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

Kévin Uguen 1 Claire Jubin 2 Yannis Duffourd 3 Claire Bardel 4 Valérie Malan 5 Jean‐michel Dupont 6 Laila El Khattabi 6 Nicolas Chatron 7 Antonio Vitobello 3 Pierre‐antoine Rollat‐farnier 4 Céline Baulard 8 Marc Lelorch 5 Aurelie Leduc 2 Frédéric Tran Mau‐them 3 Vincent Danjean 9 Marc Délépine 8 Marianne Till 10 Vincent Meyer 2 Stanislas Lyonnet 11 Anne‐laure Mosca‐boidron 3 Julien Thevenon 12 Laurence Faivre 12 Christel Thauvin‐robinet 3 Caroline Schluth‐bolard 10 Anne Boland 13 Robert Olaso 8 Patrick Callier 3 Serge Romana 5 Jean‐françois Deleuze 2 Damien Sanlaville 10
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.
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https://hal.archives-ouvertes.fr/hal-02467795
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Submitted on : Wednesday, February 5, 2020 - 11:36:56 AM
Last modification on : Thursday, November 4, 2021 - 12:46:02 PM

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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, Wiley Periodicals, Inc. 2020, pp.1-10. ⟨10.1002/mgg3.1114⟩. ⟨hal-02467795⟩

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