Computational methods for discovering structural variation with next-generation sequencing

In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variati...

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Veröffentlicht in:	Nature methods Jg. 6; H. Suppl 11; S. S13 - S20
Hauptverfasser:	Medvedev, Paul, Stanciu, Monica, Brudno, Michael
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	New York Nature Publishing Group US 01.11.2009 Nature Publishing Group
Schlagworte:	Algorithms Analysis Base Sequence Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Computational biology Computational Biology - methods DNA sequencing Genetic Variation Genome Genomes Genomics Genomics - methods Humans Hybridization Innovations Life Sciences Methods Molecular structure Nucleotide sequencing Properties Proteomics Research methodology review-article Sequence Analysis, DNA - methods Technological change Canada
ISSN:	1548-7091, 1548-7105, 1548-7105
Online-Zugang:	Volltext
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Abstract	In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions.
AbstractList	In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions.In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions. In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions. In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions. [PUBLICATION ABSTRACT]
Audience	Academic
Author	Stanciu, Monica Medvedev, Paul Brudno, Michael
Author_xml	– sequence: 1 givenname: Paul surname: Medvedev fullname: Medvedev, Paul organization: Department of Computer Science, University of Toronto – sequence: 2 givenname: Monica surname: Stanciu fullname: Stanciu, Monica organization: Department of Computer Science, University of Toronto – sequence: 3 givenname: Michael surname: Brudno fullname: Brudno, Michael email: brudno@cs.toronto.edu organization: Department of Computer Science, University of Toronto, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/19844226$$D View this record in MEDLINE/PubMed
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Copyright	Springer Nature America, Inc. 2009 COPYRIGHT 2009 Nature Publishing Group Copyright Nature Publishing Group Nov 2009
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Snippet	In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used...
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SubjectTerms	Algorithms Analysis Base Sequence Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Computational biology Computational Biology - methods DNA sequencing Genetic Variation Genome Genomes Genomics Genomics - methods Humans Hybridization Innovations Life Sciences Methods Molecular structure Nucleotide sequencing Properties Proteomics Research methodology review-article Sequence Analysis, DNA - methods Technological change
Title	Computational methods for discovering structural variation with next-generation sequencing
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