Computational Pipeline for Lynch Syndrome Detection: Integrating Alignment, Variant Calling, and Annotations

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Syndrome Detection: Integrating Alignment, Variant Calling, and Annotations</title> <meta name="description" content="Computational Pipeline for Lynch Syndrome Detection: Integrating Alignment, Variant Calling, and Annotations"> <meta name="keywords" content="Lynch Syndrome, computational pipeline, alignment, variant calling, annotation, genetic markers"> <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 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87395</div> </div> </div> </div> <div class="card publication-listing mt-3 mb-3"> <h5 class="card-header" style="font-size:.9rem">Computational Pipeline for Lynch Syndrome Detection: Integrating Alignment, Variant Calling, and Annotations</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Rofida%20Gamal">Rofida Gamal</a>, <a href="https://publications.waset.org/abstracts/search?q=Mostafa%20Mohammed"> Mostafa Mohammed</a>, <a href="https://publications.waset.org/abstracts/search?q=Mariam%20Adel"> Mariam Adel</a>, <a href="https://publications.waset.org/abstracts/search?q=Marwa%20Gamal"> Marwa Gamal</a>, <a href="https://publications.waset.org/abstracts/search?q=Marwa%20kamal"> Marwa kamal</a>, <a href="https://publications.waset.org/abstracts/search?q=Ayat%20Saber"> Ayat Saber</a>, <a href="https://publications.waset.org/abstracts/search?q=Maha%20Mamdouh"> Maha Mamdouh</a>, <a href="https://publications.waset.org/abstracts/search?q=Amira%20Emad"> Amira Emad</a>, <a href="https://publications.waset.org/abstracts/search?q=Mai%20Ramadan"> Mai Ramadan</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Lynch Syndrome is an inherited genetic condition associated with an increased risk of colorectal and other cancers. Detecting Lynch Syndrome in individuals is crucial for early intervention and preventive measures. This study proposes a computational pipeline for Lynch Syndrome detection by integrating alignment, variant calling, and annotation. The pipeline leverages popular tools such as FastQC, Trimmomatic, BWA, bcftools, and ANNOVAR to process the input FASTQ file, perform quality trimming, align reads to the reference genome, call variants, and annotate them. It is believed that the computational pipeline was applied to a dataset of Lynch Syndrome cases, and its performance was evaluated. It is believed that the quality check step ensured the integrity of the sequencing data, while the trimming process is thought to have removed low-quality bases and adaptors. In the alignment step, it is believed that the reads were accurately mapped to the reference genome, and the subsequent variant calling step is believed to have identified potential genetic variants. The annotation step is believed to have provided functional insights into the detected variants, including their effects on known Lynch Syndrome-associated genes. The results obtained from the pipeline revealed Lynch Syndrome-related positions in the genome, providing valuable information for further investigation and clinical decision-making. The pipeline's effectiveness was demonstrated through its ability to streamline the analysis workflow and identify potential genetic markers associated with Lynch Syndrome. It is believed that the computational pipeline presents a comprehensive and efficient approach to Lynch Syndrome detection, contributing to early diagnosis and intervention. The modularity and flexibility of the pipeline are believed to enable customization and adaptation to various datasets and research settings. Further optimization and validation are believed to be necessary to enhance performance and applicability across diverse populations. <iframe src="https://publications.waset.org/abstracts/178986.pdf" style="width:100%; height:400px;" frameborder="0"></iframe> <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Lynch%20Syndrome" title="Lynch Syndrome">Lynch Syndrome</a>, <a href="https://publications.waset.org/abstracts/search?q=computational%20pipeline" title=" computational pipeline"> computational pipeline</a>, <a href="https://publications.waset.org/abstracts/search?q=alignment" title=" alignment"> alignment</a>, <a href="https://publications.waset.org/abstracts/search?q=variant%20calling" title=" variant calling"> variant calling</a>, <a href="https://publications.waset.org/abstracts/search?q=annotation" title=" annotation"> annotation</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20markers" title=" genetic markers"> genetic markers</a> </p> <a href="https://publications.waset.org/abstracts/178986/computational-pipeline-for-lynch-syndrome-detection-integrating-alignment-variant-calling-and-annotations" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/178986.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">76</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 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Computational Pipeline for Lynch Syndrome Detection: Integrating Alignment, Variant Calling, and Annotations