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OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment

Florian Thibord1,2,3, Claire Perret1,2, Maguelonne Roux1,2

  • 1Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France.

RNA (New York, N.Y.)
|March 2, 2019
PubMed
Summary
This summary is machine-generated.

A new algorithm, OPTIMIR, enhances microRNA (miRNA) detection by using genetic data to improve alignment accuracy. This tool helps identify novel miRNAs and analyze genetic variations affecting miRNA expression in human samples.

Keywords:
alignmentgenetic variationsisomiRsmicroRNAnext-generation sequencing

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Next-generation sequencing is vital for characterizing microRNAs (miRNAs) in human biosamples.
  • Accurate miRNA detection and quantification are challenging due to posttranscriptional modifications and genetic variations (polymiRs).
  • These variations can significantly impact the alignment step in sequencing data analysis.

Purpose of the Study:

  • To introduce OPTIMIR, a novel algorithm designed to improve miRNA alignment accuracy.
  • To leverage biological knowledge of miRNA editing and genome-wide genotype data for enhanced analysis.
  • To address the challenges in detecting and quantifying modified and variant miRNAs.

Main Methods:

  • Developed the OPTIMIR algorithm incorporating miRNA editing knowledge and genotype data.
  • Applied OPTIMIR to analyze 391 human plasma samples previously genotyped.
  • Utilized Python for algorithm implementation, ensuring accessibility.

Main Results:

  • OPTIMIR demonstrated improved alignment accuracy for microRNAs.
  • The algorithm successfully detected genotyping errors in the analyzed samples.
  • It suggested the existence of novel miRNAs and revealed allelic imbalance in polymiR expression among heterozygous carriers.

Conclusions:

  • OPTIMIR offers a robust solution for accurate miRNA profiling, especially in the presence of genetic variations.
  • The algorithm aids in discovering new miRNAs and understanding the functional impact of polymiRs.
  • OPTIMIR is freely available, promoting wider adoption in miRNA research.