Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis - Normandie Université Access content directly
Journal Articles Human Mutation Year : 2019

Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis

Flavie Diguet
  • Function : Author
Patrick Edery
Olivier Pichon
  • Function : Author
Andrew Wilkie
  • Function : Author
Gaetan Lesca

Abstract

Human retrocopies, that is messenger RNA transcripts benefitting from the long interspersed element 1 machinery for retrotransposition, may have specific consequences for genomic testing. Next genetration sequencing (NGS) techniques allow the detection of such mobile elements but they may be misinterpreted as genomic duplications or be totally overlooked. We report eight observations of retrocopies detected during diagnostic NGS analyses of targeted gene panels, exome, or genome sequencing. For seven cases, while an exons-only copy number gain was called, read alignment inspection revealed a depth of coverage shift at every exon-intron junction where indels were also systematically called. Moreover, aberrant chimeric read pairs spanned entire introns or were paired with another locus for terminal exons. The 8th retrocopy was present in the reference genome and thus showed a normal NGS profile. We emphasize the existence of retrocopies and strategies to accurately detect them at a glance during genetic testing and discuss pitfalls for genetic testing.

Dates and versions

hal-02339267 , version 1 (30-10-2019)

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Cite

Nicolas Chatron, Kevin Cassinari, Olivier Quenez, Stéphanie Baert‐desurmont, Claire Bardel, et al.. Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis. Human Mutation, 2019, 40 (11), pp.1993-2000. ⟨10.1002/humu.23845⟩. ⟨hal-02339267⟩
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