title: Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests.
abstract: High-density SNP genotyping technology provides a low-cost, effective tool for conducting Genome Wide Association (GWA) studies. The wide adoption of GWA studies has indeed led to discoveries of disease- or trait-associated SNPs, some of which were subsequently shown to be causal. However, the nearly universal shortcoming of many GWA studies--missing heritability--has prompted great interest in searching for other types of genetic variation, such as copy number variation (CNV). Certain CNVs have been reported to alter disease susceptibility. Algorithms and tools have been developed to identify CNVs using SNP array hybridization intensity data. Such an approach provides an additional source of data with almost no extra cost. In this unit, we demonstrate the steps for calling CNVs from Illumina SNP array data using PennCNV and performing association analysis using R and PLINK.
authors: Department of Pathology and Laboratory Medicine and Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
authors: Chiao-Feng
authors: CF
authors: Lin
authors: Department of Biostatistics and Epidemiology and Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
authors: Adam C
authors: AC
authors: Naj
authors: Department of Pathology and Laboratory Medicine and Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
authors: Li-San
authors: LS
authors: Wang
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D005787:Gene Frequency; D055106:Genome-Wide Association Study / Q000379:methods; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide
keywords: CNV calling; SNP genotyping array; association study; burden analysis; copy number variations (CNV); genome-wide association studies