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Microarrays 2013, 2(3), 171-185; doi:10.3390/microarrays2030171
Review

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

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Received: 2 May 2013; in revised form: 4 June 2013 / Accepted: 5 June 2013 / Published: 25 June 2013
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Abstract: 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.
Keywords: copy number variation (CNV); algorithm; segmental duplication; single nucleotide polymorphism (SNP); cattle genome copy number variation (CNV); algorithm; segmental duplication; single nucleotide polymorphism (SNP); cattle genome
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Xu, L.; Hou, Y.; Bickhart, D.M.; Song, J.; Liu, G.E. Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. Microarrays 2013, 2, 171-185.

AMA Style

Xu L, Hou Y, Bickhart DM, Song J, Liu GE. Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. Microarrays. 2013; 2(3):171-185.

Chicago/Turabian Style

Xu, Lingyang; Hou, Yali; Bickhart, Derek M.; Song, Jiuzhou; Liu, George E. 2013. "Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data." Microarrays 2, no. 3: 171-185.

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