Copy-number-aware differential analysis of quantitative DNA sequencing data

Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on...

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Detalles Bibliográficos
Autores principales: Robinson, Mark D., Strbenac, Dario, Stirzaker, Clare, Statham, Aaron L., Song, Jenny, Speed, Terence P., Clark, Susan J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2012
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514678/
https://www.ncbi.nlm.nih.gov/pubmed/22879430
http://dx.doi.org/10.1101/gr.139055.112
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author Robinson, Mark D.
Strbenac, Dario
Stirzaker, Clare
Statham, Aaron L.
Song, Jenny
Speed, Terence P.
Clark, Susan J.
author_facet Robinson, Mark D.
Strbenac, Dario
Stirzaker, Clare
Statham, Aaron L.
Song, Jenny
Speed, Terence P.
Clark, Susan J.
author_sort Robinson, Mark D.
collection PubMed
description Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities and can therefore bias differential detection results. We have developed a flexible approach called ABCD-DNA (affinity-based copy-number-aware differential quantitative DNA sequencing analyses) that integrates CNV and other systematic factors directly into the differential enrichment engine.
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spelling pubmed-35146782012-12-20 Copy-number-aware differential analysis of quantitative DNA sequencing data Robinson, Mark D. Strbenac, Dario Stirzaker, Clare Statham, Aaron L. Song, Jenny Speed, Terence P. Clark, Susan J. Genome Res Method Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities and can therefore bias differential detection results. We have developed a flexible approach called ABCD-DNA (affinity-based copy-number-aware differential quantitative DNA sequencing analyses) that integrates CNV and other systematic factors directly into the differential enrichment engine. Cold Spring Harbor Laboratory Press 2012-12 /pmc/articles/PMC3514678/ /pubmed/22879430 http://dx.doi.org/10.1101/gr.139055.112 Text en © 2012, Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Method
Robinson, Mark D.
Strbenac, Dario
Stirzaker, Clare
Statham, Aaron L.
Song, Jenny
Speed, Terence P.
Clark, Susan J.
Copy-number-aware differential analysis of quantitative DNA sequencing data
title Copy-number-aware differential analysis of quantitative DNA sequencing data
title_full Copy-number-aware differential analysis of quantitative DNA sequencing data
title_fullStr Copy-number-aware differential analysis of quantitative DNA sequencing data
title_full_unstemmed Copy-number-aware differential analysis of quantitative DNA sequencing data
title_short Copy-number-aware differential analysis of quantitative DNA sequencing data
title_sort copy-number-aware differential analysis of quantitative dna sequencing data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514678/
https://www.ncbi.nlm.nih.gov/pubmed/22879430
http://dx.doi.org/10.1101/gr.139055.112
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