MPAgenomics

MPAgenomics performs multi-patient analysis of copy number variations and single nucleotide polymorphisms (SNPs) as an R package, using segmentation and penalized regression to identify genomic markers.

Key Features:

• Efficient Segmentation: Automates parameter selection and segments multi-patient genomic data to identify regions of copy-number gain and loss.
• Genomic Marker Selection: Employs penalized regression methods to select genomic markers associated with outcomes across multiple patient profiles.
• SNP array integration: Leverages recent-generation SNP arrays to jointly analyze genotyping measures and copy-number variations.

Scientific Applications:

• Cancer genomics: Identification of recurrent copy-number alterations and SNPs associated with tumor phenotypes across patient cohorts.
• Personalized medicine: Detection of genomic markers that may inform therapeutic response and patient stratification.
• Population genetics: Analysis of population-level variation in copy number and SNP profiles across multiple individuals.

Methodology:

Integration of existing R packages via custom wrappers, automatic parameter choice for segmentation, and use of penalized regression methods for marker selection.