota, and other Japanologists. Texts specific to Japan can improve student comprehension and interpretation of manga. The author describes methods of teaching manga using comparative analysis resources from their Japanese culture classroom. Based on experiences there, they show the use the ideas of Japanese scholars for formal analysis in order to enhance discussions of the manga page, including topics of panels, onomatopoeia, and genre conventions. American comics heavily stress sequentiality, but manga use pages, panels, and words differently to emphasize mood. By preparing for the manga classroom differently, we can offer our students tools specific to expand discussions of Japanese culture.
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Flament, Martine F., and Philippe Robaey. "Obsessive–compulsive disorder and tics in children and adolescents." In New Oxford Textbook of Psychiatry, 1680–93. Oxford University Press, 2012. http://dx.doi.org/10.1093/med/9780199696758.003.0219.
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Paediatric OCD is the disorder, in child psychiatry, whose clinical picture most closely resembles its adult counterpart. Despite a relative diversity, the symptom pool is remarkably finite, and very similar to that seen in older individuals. Prevalence, comorbidity, and response to behavioural and drug treatment also appear similar across the lifespan. For tic disorders, there is continuity between child and adult presentations, but the disease is much more prone to resolve spontaneously, or to be less disruptive in adulthood. Both OCD and tics occur more often in males than in females, and are likely to be linked to an array of neurobiological abnormalities, many of which remain to be understood. Invaluable benefits can now be obtained from available behavioural and pharmacological treatments, but complete remission remains uncertain and long-term management may be required. Thus, the treatment of OCD and tics in children and adolescents remains a clinical challenge. It requires careful assessment of the targeted symptoms and, in many cases, comorbidity; attention to the quality of the child's functioning at home and with peers; use of specific CBT interventions, which are not readily available (or accessible) in all communities; patience and caution in the choice and adjustment of medication; and vigilance in watching potential side effects. Given the possible chronicity of OCD and/or tic disorders, and their changing patterns in severity and impact over the childhood and adolescent years, optimal treatment generally requires a long-term ongoing relationship with the child and family. Current conceptualizations of OCD and tic disorders have been shaped by advances in systems neuroscience and functional in vivo neuroimaging. Continued success in these areas should lead to the targetting of specific brain circuits for more intensive research. This should include testing novel pharmacological agents, tracking treatment response using neuroimaging techniques, and possibly investigating circuit-based therapies using deep-brain stimulation for refractory cases. The identification of the PANDAS subgroup of patients, with an abrupt onset and dramatic exacerbations, certainly brings new insights into the pathophysiology of OCD and tic disorders, and may lead to new assessment and treatment strategies. The increasing evidence for susceptibility genes in OCD and tic disorders will also doubtless point to new therapeutic directions. Furthermore, it is likely that many of the empirical findings used in research on paediatric OCD and tic disorders will be relevant to a better understanding of both normal development, and other disorders of childhood onset.
Conference papers on the topic "Targeted gene panels"
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Barry, Andrew John, Kruti M. Patel, Amy B. Emerman, Scott Adams, Sarah Bowman, Evan Mauceli, Fiona Stewart, et al. "Abstract 3416: Customizable gene panels overcome challenges associated with targeted resequencing." 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.am2018-3416.
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Spayd, Katherine J., Irina Vasenkova, Tatiana Shvetsova, Randall C. Bachmeyer, Richard M. Myers, D. Troy Moore, and Katherine E. Varley. "Abstract LB-412: TargetRich™ cancer gene panels: targeted next generation sequencing in cancer samples." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-lb-412.
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Kermani, Bahram G., Evans L. Roberts, Theresa A. Boyle, and Anthony M. Magliocco. "Abstract 4280: Improving the sensitivity of wide targeted cancer gene panels via novel genome analysis tools." 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.am2018-4280.
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Helman, Elena, Michael James Clark, Sean Boyle, Richard Chen, Shujun Luo, Christian Haudenschild, Jason Harris, Gabor Bartha, Deanna Church, and John West. "Abstract A2-39: Augmented targeted NGS in cancer diagnostics: Comparing gene panels and whole exome sequencing for accurate detection of driver mutations." In Abstracts: AACR Special Conference: Translation of the Cancer Genome; February 7-9, 2015; San Francisco, CA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.transcagen-a2-39.
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Sjöström, M., J. Staaf, P. Edén, F. Wärnberg, J. Bergh, P. Malmström, M. Fernö, E. Niméus, and I. Fredriksson. "Abstract P4-09-08: A targeted breast cancer radiosensitivity gene expression panel." In Abstracts: 2017 San Antonio Breast Cancer Symposium; December 5-9, 2017; San Antonio, Texas. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.sabcs17-p4-09-08.
