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2018 | OriginalPaper | Buchkapitel

Identification of Factors that Affect Reproducibility of Mutation Calling Methods in Data Originating from the Next-Generation Sequencing

verfasst von : Roman Jaksik, Krzysztof Psiuk-Maksymowicz, Andrzej Swierniak

Erschienen in: Computer and Information Sciences

Verlag: Springer International Publishing

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Abstract

Identification of somatic mutations, based on data from next-generation sequencing of the DNA, has become one of the fundamental research strategies in oncology, with the goal to seek mechanisms underlying the process of carcinogenesis and resistance to commonly used therapies. Despite significant advances in the development of sequencing methods and data processing algorithms, the reproducibility of experiments is relatively low and depending significantly on the methods used to identify changes in the structure of the DNA. This is mainly due to the influence of three factors: (1) high heterogeneity of tumors due to which some mutations are characteristic for a small number of cells, (2) bias associated with the process of exome isolation and (3) specificity of data pre-processing strategies.

The aim of the work was to determine the impact of these factors on the identification of somatic mutations, allowing to determine the reasons for low reproducibility in such studies.

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Titel: Identification of Factors that Affect Reproducibility of Mutation Calling Methods in Data Originating from the Next-Generation Sequencing
verfasst von: Roman Jaksik
Krzysztof Psiuk-Maksymowicz
Andrzej Swierniak
Verlag: Springer International Publishing
Buch: Computer and Information Sciences
Print ISBN: 978-3-030-00839-0

Electronic ISBN: 978-3-030-00840-6

Copyright-Jahr: 2018
DOI: https://doi.org/10.1007/978-3-030-00840-6_29

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