Subtypes of Smoldering Multiple Myeloma

Repo for Manuscript:

Bustoros, M., Anand, S., et al. "Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes." Nature communications 13.1 (2022): 1-10.

Link to pre-print.

Link to Nature Communications publication.

Contact: Shankara Anand - sanand@broadinstitute.org

---

Table of DNA-based SMM subtypes

Note: we included in this table the names used in previous iterations and seen in the code base.

---

Repo Structure:

data - see ./data/README.md

funcs - folder with python/R helper functions or scripts written

Fig1

• 1_clustering.ipynb: notebook with clustering, QC, fisher exact tests for DNA features
• 2_misc.ipynb: misc cohort plots
• 3*_mutational_signatures.ipynb: mutational signature analysis with subtypes

Fig2

• 1_process_rna.ipynb: python notebook describing RNA processing & QC
• 2_diffexp_pathways_rna.ipynb: R notebook with differential expression, fGSEA, & other plots for Fig2 & related supplements

Fig3

• 1_clinical_classifier.ipynb: subtype classifier for clinical outcomes
• Run 00-fig-km.R, 01-fig-traj.R, then 02-fig-pairs.R