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Evaluation of copy number variation detection for a SNP array platform

Xin Zhang1, Renqian Du1, Shilin Li1, Feng Zhang1, Li Jin1 and Hongyan Wang12*

Author Affiliations

1 State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China

2 Children’s Hospital of Fudan University, 399 Wanyuan Road, Shanghai 201102, China

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BMC Bioinformatics 2014, 15:50  doi:10.1186/1471-2105-15-50

Published: 21 February 2014

Abstract

Background

Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform.

We selected four publicly available software packages designed for CNV calling from an Affymetrix SNP array, including Birdsuite, dChip, Genotyping Console (GTC) and PennCNV. The publicly available dataset generated by Array-based Comparative Genomic Hybridization (CGH), with a resolution of 24 million probes per sample, was considered to be the “gold standard”. Compared with the CGH-based dataset, the success rate, average stability rate, sensitivity, consistence and reproducibility of these four software packages were assessed compared with the “gold standard”. Specially, we also compared the efficiency of detecting CNVs simultaneously by two, three and all of the software packages with that by a single software package.

Results

Simply from the quantity of the detected CNVs, Birdsuite detected the most while GTC detected the least. We found that Birdsuite and dChip had obvious detecting bias. And GTC seemed to be inferior because of the least amount of CNVs it detected. Thereafter we investigated the detection consistency produced by one certain software package and the rest three software suits. We found that the consistency of dChip was the lowest while GTC was the highest. Compared with the CNVs detecting result of CGH, in the matching group, GTC called the most matching CNVs, PennCNV-Affy ranked second. In the non-overlapping group, GTC called the least CNVs. With regards to the reproducibility of CNV calling, larger CNVs were usually replicated better. PennCNV-Affy shows the best consistency while Birdsuite shows the poorest.

Conclusion

We found that PennCNV outperformed the other three packages in the sensitivity and specificity of CNV calling. Obviously, each calling method had its own limitations and advantages for different data analysis. Therefore, the optimized calling methods might be identified using multiple algorithms to evaluate the concordance and discordance of SNP array-based CNV calling.

Keywords:
CNV; CGH; Evaluation; Comparison; Performance test; Reproducibility test; Success rate; Birdsuite; dChip; GTC; PennCNV