[Detection and Interpretation of Somatic Variants in Molecular Pathology]

Overview

Journal Pathologe

Specialty Pathology

Date 2019 May 1

PMID 31037375

Authors

S Merkelbach-Bruse

J Rehker

J Siemanowski

F Klauschen

Affiliations

Soon will be listed here.

Abstract

Background: Due to the increasing amount of data and sources of information, data evaluation is a crucial step in parallel sequencing.

Objectives: Illustration of pitfalls in evaluating the variant list of parallel sequencing and recommendations regarding software tools and databases.

Methods: Description of filtering steps used, demonstration of criteria and recommendations for annotation by examples from everyday work, comparative analysis of databases with somatic variants, description of the installation of an individualized database.

Results: Variant filtering is a multistep process using information from different databases. The plausibility of variant calling should be verified using the Integrative Genomics Viewer and variants should be described according to the Human Genome Variation Society (HGVS) recommendations. Different databases, which all show advantages and disadvantages, are available for variant interpretation. An individualized database can be built up with the open-source tool cBioPortal.

Conclusions: Different tools and databases might be used for the analysis of parallel sequencing data. The application depends on, amongst other things, the local situation and has to be extensively validated.

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