Search results for: Aggeliki Delimitsou

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Delimitsou</title> <meta name="description" content="Search results for: Aggeliki Delimitsou"> <meta name="keywords" content="Aggeliki Delimitsou"> <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1, user-scalable=no"> <meta charset="utf-8"> <link href="https://cdn.waset.org/favicon.ico" type="image/x-icon" rel="shortcut icon"> <link href="https://cdn.waset.org/static/plugins/bootstrap-4.2.1/css/bootstrap.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/plugins/fontawesome/css/all.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/css/site.css?v=150220211555" rel="stylesheet"> </head> <body> <header> <div class="container"> <nav class="navbar navbar-expand-lg navbar-light"> <a class="navbar-brand" href="https://waset.org"> <img src="https://cdn.waset.org/static/images/wasetc.png" alt="Open Science Research Excellence" title="Open Science Research Excellence" /> </a> <button class="d-block d-lg-none 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action="https://publications.waset.org/abstracts/search"> <div id="custom-search-input"> <div class="input-group"> <i class="fas fa-search"></i> <input type="text" class="search-query" name="q" placeholder="Author, Title, Abstract, Keywords" value="Aggeliki Delimitsou"> <input type="submit" class="btn_search" value="Search"> </div> </div> </form> </div> </div> <div class="row mt-3"> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Commenced</strong> in January 2007</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Frequency:</strong> Monthly</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Edition:</strong> International</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Paper Count:</strong> 2</div> </div> </div> </div> <h1 class="mt-3 mb-3 text-center" style="font-size:1.6rem;">Search results for: Aggeliki Delimitsou</h1> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">2</span> Competitive DNA Calibrators as Quality Reference Standards (QRS™) for Germline and Somatic Copy Number Variations/Variant Allelic Frequencies Analyses</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Eirini%20Konstanta">Eirini Konstanta</a>, <a href="https://publications.waset.org/abstracts/search?q=Cedric%20Gouedard"> Cedric Gouedard</a>, <a href="https://publications.waset.org/abstracts/search?q=Aggeliki%20Delimitsou"> Aggeliki Delimitsou</a>, <a href="https://publications.waset.org/abstracts/search?q=Stefania%20Patera"> Stefania Patera</a>, <a href="https://publications.waset.org/abstracts/search?q=Samuel%20Murray"> Samuel Murray</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=calibrator" title="calibrator">calibrator</a>, <a href="https://publications.waset.org/abstracts/search?q=CNV" title=" CNV"> CNV</a>, <a href="https://publications.waset.org/abstracts/search?q=gene%20copy%20number" title=" gene copy number"> gene copy number</a>, <a href="https://publications.waset.org/abstracts/search?q=VAF" title=" VAF"> VAF</a> </p> <a href="https://publications.waset.org/abstracts/134208/competitive-dna-calibrators-as-quality-reference-standards-qrs-for-germline-and-somatic-copy-number-variationsvariant-allelic-frequencies-analyses" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/134208.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">152</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">1</span> Comparison and Validation of a dsDNA biomimetic Quality Control Reference for NGS based BRCA CNV analysis versus MLPA</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=A.%20Delimitsou">A. Delimitsou</a>, <a href="https://publications.waset.org/abstracts/search?q=C.%20Gouedard"> C. Gouedard</a>, <a href="https://publications.waset.org/abstracts/search?q=E.%20Konstanta"> E. Konstanta</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20Koletis"> A. Koletis</a>, <a href="https://publications.waset.org/abstracts/search?q=S.%20Patera"> S. Patera</a>, <a href="https://publications.waset.org/abstracts/search?q=E.%20Manou"> E. Manou</a>, <a href="https://publications.waset.org/abstracts/search?q=K.%20Spaho"> K. Spaho</a>, <a href="https://publications.waset.org/abstracts/search?q=S.