Abstract

Copy number variation is one of the common types of structure variation in the human genome. There have been many technologies developed to detect copy number variations and one of them is the SNP array. With the progression of chip technology, we can quickly obtain genome-wide information. A number of algorithms proposed to efficiently extract chromosome copy number variation information from the huge SNP data. The goal of this study is to know how these CNV detection algorithms perform. In this article, we compare four algorithms on HapMap 270 samples from Affymetrix SNP 6.0 array data. The performance is evaluated based on the consistency of the trios and the concordance rate with two published data. According to our analysis, there is not a single CNV detection algorithm outperforming all the other CNV calling methods.

BIOCONDUCTOR, http://www.bioconductor.org/
COKGEN, http://mendel.gene.cwru.edu/laframboiselab/software.php
Colella, S., C. Yau, et al. (2007). "QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data." Nucleic Acids Res 35(6): 2013-2025.
Fellermann, K., D. E. Stange, et al. (2006). "A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon." Am J Hum Genet 79(3): 439-448.
Feuk, L., A. R. Carson, et al. (2006). "Structural variation in the human genome." Nat Rev Genet 7(2): 85-97.
GenoCN, http://www.bios.unc.edu/~wsun/software/genoCN.htm
Huang, J., W. Wei, et al. (2006). "CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays." BMC Bioinformatics 7: 83.
Kidd, J. M., G. M. Cooper, et al. (2008). "Mapping and sequencing of structural variation from eight human genomes." Nature 453(7191): 56-64.
Korn, J. M., F. G. Kuruvilla, et al. (2008). "Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs." Nat Genet 40(10): 1253-1260.
Laframboise, T., D. Harrington, et al. (2007). "PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data." Biostatistics 8(2): 323-336.
McCarroll, S. A., F. G. Kuruvilla, et al. (2008). "Integrated detection and population-genetic analysis of SNPs and copy number variation." Nat Genet 40(10): 1166-1174.
Olshen, A. B., E. S. Venkatraman, et al. (2004). "Circular binary segmentation for the analysis of array-based DNA copy number data." Biostatistics 5(4): 557-572.
PennCNV, http://www.openbioinformatics.org/penncnv/penncnv_download.html
PennCNV-Affy, http://www.openbioinformatics.org/penncnv/penncnv_tutorial_affy_gw6.html
Pique-Regi, R., J. Monso-Varona, et al. (2008). "Sparse representation and Bayesian detection of genome copy number alterations from microarray data." Bioinformatics 24(3): 309-318.
QuantiSNP, http://groups.google.co.uk/group/quantisnp/web/software-updates
Rovelet-Lecrux, A., D. Hannequin, et al. (2006). "APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy." Nat Genet 38(1): 24-26.
Sebat, J., B. Lakshmi, et al. (2007). "Strong association of de novo copy number mutations with autism." Science 316(5823): 445-449.
Simon-Sanchez, J., S. Scholz, et al. (2008). "Genomewide SNP assay reveals mutations underlying Parkinson disease." Hum Mutat 29(2): 315-322.
Sun, W., F. A. Wright, et al. (2009). "Integrated study of copy number states and genotype calls using high-density SNP arrays." Nucleic Acids Res 37(16): 5365-5377.
Walsh, T., J. M. McClellan, et al. (2008). "Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia." Science 320(5875): 539-543.
Wang, K., M. Li, et al. (2007). "PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data." Genome Res 17(11): 1665-1674.
Winchester, L., C. Yau, et al. (2009). "Comparing CNV detection methods for SNP arrays." Brief Funct Genomic Proteomic 8(5): 353-366.
Yavas, G., M. Koyuturk, et al. (2009). "An optimization framework for unsupervised identification of rare copy number variation from SNP array data." Genome Biol 10(10): R119.