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Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data

Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detecti...

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Autores principales: Xu, Lingyang, Hou, Yali, Bickhart, Derek M., Song, Jiuzhou, Liu, George E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003459/
https://www.ncbi.nlm.nih.gov/pubmed/27605188
http://dx.doi.org/10.3390/microarrays2030171
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author Xu, Lingyang
Hou, Yali
Bickhart, Derek M.
Song, Jiuzhou
Liu, George E.
author_facet Xu, Lingyang
Hou, Yali
Bickhart, Derek M.
Song, Jiuzhou
Liu, George E.
author_sort Xu, Lingyang
collection PubMed
description Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed.
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spelling pubmed-50034592016-09-06 Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data Xu, Lingyang Hou, Yali Bickhart, Derek M. Song, Jiuzhou Liu, George E. Microarrays (Basel) Review Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed. MDPI 2013-06-25 /pmc/articles/PMC5003459/ /pubmed/27605188 http://dx.doi.org/10.3390/microarrays2030171 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0/ This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Review
Xu, Lingyang
Hou, Yali
Bickhart, Derek M.
Song, Jiuzhou
Liu, George E.
Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
title Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
title_full Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
title_fullStr Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
title_full_unstemmed Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
title_short Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
title_sort comparative analysis of cnv calling algorithms: literature survey and a case study using bovine high-density snp data
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003459/
https://www.ncbi.nlm.nih.gov/pubmed/27605188
http://dx.doi.org/10.3390/microarrays2030171
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