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Multi-dimensional and integrative pipeline for NGS-based datasets to explore cell fate decisions

Abstract : Epigenomics would help us understand why various cells types exhibit different behaviours. Aberrant changes in reversible epigenetic modifications observed in cancer raised focus towards epigenetic targeted therapy. As epigenetic studies may involve comparing multi-profile sequencing data, thereis an imminent need for novel approaches and tools to address underlying technical variabilities. Wehave developed NGS-QC, a QC system to infer the experimental quality of the data and Epimetheus, a quantile-based multi-profile normalization tool for histone modification datasets to correct technical variation among samples. Further, we have employed these developed tools in an allele-specific analysis to understand the epigenetic status of X chromosome inactivation in breast cancer cells where disappearance of Xi is frequent. Our analysis has revealed perturbation in epigenetic landscape of X and aberrant gene reactivation in Xi including the ones that are associated with cancer promotion.
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  • HAL Id : tel-01423907, version 1



Mohamed Ashick Mohamed Saleem. Multi-dimensional and integrative pipeline for NGS-based datasets to explore cell fate decisions. Quantitative Methods [q-bio.QM]. Université de Strasbourg, 2015. English. ⟨NNT : 2015STRAJ072⟩. ⟨tel-01423907⟩



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