SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read map-pability.

Daria Iakovishina 1 Isabelle Janoueix-Lerosey 2, 3 Emmanuel Barillot 2, 4, 5, 6 Mireille Regnier 1 Valentina Boeva 2, 4, 5, 6
1 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France, X - École polytechnique, CNRS - Centre National de la Recherche Scientifique : UMR8623
Abstract : Whole genome sequencing of paired-end reads can be applied to characterize the landscape of large somatic rearrangements of cancer genomes. Several methods for detecting structural variants with whole genome sequencing data have been developed. So far, none of these methods has combined information about abnormally mapped read pairs connecting rearranged regions and associated global copy number changes automatically inferred from the same sequencing data file. Our aim was to create a computational method that could use both types of information, i.e., normal and abnormal reads, and demonstrate that by doing so we can highly improve both sensitivity and specificity rates of structural variant prediction. We developed a computational method, SV-Bay, to detect structural variants from whole genome sequencing mate-pair or paired-end data using a probabilistic Bayesian approach. This approach takes into account depth of coverage by normal reads and abnormalities in read pair mappings. To estimate the model likelihood, SV-Bay considers GC-content and read mappability of the genome, thus making important corrections to the expected read count. For the detection of somatic variants, SV-Bay makes use of a matched normal sample when it is available. We validated SV-Bay on simulated datasets and an experimental mate-pair dataset for the CLB-GA neuroblastoma cell line. The comparison of SV-Bay with several other methods for structural variant detection demonstrated that SV-Bay has better prediction accuracy both in terms of sensitivity and false positive detection rate. https://github.com/InstitutCurie/SV-Bay CONTACT: SV.Bay@curie.fr SUPPLEMENTARY INFORMATION: Available at Bioinformatics online.
Type de document :
Article dans une revue
Bioinformatics (Oxford, England), 2016
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https://hal.inria.fr/hal-01253126
Contributeur : Mireille Regnier <>
Soumis le : vendredi 8 janvier 2016 - 16:38:20
Dernière modification le : lundi 18 juin 2018 - 10:32:23

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  • HAL Id : hal-01253126, version 1
  • PUBMED : 26740523

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Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Regnier, Valentina Boeva. SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read map-pability.. Bioinformatics (Oxford, England), 2016. 〈hal-01253126〉

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