Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests.
Title | Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests. |
Publication Type | Journal Article |
Year of Publication | 2013 |
Authors | Lin, C-F, Naj, AC, San Wang, L- |
Journal | Curr Protoc Hum Genet |
Volume | 79 |
Pagination | Unit 1.27. |
Date Published | 2013 Oct 18 |
ISSN | 1934-8258 |
Keywords | Algorithms, DNA Copy Number Variations, Gene Frequency, Genome-Wide Association Study, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide |
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. |
DOI | 10.1002/0471142905.hg0127s79 |
Alternate Journal | Curr Protoc Hum Genet |
PubMed ID | 24510649 |
PubMed Central ID | PMC4015338 |
Grant List | U01 AG032984 / AG / NIA NIH HHS / United States U24 AG041689 / AG / NIA NIH HHS / United States |