Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer

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http://hdl.handle.net/10138/306620

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Katainen , R , Donner , I , Cajuso , T , Kaasinen , E , Palin , K , Mäkinen , V , Aaltonen , L A & Pitkänen , E 2018 , ' Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer ' , Nature Protocols , vol. 13 , no. 11 , pp. 2580-2600 . https://doi.org/10.1038/s41596-018-0052-3

Title: Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer
Author: Katainen, Riku; Donner, Iikki; Cajuso, Tatiana; Kaasinen, Eevi; Palin, Kimmo; Mäkinen, Veli; Aaltonen, Lauri A.; Pitkänen, Esa
Contributor: University of Helsinki, Genome-Scale Biology (GSB) Research Program
University of Helsinki, Genome-Scale Biology (GSB) Research Program
University of Helsinki, Genome-Scale Biology (GSB) Research Program
University of Helsinki, Genome-Scale Biology (GSB) Research Program
University of Helsinki, Lauri Antti Aaltonen / Principal Investigator
University of Helsinki, Genome-scale Algorithmics research group / Veli Mäkinen
University of Helsinki, Lauri Antti Aaltonen / Principal Investigator
University of Helsinki, Lauri Antti Aaltonen / Principal Investigator
Date: 2018-11
Language: eng
Number of pages: 21
Belongs to series: Nature Protocols
ISSN: 1754-2189
URI: http://hdl.handle.net/10138/306620
Abstract: Next-generation sequencing (NGS) is routinely applied in life sciences and clinical practice, but interpretation of the massive quantities of genomic data produced has become a critical challenge. The genome-wide mutation analyses enabled by NGS have had a revolutionary impact in revealing the predisposing and driving DNA alterations behind a multitude of disorders. The workflow to identify causative mutations from NGS data, for example in cancer and rare diseases, commonly involves phases such as quality filtering, case-control comparison, genome annotation, and visual validation, which require multiple processing steps and usage of various tools and scripts. To this end, we have introduced an interactive and user-friendly multi-platform-compatible software, BasePlayer, which allows scientists, regardless of bioinformatics training, to carry out variant analysis in disease genetics settings. A genome-wide scan of regulatory regions for mutation clusters can be carried out with a desktop computer in -10 min with a dataset of 3 million somatic variants in 200 whole-genome-sequenced (WGS) cancers.
Subject: GENETIC-VARIANTS
READ ALIGNMENT
CANCER
DISEASE
PATHOGENICITY
VISUALIZATION
FRAMEWORK
FEATURES
ELEMENTS
CALLS
3111 Biomedicine
1182 Biochemistry, cell and molecular biology
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