Recurrent non-coding mutational hotspots drive chromosomal rearrangement and disease progression in multiple myeloma

This repository contains data utilized in the analysis for the manuscript titled "Recurrent non-coding mutational hotspots drive chromosomal rearrangement and disease progression in multiple myeloma" published in Genome Biology. The data can be used in conjuction with the source code and analysis scripts found at the GitHub repository https://github.com/pblaney/myelomaNoncodingGenome. File Descriptions: genome_tiles.rds - fishHook object of 10kbp tiled windows where each successive window is shifted 500bp of the previous reptome_fish.hg38.rds - fishHook object of replication timing across 96 cell lines, from Roadmap Epigenomics Project seqome_fish.hg38.rds - fishHook object of sequence context (mono, di and tri) encodome_fish.hg38.rds - fishHook object of 15 ChromHMM states across 127 cell lines and tissues, from ENCODE completeGeneSegments.rds - GenomicRanges object of GRCh38 coordinates of Ensembl v108 genes body segments (CDS, Introns, UTRs) *_[snv/indel]_results.sushi.rds - Output from fishHook model for SNVs and InDels across Pan-Myeloma data series, per disease stage, and in a set of normal lymphocytes. nonMerSimulationWidthDistro.rds - Dataframe with the widths of simulated non-MERs nonMerSimulation96Sbs.rds - Dataframe with the 96 different contexts of mutations within simulated non-MERs nonMerSimulationMmsigSbs.rds - Dataframe with the mmsig fitted mutational signatures within simulated non-MERs mer_vs_non_mer_se_lola.rds - LOLA object of enrichment test for super-enhancers at MERs compared to simulated non-MERs clusteredEvents.rds - Dataframe of genomic coordinates of all clustered mutation events called from SigProfilerCluster sv_hotspots.CoMMpass.hg38.rds - GenomicRanges object of GRCh38 coordinates of SV hotspots called in CoMMpass study newly diagnosed multiple myeloma patients complex_hotspots.CoMMpass.hg38.rds - GenomicRanges object of GRCh38 coordinates of complex event SV hotspots called in CoMMpass study newly diagnosed multiple myeloma patients hq_total_sv_bp_dt.rds - Dataframe with consensus, high-quality SVs hq_total_sv_bp_gr.rds - GenomicRanges object of consensus, high-quality SVs nonMerSimulationTrxDistro.rds - Dataframe with the simulated non-MERs used for enrichment test of SVs nonMerSimulationTrxDistances.rds - Dataframe with distances from simulated non-MERs to SVs nonMerSimulationTrxDistanceDensity.rds - Dataframe with density of distances from simulated non-MERs to SVs nonMerSimulationTrxLoessDensity.rds - Dataframe with LOESS density of distances from simulated non-MERs to SVs commpass_paired_wgs_rna_myc_deg.rds - Object with DESeq2 output for expression analysis between patients with MYC translocations with TXNDC5/TENT5C, IGH/IGK/IGL, and those with no event at MYC. mm_epilogos.rds - Dataframe with the Epilogos calculated from multiple myeloma patients ChromHMM states GSM1755012_LP1_GROseq_plus_hg38.rds - GenomicRanges object of GRO-seq data (plus strand) from LP-1 myeloma cell line GSM1755012_LP1_GROseq_minus_hg38.rds - GenomicRanges object of GRO-seq data (minus strand) from LP-1 myeloma cell line