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Identifier 000425729
Title An open and interactive pipeline for variant analysis and downstream exome sequencing analysis
Author Αστρινάκη, Μαρία
Thesis advisor Ποταμιάς, Γεώργιος
Καφετζόπουλος, Δημήτριος
Abstract Next Generation Sequencing (NGS) is a technique for the profiling of the DNA sequence of an organism that has been constantly developed and optimized over the last 20 years. Today, the quality, automation and cost-effectiveness of this technique has reached a level that can be directly applied in diagnostic and therapeutic protocols of modern health-care systems. A typical NGS pipeline starts with sample preparation and concludes with a report that is delivered to the clinician. This report contains all findings, usually genetic mutations, with important implications and clinical relevance to the condition of the patient. Two of the most important intermediate steps of this procedure is the annotation and prioritization of the identified mutations. Annotation is the process of complementing a list of mutations with information available in existing and open genetic databases. Prioritization is the process of applying various criteria to the variants in order to rank them according to their pathogenicity. Usually the variants reported to the clinicians are the ones that have the highest rankings. Although all steps of the NGS pipeline have been thoroughly standardized for a wide set of sequencing platforms and diagnostic scenaria, prioritization remains on of the most subjective and under-standardized step. As of today, the most known systematization process for variant prioritization is the set of guidelines introduced by the American College of Medical Genetics and Genomics (ACMG). However, these guidelines are far from complete and contain many vague directions that are open to interpretation by clinical geneticists. The subjective interpretation of these guidelines combined with the plethora of annotation information for tens of thousands of mutations, creates a bewildered terrain for the researcher. To alleviate this, we create an environment, call Zazz which serves two purposes. The first is to store in a relational database the variants and the annotation information of a set of samples. The second is to offer a query and exploration environment where users can apply and fine-tune the prioritization guidelines. Zazz offers a simple User Interface through which the user can apply complex queries and also offers an interactive exploration envirοnment that visualizes variants through modern javascript graph toolkits. Zazz is also integrated with a graphic genome browser. We demonstrate the efficiency of Zazz with exome sequencing data annotated with the IonReporter suite and the open annotation tools VEP and ANNOVAR. We also show how Zazz can accommodate custom annotation fields by importing data from a custom parser of the ClinVar database which extracts fields that other annotation platforms omit. Overall Zazz is a platform that helps clinical geneticists to browse a huge amount of information with the purpose of creating concise reports, in a timely manner
Language English
Subject Exomes
Next generation sequensing
Variant priorizitation open software
Αλληλούχιση επόμενης γενιάς
Ταξινόμηση παραλλαγών ανοιχτού λογισμικού
Issue date 2019-12-11
Collection   Faculty/Department--School of Medicine--Department of Medicine--Post-graduate theses
  Type of Work--Post-graduate theses
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