Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization - Archive ouverte HAL Access content directly
Journal Articles Molecular Genetics & Genomic Medicine Year : 2020

Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

Yannis Duffourd
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Laila El Khattabi
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Marc Délépine
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  • PersonId : 919144
Anne Boland
Patrick Callier
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Abstract

Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base-pair resolution, but the use of short-read sequencing is limited by repetitive sequences, and long-read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked-reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short-read to linked-read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short-read WGS.

Dates and versions

hal-02467795 , version 1 (05-02-2020)

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Kévin Uguen, Claire Jubin, Yannis Duffourd, Claire Bardel, Valérie Malan, et al.. Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization. Molecular Genetics & Genomic Medicine, 2020, pp.1-10. ⟨10.1002/mgg3.1114⟩. ⟨hal-02467795⟩
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