De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

Ameur, Adam; Che, Huiwen; Martin, Marcel; Bunikis, Ignas; Dahlberg, Johan; Höijer, Ida; Häggqvist, Susana; Vezzi, Francesco; Nordlund, Jessica; Olason, Pall; Feuk, Lars; Gyllensten, Ulf

doi:10.3390/genes9100486

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De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

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Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 752 36 Uppsala, Sweden

Science for Life Laboratory, Department of Biochemistry and Biophysics (DBB), Stockholm University, 114 19 Stockholm, Sweden

Science for Life Laboratory, Department of Medical Sciences, Molecular Medicine, Uppsala University, 752 36 Uppsala, Sweden

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Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden

Author to whom correspondence should be addressed.

Genes 2018, 9(10), 486; https://doi.org/10.3390/genes9100486

Received: 28 August 2018 / Revised: 21 September 2018 / Accepted: 5 October 2018 / Published: 9 October 2018

(This article belongs to the Special Issue Advances in Single Molecule, Real-Time (SMRT) Sequencing)

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Abstract

The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data. View Full-Text

Keywords: de novo assembly; SMRT sequencing; GRCh38; human reference genome; human whole-genome sequencing; population sequencing; Swedish population

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Ameur, A.; Che, H.; Martin, M.; Bunikis, I.; Dahlberg, J.; Höijer, I.; Häggqvist, S.; Vezzi, F.; Nordlund, J.; Olason, P.; Feuk, L.; Gyllensten, U. De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data. Genes 2018, 9, 486. https://doi.org/10.3390/genes9100486

AMA Style

Ameur A, Che H, Martin M, Bunikis I, Dahlberg J, Höijer I, Häggqvist S, Vezzi F, Nordlund J, Olason P, Feuk L, Gyllensten U. De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data. Genes. 2018; 9(10):486. https://doi.org/10.3390/genes9100486

Chicago/Turabian Style

Ameur, Adam, Huiwen Che, Marcel Martin, Ignas Bunikis, Johan Dahlberg, Ida Höijer, Susana Häggqvist, Francesco Vezzi, Jessica Nordlund, Pall Olason, Lars Feuk, and Ulf Gyllensten. 2018. "De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data" Genes 9, no. 10: 486. https://doi.org/10.3390/genes9100486

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De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

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