OPTIMIR

OPTIMIR integrates genome-wide genotype data into microRNA (miRNA) sequence alignment to improve the accuracy of miRNA characterization from next-generation sequencing data.

Key Features:

• Integration of Genotype Data: Incorporates genome-wide genotype data to account for polymiRs (polymorphic microRNAs) during alignment.
• Accounting for Posttranscriptional Modifications: Integrates biological knowledge of miRNA posttranscriptional modifications and editing processes to refine alignments.
• Detection of Genotyping Errors: Identifies potential genotyping errors within samples to improve the reliability of downstream analyses.
• Novel miRNA Discovery: Suggests candidate novel miRNAs based on alignment patterns and discrepancies.
• Allelic Imbalance Analysis: Highlights allelic imbalance expression in heterozygous carriers of polymiRs.
• Next-Generation Sequencing Support: Processes miRNA reads derived from next-generation sequencing technologies for human biosamples.

Scientific Applications:

• miRNA profiling in human biosamples: Characterization of miRNA expression in human plasma and other biosamples using NGS data.
• Genetic variation studies: Investigation of how polymiRs and genetic variants affect miRNA expression and regulation.
• Quality control of genotype data: Detection of genotyping inconsistencies to support sample QC in genomic studies.
• Novel miRNA identification: Support for discovering previously unannotated miRNA candidates.
• Personalized medicine research: Analysis of allelic imbalance and individual-specific miRNA regulation relevant to personalized medicine.

Methodology:

Implemented in Python, OPTIMIR processes next-generation sequencing miRNA reads while integrating genome-wide genotyping array data and miRNA editing/posttranscriptional modification knowledge to refine alignments and detect polymiRs and genotyping inconsistencies.