Wang, Z., Andrews, P. orcid.org/0000-0001-7215-4410, Kendall, J. et al. (6 more authors) (2016) SMASH, a fragmentation and sequencing method for genomic copy number analysis. Genome Research, 26 (6). pp. 844-851. ISSN 1088-9051
Abstract
Copy number variants (CNVs) underlie a significant amount of genetic diversity and disease. CNVs can be detected by a number of means, including chromosomal microarray analysis (CMA) and whole-genome sequencing (WGS), but these approaches suffer from either limited resolution (CMA) or are highly expensive for routine screening (both CMA and WGS). As an alternative, we have developed a next-generation sequencing-based method for CNV analysis termed SMASH, for short multiply aggregated sequence homologies. SMASH utilizes random fragmentation of input genomic DNA to create chimeric sequence reads, from which multiple mappable tags can be parsed using maximal almost-unique matches (MAMs). The SMASH tags are then binned and segmented, generating a profile of genomic copy number at the desired resolution. Because fewer reads are necessary relative to WGS to give accurate CNV data, SMASH libraries can be highly multiplexed, allowing large numbers of individuals to be analyzed at low cost. Increased genomic resolution can be achieved by sequencing to higher depth.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2016 Wang et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Biomedical Science (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 27 Jul 2016 10:57 |
Last Modified: | 27 Jul 2016 10:57 |
Published Version: | http://dx.doi.org/10.1101/gr.201491.115 |
Status: | Published |
Publisher: | Cold Spring Harbor Laboratory Press |
Refereed: | Yes |
Identification Number: | 10.1101/gr.201491.115 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:102963 |