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


Robinson, Mark D; Strbenac, Dario; Stirzaker, Clare; Statham, Aaron L; Song, Jenny Z; Speed, Terence P; Clark, Susan J (2012). Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Research, 22(12):2489-2496.

Abstract

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.

Abstract

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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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Molecular Life Sciences
Dewey Decimal Classification:570 Life sciences; biology
Uncontrolled Keywords:Statistics; Epigenomics; Next generation sequencing
Language:English
Date:9 August 2012
Deposited On:06 Sep 2012 09:16
Last Modified:16 Feb 2018 23:46
Publisher:Cold Spring Harbor Laboratory Press
ISSN:1088-9051
OA Status:Hybrid
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1101/gr.139055.112
PubMed ID:22879430

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