MMRFBiolinks: an R-package for integrating and analyzing MMRF-CoMMpass data

Area of Science:

• Bioinformatics
• Genomics
• Cancer Research

Background:

• Multiple myeloma (MM) is a significant hematological cancer requiring advanced bioinformatic tools for mechanistic and drug response studies.
• Publicly available genomic data from sources like MMRF and NCI-GDC offers valuable insights into MM.

Purpose of the Study:

• To introduce MMRFBiolinks, an R package designed for the integrative analysis of multiple myeloma genomic datasets.
• To provide enhanced functionalities for data retrieval, analysis, and visualization beyond existing platforms.

Main Methods:

• Development of the MMRFBiolinks R package, extending TCGABiolinks with 13 new functions.
• Integration of data from the Multiple Myeloma Research Foundation (MMRF) CoMMpass study and the National Cancer Institute Genomic Data Commons (NCI-GDC).
• Implementation of integrative analysis methods including array-array intensity correlation and Kaplan-Meier survival analysis.

Main Results:

• MMRFBiolinks enables comprehensive analysis workflows for MMRF data, including gene survival analysis and best overall response correlation.
• The package successfully overcomes limitations of existing analysis tools at NCI-GDC and MMRF-RG.
• Two case studies demonstrate the utility in identifying survival-related genes and analyzing treatment response correlations.

Conclusions:

• MMRFBiolinks significantly facilitates the retrieval, downloading, and analysis of multiple myeloma genomic data.
• The package enhances the understanding of multiple myeloma onset mechanisms and drug responses.
• It provides a more accessible and comprehensive platform for researchers working with MMRF genomic data.