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

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  • معلومة اضافية
    • Contributors:
      Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN); Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition CHU Pitié Salpêtrière (IHU ICAN); CHU Pitié-Salpêtrière AP-HP; Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière AP-HP; Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU); Sorbonne Université (SU); Bordeaux population health (BPH); Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM); Aix Marseille Université (AMU); Laboratoire d'hématologie biologique Hôpital de la Timone - Hôpital Nord - APHM; Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Hôpital de la Timone CHU - APHM (TIMONE); Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN); Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM); Centre d'Etude du Polymorphisme Humain (CEPH); Université Paris Diderot - Paris 7 (UPD7)-Institut Universitaire d'Hématologie (IUH); Université Paris Diderot - Paris 7 (UPD7)-Fondation Jean Dausset; ANR-10-LABX-0013,GENMED,Medical Genomics(2010)
    • بيانات النشر:
      CCSD
      Cold Spring Harbor Laboratory Press
    • الموضوع:
      2019
    • Collection:
      Inserm: HAL (Institut national de la santé et de la recherche médicale)
    • نبذة مختصرة :
      International audience ; 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 posttranscriptional 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).
    • Relation:
      info:eu-repo/semantics/altIdentifier/pmid/30819774; PUBMED: 30819774
    • الرقم المعرف:
      10.1261/rna.069708.118
    • الدخول الالكتروني :
      https://hal.sorbonne-universite.fr/hal-02145961
      https://hal.sorbonne-universite.fr/hal-02145961v1/document
      https://hal.sorbonne-universite.fr/hal-02145961v1/file/RNA-2019-Thibord-657-68.pdf
      https://doi.org/10.1261/rna.069708.118
    • Rights:
      info:eu-repo/semantics/OpenAccess
    • الرقم المعرف:
      edsbas.42219A44