{"doi":"10.1038/ncomms11938","title":"Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks","abstract":"<jats:title>Abstract</jats:title><jats:p>Chronic lymphocytic leukaemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, here we present genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients measured by the ATAC-seq assay. We also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting data set, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions.<jats:italic>IGHV</jats:italic>mutation status—which distinguishes the two major subtypes of CLL—was accurately predicted by the chromatin profiles and gene regulatory networks inferred for<jats:italic>IGHV</jats:italic>-mutated versus<jats:italic>IGHV</jats:italic>-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we discovered widespread heterogeneity in the chromatin landscape of CLL, established a community resource for studying epigenome deregulation in leukaemia and demonstrated the feasibility of large-scale chromatin accessibility mapping in cancer cohorts and clinical research.</jats:p>","journal":"Nature Communications","year":2016,"id":601154,"datarank":0.7584368708022463,"base_score":5.056245805348308,"endowment":5.056245805348308,"self_citation_contribution":0.7584368708022463,"citation_network_contribution":0.0,"self_endowment_contribution":0.7584368708022463,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":156,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":77592,"name":"Christian Schmidl","orcid":"0000-0002-0522-202X","position":1,"is_corresponding":false},{"id":673855,"name":"Jonathan C. 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Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions.<jats:italic>IGHV</jats:italic>mutation status—which distinguishes the two major subtypes of CLL—was accurately predicted by the chromatin profiles and gene regulatory networks inferred for<jats:italic>IGHV</jats:italic>-mutated versus<jats:italic>IGHV</jats:italic>-unmutated samples identified characteristic differences between these two disease subtypes. 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