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Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
- Source :
- Liu, S, Huang, S, Rao, J, Ye, W, Schierup, M H, Villesen, P, Xu, X, Li, N, Kristiansen, K, Sørensen, T I A, Hansen, T, Pedersen, O, Brunak, S, Gupta, R, Rasmussen, S, Lund, O, Bolund, L, Børglum, A D, Eiberg, H, Nørgaard Flindt, E, Xu, R, Sun, J, Liu, H, Jiang, H, Wang, O, Cheng, X, Demontis, D, Besenbacher, S, Mailund, T, Friborg, R M, Pedersen, C N S, Liu, S, Chang, Y, Li, S, Guo, X, Cao, H, Ye, C, Maretty, L, Andreas Sibbesen, J, Albrechtsen, A, Bork-Jensen, J, Theil Have, C, Gonzalez-Izarzugaza, J M, Belling, K G-I, Yadav, R, Grove, J, Dam-Als, T, Lescai, F, Krogh, A & Wang, J 2015, ' Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale ', GigaScience, vol. 4, no. 64 . https://doi.org/10.1186/s13742-015-0103-4, GigaScience, Liu, S, Huang, S, Rao, J, Ye, W, Genome Denmark Consortium (Anders Børglum, member of-), Krogh, A & Wang, J 2015, ' Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale ', GigaScience, vol. 4, pp. 64 . https://doi.org/10.1186/s13742-015-0103-4, Danish Pan Genome Consortium, Belling, K G & Rasmussen, S 2015, ' Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale ', GigaScience, vol. 4, 64 . https://doi.org/10.1186/s13742-015-0103-4
- Publication Year :
- 2015
-
Abstract
- Background Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. Findings We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Conclusions Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0103-4) contains supplementary material, which is available to authorized users.
- Subjects :
- Novel sequence
Genotype
Sequence analysis
Population
Sequence assembly
Health Informatics
Single-nucleotide polymorphism
Genomics
Computational biology
Biology
de novo assembly
Genome
Structural variation
SDG 3 - Good Health and Well-being
Technical Note
De novo assembly
Humans
education
Genetics
education.field_of_study
Genome, Human
Genetic Variation
High-Throughput Nucleotide Sequencing
Computer Science Applications
Human genome
Sequence Analysis
Software
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Liu, S, Huang, S, Rao, J, Ye, W, Schierup, M H, Villesen, P, Xu, X, Li, N, Kristiansen, K, Sørensen, T I A, Hansen, T, Pedersen, O, Brunak, S, Gupta, R, Rasmussen, S, Lund, O, Bolund, L, Børglum, A D, Eiberg, H, Nørgaard Flindt, E, Xu, R, Sun, J, Liu, H, Jiang, H, Wang, O, Cheng, X, Demontis, D, Besenbacher, S, Mailund, T, Friborg, R M, Pedersen, C N S, Liu, S, Chang, Y, Li, S, Guo, X, Cao, H, Ye, C, Maretty, L, Andreas Sibbesen, J, Albrechtsen, A, Bork-Jensen, J, Theil Have, C, Gonzalez-Izarzugaza, J M, Belling, K G-I, Yadav, R, Grove, J, Dam-Als, T, Lescai, F, Krogh, A & Wang, J 2015, ' Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale ', GigaScience, vol. 4, no. 64 . https://doi.org/10.1186/s13742-015-0103-4, GigaScience, Liu, S, Huang, S, Rao, J, Ye, W, Genome Denmark Consortium (Anders Børglum, member of-), Krogh, A & Wang, J 2015, ' Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale ', GigaScience, vol. 4, pp. 64 . https://doi.org/10.1186/s13742-015-0103-4, Danish Pan Genome Consortium, Belling, K G & Rasmussen, S 2015, ' Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale ', GigaScience, vol. 4, 64 . https://doi.org/10.1186/s13742-015-0103-4
- Accession number :
- edsair.doi.dedup.....025b39ae5915652596e801061b7362dd