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CNV-seq, a new method to detect copy number variation using high-throughput sequencing
BACKGROUND: DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS: Here, we describe a method to det...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667514/ https://www.ncbi.nlm.nih.gov/pubmed/19267900 http://dx.doi.org/10.1186/1471-2105-10-80 |
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author | Xie, Chao Tammi, Martti T |
author_facet | Xie, Chao Tammi, Martti T |
author_sort | Xie, Chao |
collection | PubMed |
description | BACKGROUND: DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS: Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. CONCLUSION: Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes. |
format | Text |
id | pubmed-2667514 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26675142009-04-10 CNV-seq, a new method to detect copy number variation using high-throughput sequencing Xie, Chao Tammi, Martti T BMC Bioinformatics Methodology Article BACKGROUND: DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS: Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. CONCLUSION: Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes. BioMed Central 2009-03-06 /pmc/articles/PMC2667514/ /pubmed/19267900 http://dx.doi.org/10.1186/1471-2105-10-80 Text en Copyright © 2009 Xie and Tammi; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Xie, Chao Tammi, Martti T CNV-seq, a new method to detect copy number variation using high-throughput sequencing |
title | CNV-seq, a new method to detect copy number variation using high-throughput sequencing |
title_full | CNV-seq, a new method to detect copy number variation using high-throughput sequencing |
title_fullStr | CNV-seq, a new method to detect copy number variation using high-throughput sequencing |
title_full_unstemmed | CNV-seq, a new method to detect copy number variation using high-throughput sequencing |
title_short | CNV-seq, a new method to detect copy number variation using high-throughput sequencing |
title_sort | cnv-seq, a new method to detect copy number variation using high-throughput sequencing |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667514/ https://www.ncbi.nlm.nih.gov/pubmed/19267900 http://dx.doi.org/10.1186/1471-2105-10-80 |
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