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Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations


Using Oxford Nanopore sequencing, Noyvert et al. captured SVs in 888 samples from the 1000 Genomes Project, creating a reference panel that was then used for the first large-scale genome-wide SV-association study. The authors identified thousands of disease-related DNA alterations, and SV analysis highlighted potential causal genes for respiratory diseases that were missed in previous studies.

Key points:

  • Previous genome-wide association studies (GWAS) focused on SNVs because SVs are often longer than the maximum read length of short-read sequencing methods.

  • By nanopore sequencing 888 samples from mixed ancestry backgrounds, the authors created an SV panel that was used to impute SVs in nearly 500,000 UK Biobank participants.

  • The authors identified 3,858 SV associations across 32 disease-relevant traits, of which 1,258 were novel.

  • SV analysis highlighted CFDP1, MEGF6, AAGAB, and FLI1 as potential causal genes for respiratory diseases that were missed by previous GWAS.

  • Studying SVs could improve genetic risk prediction and identification of potential drug targets in the future.

Sample type: human DNA from the 1000 genomes project

Kit: Ligation Sequencing Kit

Authors: Boris Noyvert, A Mesut Erzurumluoglu, Dmitriy Drichel, Steffen Omland, Till F M Andlauer, Stefanie Mueller, Lau Sennels, Christian Becker, Aleksandr Kantorovich, Boris A Bartholdy, Ingrid Brænne, Julio Cesar Bolivar-Lopez, Costas Mistrellides, Gillian M Belbin, Jeremiah H Li, Joseph K Pickrell, Jatin Arora, Yao Hu, Boehringer Ingelheim – Global Computational Biology and Digital Sciences, Clive R Wood, Jan M Kriegl, Nikhil Podduturi, Jan N Jensen, Jan Stutzki, Zhihao Ding

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