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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.

Original publication

DOI

10.1002/humu.23845

Type

Journal article

Journal

Hum Mutat

Publication Date

11/2019

Volume

40

Pages

1993 - 2000

Keywords

copy number gain, genetic testing pitfalls, genome mobility, retrocopies, Adolescent, Adult, Aged, Child, Child, Preschool, Diagnostic Tests, Routine, Female, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Testing, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Infant, Male, Middle Aged, Retroelements, Young Adult