Abstract
This article describes the use of a comprehensive approach for the identification of differentiating gene related blocks of SNPs based on Fisher’s p-value integration with a pooled correlation approximation. This pre-selection step is proposed as an alternative to advanced haplotype analyses for computational complexity reduction. The method, previously used for pathway regulation inference in eQTL data, is with the necessary modification especially suited for high-dimensional population genetics studies with a case/control design, where extensive numbers of SNPs are identified, leading to numerous haplotype blocks to be tested. This approach extends standard allele frequency analysis to more advanced haplotype identification. The novel method succeeds at reducing the runtime while maintaining a high level of biological result accuracy when compared against the exact test for haplotypes.
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Acknowledgements
This work was funded by The Polish National Centre for Research and Development grant no. PBS3/A7/29/2015/ID-247184 (AP) and National Science Centre, Poland grant no. 2015/19/B/ST6/01736 (JP). Calculations were carried out using GeCONiI infrastructure (POIG02.03.01-24-099).
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Papiez, A. et al. (2019). Can an Integrative SNP Approach Substitute Standard Identification in Comprehensive Case/Control Analyses?. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., González, P. (eds) Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. PACBB2018 2018. Advances in Intelligent Systems and Computing, vol 803. Springer, Cham. https://doi.org/10.1007/978-3-319-98702-6_15
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DOI: https://doi.org/10.1007/978-3-319-98702-6_15
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