MMRFVariant: Prioritizing variants in Multiple Myeloma

Background: Multiple Myeloma (MM) is a blood malignancy that occurs in the plasma cells of bone marrow. Due to the drug resistance and frequent relapses, MM remains a key area of therapeutic challenge. Analysis of variants could reveal important prognostic features in MM. A reliable interpretation on how a variant affects a protein remains yet a not trivial task. The usage of appropriate bioinformatic tools for the analysis of variants data, sourcing from the Multiple Myeloma Research Foundation (MMRF) CoMMpass (Clinical Outcomes in MM to Personal Assessment of Genetic Profile) study, a large-scale observation project focusing on MM, offers great opportunities. To the best of our knowledge, a specific tool dealing with variants data sourcing from MMRF-CoMMpass datasets does not exist yet. Material and methods: MMRFVariant is a novel R package able to identify and prioritize the disease-causing variants in MM with the aim of providing valuable insights for the MM variants interpretation. MMRFVariant deals with the datasets (IA15 release) retrieved from the MMRF-CoMMpass Study. The MM variants analysis exploits pathogenicity predictions scores and survival analysis results. Conclusion and Discussion: MMRFVariant provides five functionalities that produce graphical and tabular results: the impact-effect correlation plot, the Kaplan–Meier (KM) survival curves, the heatmap of the occurrence number and the impact table can be computed. The potentiality of the tool is highlighted in a case study in which a set of six genes is selected due to their notoriety in the MM pathogenicity: the results provided by MMRFVariant are confirmed by what is reported in other studies.