RT Journal Article
SR Electronic
T1 OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 479097
DO 10.1101/479097
A1 Florian Thibord
A1 Claire Perret
A1 Maguelonne Roux
A1 Pierre Suchon
A1 Marine Germain
A1 Jean-François Deleuze
A1 Pierre-Emmanuel Morange
A1 David-Alexandre Trégouët
A1 on behalf of the GENMED Consortium
YR 2019
UL http://biorxiv.org/content/early/2019/02/05/479097.abstract
AB Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs’ detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy.OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers.OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).