A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read d...

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Main Authors: Plagnol, Vincent, Curtis, James, Epstein, Michael, Mok, Kin Y., Stebbings, Emma, Grigoriadou, Sofia, Wood, Nicholas W., Hambleton, Sophie, Burns, Siobhan O., Thrasher, Adrian J., Kumararatne, Dinakantha, Doffinger, Rainer, Nejentsev, Sergey
Format: Online
Language:English
Published: Oxford University Press 2012
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476336/
id pubmed-3476336
recordtype oai_dc
spelling pubmed-34763362012-12-12 A robust model for read count data in exome sequencing experiments and implications for copy number variant calling Plagnol, Vincent Curtis, James Epstein, Michael Mok, Kin Y. Stebbings, Emma Grigoriadou, Sofia Wood, Nicholas W. Hambleton, Sophie Burns, Siobhan O. Thrasher, Adrian J. Kumararatne, Dinakantha Doffinger, Rainer Nejentsev, Sergey Original Papers Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls. Oxford University Press 2012-11-01 2012-08-31 /pmc/articles/PMC3476336/ /pubmed/22942019 http://dx.doi.org/10.1093/bioinformatics/bts526 Text en © The Author 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Plagnol, Vincent
Curtis, James
Epstein, Michael
Mok, Kin Y.
Stebbings, Emma
Grigoriadou, Sofia
Wood, Nicholas W.
Hambleton, Sophie
Burns, Siobhan O.
Thrasher, Adrian J.
Kumararatne, Dinakantha
Doffinger, Rainer
Nejentsev, Sergey
spellingShingle Plagnol, Vincent
Curtis, James
Epstein, Michael
Mok, Kin Y.
Stebbings, Emma
Grigoriadou, Sofia
Wood, Nicholas W.
Hambleton, Sophie
Burns, Siobhan O.
Thrasher, Adrian J.
Kumararatne, Dinakantha
Doffinger, Rainer
Nejentsev, Sergey
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
author_facet Plagnol, Vincent
Curtis, James
Epstein, Michael
Mok, Kin Y.
Stebbings, Emma
Grigoriadou, Sofia
Wood, Nicholas W.
Hambleton, Sophie
Burns, Siobhan O.
Thrasher, Adrian J.
Kumararatne, Dinakantha
Doffinger, Rainer
Nejentsev, Sergey
author_sort Plagnol, Vincent
title A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
title_short A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
title_full A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
title_fullStr A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
title_full_unstemmed A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
title_sort robust model for read count data in exome sequencing experiments and implications for copy number variant calling
description Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.
publisher Oxford University Press
publishDate 2012
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476336/
_version_ 1611917593954746368

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