%20Murray"> S. Murray</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Background: There remains a lack of International Standard Control Reference materials for Next Generation Sequencing-based approaches or device calibration. We have designed and validated dsDNA biomimetic reference materials for targeted such approaches incorporating proprietary motifs (patent pending) for device/test calibration. They enable internal single-sample calibration, alleviating sample comparisons to pooled historical population-based data assembly or statistical modelling approaches. We have validated such an approach for BRCA Copy Number Variation analytics using iQRS™-CNVSUITE versus Mixed Ligation-dependent Probe Amplification. Methods: Standard BRCA Copy Number Variation analysis was compared between mixed ligation-dependent probe amplification and next generation sequencing using a cohort of 198 breast/ovarian cancer patients. Next generation sequencing based copy number variation analysis of samples spiked with iQRS™ dsDNA biomimetics were analysed using proprietary CNVSUITE software. Mixed ligation-dependent probe amplification analyses were performed on an ABI-3130 Sequencer and analysed with Coffalyser software. Results: Concordance of BRCA – copy number variation events for mixed ligation-dependent probe amplification and CNVSUITE indicated an overall sensitivity of 99.88% and specificity of 100% for iQRS™-CNVSUITE. The negative predictive value of iQRS-CNVSUITE™ for BRCA was 100%, allowing for accurate exclusion of any event. The positive predictive value was 99.88%, with no discrepancy between mixed ligation-dependent probe amplification and iQRS™-CNVSUITE. For device calibration purposes, precision was 100%, spiking of patient DNA demonstrated linearity to 1% (±2.5%) and range from 100 copies. Traditional training was supplemented by predefining the calibrator to sample cut-off (lock-down) for amplicon gain or loss based upon a relative ratio threshold, following training of iQRS™-CNVSUITE using spiked iQRS™ calibrator and control mocks. BRCA copy number variation analysis using iQRS™-CNVSUITE™ was successfully validated and ISO15189 accredited and now enters CE-IVD performance evaluation. Conclusions: The inclusion of a reference control competitor (iQRS™ dsDNA mimetic) to next generation sequencing-based sequencing offers a more robust sample-independent approach for the assessment of copy number variation events compared to mixed ligation-dependent probe amplification. The approach simplifies data analyses, improves independent sample data analyses, and allows for direct comparison to an internal reference control for sample-specific quantification. Our iQRS™ biomimetic reference materials allow for single sample copy number variation analytics and further decentralisation of diagnostics to single patient sample assessment. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=validation" title="validation">validation</a>, <a href="https://publications.waset.org/abstracts/search?q=diagnostics" title=" diagnostics"> diagnostics</a>, <a href="https://publications.waset.org/abstracts/search?q=oncology" title=" oncology"> oncology</a>, <a href="https://publications.waset.org/abstracts/search?q=copy%20number%20variation" title=" copy number variation"> copy number variation</a>, <a href="https://publications.waset.org/abstracts/search?q=reference%20material" title=" reference material"> reference material</a>, <a href="https://publications.waset.org/abstracts/search?q=calibration" title=" calibration"> calibration</a> </p> <a href="https://publications.waset.org/abstracts/171085/comparison-and-validation-of-a-dsdna-biomimetic-quality-control-reference-for-ngs-based-brca-cnv-analysis-versus-mlpa" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/171085.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">66</span> </span> </div> </div> </div> </main> <footer> <div id="infolinks" class="pt-3 pb-2"> <div class="container"> <div style="background-color:#f5f5f5;" class="p-3"> <div class="row"> <div class="col-md-2"> <ul class="list-unstyled"> About <li><a href="https://waset.org/page/support">About Us</a></li> <li><a href="https://waset.org/page/support#legal-information">Legal</a></li> <li><a target="_blank" rel="nofollow" href="https://publications.waset.org/static/files/WASET-16th-foundational-anniversary.pdf">WASET celebrates its 16th foundational 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Search results for: Aggeliki Delimitsou