Repository for analysis in "Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma" from Boyle, E.M., Blaney, P., and Stoeckle, J. et al.
The crux of all data analysis and visualization were performed in R with the source code found in quantitativeAnalysisOfEpigeneticLandscapeOnChromosome1.Rmd. A knitted PDF version quantitativeAnalysisOfEpigeneticLandscapeOnChromosome1.pdf is also included to easily relate code blocks to figures included in the manuscript.
The copy-number and structural variant hotspots were learned from WGS data of 752 MM patients enrolled in the MMRF's CoMMpass trial and originally described in Revealing the impact of structural variants in multiple myeloma from Rustad et al..
HumanMethylation27 array data was collected from peripheral blood derived B cells, plasma cells from non-malignant donors, patient samples of MGUS, NDMM, PCL, and 9 different myeloma cell lines originally described in Aberrant global methylation patterns affect the molecular pathogenesis and prognosis of multiple myeloma from Walker et al..
Hi-C data was obtained for normal B-cell states including peripheral blood derived naïve B-cells, memory B-cells, germinal-center B-cells, and tonsillar plasma cells from EGA dataset EGAD00001006485. Additional data was included for three myeloma cell lines from GSE87585 and EGAD00001003597.
Super-enhancer elements were characterized using H3K27ac signal peaks across 10 NDMM patients and U266, RPMI8226, and KMS11 cell lines as originally described in Myeloma-specific superenhancers affect genes of biological and clinical relevance in myeloma from Jia et al.