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.
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No previously unpublished data sets were generated or analyzed during the current study.
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Key references using this protocol
1. Katainen, R. et al. Nat. Genet. 47, 818–821 (2015): https://doi.org/10.1038/ng.3335
2. Pradhan, B. et al. Sci. Rep. 7, 14521 (2017): https://doi.org/10.1038/s41598-017-15076-3
3. Donner, I. et al. Genes Chromosomes Cancer 56, 453–459 (2017): https://doi.org/10.1002/gcc.22448
We thank T. Kivioja for his guidance in regard to the SELEX data and A. Ollikainen for the voice-over in the demonstration videos. We thank B. Pradhan and L. Kauppi for sharing their unpublished Nanopore data. We also thank M. Aavikko, L. van den Berg, D. Berta, O. Kilpivaara, J. Kondelin, H. Kuisma, Y. Li, M. Mehine, H. Metsola, J. Ravantti, L. Sipilä, T. Tanskanen, P. Vahteristo and N. Välimäki for testing BasePlayer and giving suggestions and additional support. We acknowledge ZeroTurnaround for creating the JRebel plugin for Eclipse (IDE). This work was supported by grants from the Biomedicum Helsinki Foundation; the Cancer Society of Finland; the Emil Aaltonen Foundation; the Juhani Aho Foundation for Medical Research; the Sigrid Juselius Foundation; the Academy of Finland (Finnish Center of Excellence Program 2012–2017, 250345); the European Research Council (ERC, 268648); a European Union Framework Programme 7 Collaborative Project (SYSCOL, 258236); the Nordic Information for Action eScience Center (NIASC); and a Nordic Center of Excellence grant financed by NordForsk (62721 to K.P.).