CNV-seq, a new method to detect copy number variation using high-throughput sequencing

Chao Xie,Martti T Tammi

doi:10.1186/1471-2105-10-80

Chao Xie, Martti T Tammi

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https://doi.org/10.1186/1471-2105-10-80

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BackgroundDNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations.ResultsHere, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads.ConclusionSimulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.

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DNA copy number variation (CNV) has been recognized as an important source of genetic variation
The method is based on a robust statistical model that allows confidence assessment of observed copy number ratios and is conceptually derived from Array comparative genomic hybridization (aCGH) (Figure 1)
We have developed a method to detect CNV using shotgun data

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Introduction

DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. DNA copy number variation (CNV) has long been known as a source of genetic variation, but its importance has only been recognized recently [1,2]. The rapid development of new sequencing technologies is continuously increasing the speed of sequencing and decreasing the cost. The nextgeneration sequencing, such as 454 [8], Solexa [9] and SOLiD [10] have already showed advantages over microarrays in several aspects.

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