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Pankov, Aleksandr, Yongming Sun, Yuan-Chieh Ku, Warren Tom, Jianping Zheng, Timothy Looney, Janice Au-Yong, Fiona Hyland, and Ann Mongan. "Abstract B17: Validation of targeted gene expression profiling panel for identifying biomarker signatures of immunotherapy responders." In Abstracts: AACR Special Conference on Tumor Immunology and Immunotherapy; October 20-23, 2016; Boston, MA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/2326-6074.tumimm16-b17.
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Carvalho, Tamyres MIngorance, Tayana Schultz Jukoski, Guillermo Ortiz Brasil, Flavia Kuroda, and Enilze M. S. F. Ribeiro. "EXPRESSION OF miRNAS SUGGESTS A POTENTIAL ROLE IN BREAST CANCER." In Scientifc papers of XXIII Brazilian Breast Congress - 2021. Mastology, 2021. http://dx.doi.org/10.29289/259453942021v31s1050.
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Introduction: MicroRNAs (miRNAs) are regulators of gene expression in biological processes, mainly repressing translation or degrading messenger RNA (mRNA) from their target genes. Their deregulation is associated with a wide variety of diseases, including cancer. Breast cancer (BC) is the most common cancer among women worldwide. Understanding the mechanisms involved in this pathology is essential for the discovery of new diagnostic and prognostic markers. Objectives: Investigate the differential expression of selected miRNAs in luminal A (LA) and triple-negative breast cancer (TNBC). Methods: We evaluated the expression of miR-320a, miR-4433b-5p, miR-142-5p, and miR-150-5p in 31 BC samples (19 LA and 12 TNBC) and 29 adjacent non-tumor breast cancer (NT). The miRNAs were selected after in silico study. RT-qPCR was the method of choice, using RNU48 as endogenous control, and the BT-474 cell line was used as a calibrator between plates. The 2−ΔΔCt method was used to estimate miRNA expression level. Individual receiver operating characteristic (ROC) curves were calculated based on RQ values to investigate the diagnostic value of miRNAs. Results: miR-142-5p, miR-150-5p, miR-320a, and miR-4433b-5p were downregulated in BC compared to NT samples. All studied miRNAs were able to discriminate between BC and NT samples with sensitivity and sensibility (AUC – Area under curve >0.7 and p <0.05). A panel including all miRNAs improved the AUC to identify TNBC patients compared to NT (AUC=0.9240, sensitivity 94.44%, specificity 100%). We found no difference comparing miRNAs between LA and TNBC BC subtypes. There was no association between expression levels and prognostic parameters (age, histological grade, size of the tumor, axillary lymph node status). Conclusions: Our data suggest that downregulation of miR-142-5p, miR-150-5p, miR-320a, and miR-4433b-5p can be involved in BC for not repressing the expression of target genes. Functional studies will contribute to elucidate their involvement in BC.
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Chen, Peilin, Jaibiao Gong, David Wang, Devin Do, Lianne McLean, and Tom Goralski. "Abstract 4651: Development of a targeted NGS panel for solid tumor actionable gene targets using multiplex PCR-based enrichment in an integrated fluidic circuit." 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.am2018-4651.
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Oades, Kahuku, Lien Vo, Jerry Lee, Mark Landers, Yipeng Wang, Byung-In Lee, and Joseph Monforte. "Abstract 4143: Targeted RNA sequencing for expression analysis of breast cancer patient samples using a biomarker gene panel." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4143.
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Costa, Jose, Joana Reis, Margarida Fernandes, Rafaela Silva, Luis Cirnes, Ruchi Chaudhary, Fatima Carneiro, and Jose C. Machado. "Abstract 1712: Assessing tumor mutation load using an NGS-based, routine-friendly target gene panel." 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.am2018-1712.
Full textReports on the topic "Targeted gene panels"
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Lers, Amnon, and Pamela J. Green. Analysis of Small RNAs Associated with Plant Senescence. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7593393.bard.
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Senescence is an agriculturally significant process due to its negative impact to crop yield and postharvest quality. The genetic regulatory systems controlling senescence induction and progress respond to both developmental and environmental stress signals and involve numerous gene expression changes. Knowledge about the key molecular factors which control senescence is very limited. MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, responses to environmental stresses, and senescence. The long-term goal of this work is to elucidate roles of small RNAs associated with plant senescence. The hypothesis underlying this research is that miRNA-mediated regulation makes important contributions to the senescence process in plants. Specific, original research objectives included: 1) Profiling of small RNAs from senescing plants; 2) Data Analysis and public access via a user-friendly web interface; 3) Validation of senescence-associated miRNAs and target RNAs; 4) Development of transgenic plants for functional analysis of miRNAs in Arabidopsis. Major revisions made in the research compared to the original work plan included 1) Exclusion of the planned work with tomato as recommended by the BARD review panel; 2) Performing miRNA study also in senescing Arabidopsis siliques, in addition to senescing leaves. To identify senescenceregulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences. Parallel Analysis of RNA Ends (PARE) libraries, which enable the large-scale examination of miRNA-guided cleavage products, were also constructed and sequenced, resulting in over 750 million genome-matched sequences. These massive datasets lead to the identification of new miRNAs, as well as new regulation of known miRNAs and their target genes during senescence, many of which have established roles in nutrient responsiveness and cell structural integrity. In keeping with remobilization of nutrients thought to occur during senescence, many miRNAs and targets had opposite expression pattern changes between leaf and silique tissues during the progression of senescence. Taken together, these findings highlight the integral role that miRNAs may play in the remobilization of resources and alteration of cellular structure that is known to occur in senescence. Experiments were initiated for functional analysis of specific senescence-associated miRNAs and respective target genes. Transgenic Arabidopsis plants were generated in which miR408, found in this study to be significantly induced in leaf senescence, was over-expressed either constitutively or under a senescence-specific promoter. These plants are currently being characterized for any altered phenotypes. In addition T-DNA knock out mutants for various target genes identified in this research are being analyzed. This work provides insights about specific miRNAs that contribute to leaf and silique senescence. The knowledge generated may suggest new strategies to monitor and alter the progression of senescence in crops for agricultural improvement.
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Shpigel, Nahum, Raul Barletta, Ilan Rosenshine, and Marcelo Chaffer. Identification and characterization of Mycobacterium paratuberculosis virulence genes expressed in vivo by negative selection. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7696510.bard.
Full textAbstract:
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of a severe inflammatory bowel disease (IBD) in ruminants, known as Johne’s disease or paratuberculosis. Johne’s disease is considered to be one of the most serious diseases affecting dairy cattle both in Israel and worldwide. Heavy economic losses are incurred by dairy farmers due to the severe effect of subclinical infection on milk production, fertility, lower disease resistance and early culling. Its influence in the United States alone is staggering, causing an estimated loss of $1.5 billion to the agriculture industry every year. Isolation of MAP from intestinal tissue and blood of Crohn's patients has lead to concern that it plays a potential pathogenic role in promoting human IDB including Crohn’s disease. There is great concern following the identification of the organism in animal products and shedding of the organism to the environment by subclinically infected animals. Little is known about the molecular basis for MAP virulence. The goal of the original proposed research was to identify MAP genes that are required for the critical stage of initial infection and colonization of ruminants’ intestine by MAP. We proposed to develop and use signature tag mutagenesis (STM) screen to find MAP genes that are specifically required for survival in ruminants upon experimental infection. This research projected was approved as one-year feasibility study to prove the ability of the research team to establish the animal model for mutant screening and alternative in-vitro cell systems. In Israel, neonatal goat kids were repeatedly inoculated with either one of the following organisms; MAP K-10 strain and three transposon mutants of K-10 which were produced and screened by the US PI. Six months after the commencement of inoculation we have necropsied the goats and taken multiple tissue samples from the jejunum, ileum and mesenteric lymph nodes. Both PCR and histopathology analysis indicated on efficient MAP colonization of all the inoculated animals. We have established several systems in the Israeli PI’s laboratory; these include using IS900 PCR for the identification of MAP and using HSP65-based PCR for the differentiation between MAV and MAP. We used Southern blot analysis for the differentiation among transposon mutants of K-10. In addition the Israeli PI has set up a panel of in-vitro screening systems for MAP mutants. These include assays to test adhesion, phagocytosis and survival of MAP to/within macrophages, assays that determine the rate of MAPinduced apoptosis of macrophages and MAP-induced NO production by macrophages, and assays testing the interference with T cell ã Interferon production and T cell proliferation by MAP infected macrophages (macrophage studies were done in BoMac and RAW cell lines, mouse peritoneal macrophages and bovine peripheral blood monocytes derived macrophages, respectively). All partners involved in this project feel that we are currently on track with this novel, highly challenging and ambitious research project. We have managed to establish the above described research systems that will clearly enable us to achieve the original proposed scientific objectives. We have proven ourselves as excellent collaborative groups with very high levels of complementary expertise. The Israeli groups were very fortunate to work with the US group and in a very short time period to master numerous techniques in the field of Mycobacterium research. The Israeli group has proven its ability to run this complicated animal model. This research, if continued, may elucidate new and basic aspects related to the pathogenesis MAP. In addition the work may identify new targets for vaccine and drug development. Considering the possibility that MAP might be a cause of human Crohn’s disease, better understanding of virulence mechanisms of this organism might also be of public health interest as well.