Copy number variation association software tools | Genome-wide association study data analysis
Genome-wide association studies (GWAS) using Copy Number Variation (CNV) are becoming a central focus of genetic research. CNVs have successfully provided target genome regions for some disease conditions where simple genetic variation (i.e., SNPs) has previously failed to provide a clear association.
A statistical framework for performing case-control CNV association studies that applies likelihood ratio testing of quantitative CNV measurements in cases and controls. CNVtools can model large batch effects that do not follow group membership, which is an important consideration in large-scale association studies. It is based on methods that are robust to differential errors and noisy data and can achieve maximal theoretical power. CNVtools‘ computational efficiency is such that it would be feasible to use this software to test for CNV associations genome-wide (>10,000 loci).
Integrates: (i) data import from most common formats of Affymetrix, Illumina and aCGH arrays; (ii) a fast and accurate segmentation algorithm to call CNVs based on Genome Alteration Detection Analysis (GADA); and (iii) functions for displaying and exporting the Copy Number calls, identification of recurrent CNVs, multivariate analysis of population structure, and tools for performing association studies. The package provides the tools for creating a complete integrated pipeline from data normalization to statistical association. It can efficiently handle a massive volume of data consisting of millions of genetic markers and hundreds or thousands of samples with very accurate results.
Takes CNV calls as input and creates probe based statistics for CNV occurrence in (cases and controls, families, or population with quantitative trait) then calls CNVRs based on neighboring SNPs of similar significance. CNV calls may be from aCGH, SNP array, Exome Sequencing, or Whole Genome Sequencing.
Enables, in a combinatorial way, the analysis of single nucleotide polymorphism (SNP) genotype calls, copy numbers, polymorphic copy number variations (CNVs) and gene expression. SNPExpress is available for use with Affymetrix DNA mapping arrays, Illumina HumanHap550 Genotyping BeadChip and Affymetrix GeneChips. The software facilitates the identification of biologically and clinically relevant entities. It can be useful to genome-wide studies by providing an integrated view of data from DNA mapping and mRNA expression arrays.
A user-friendly program for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification.
Automates statistical tests for the association between single nucleotide polymorphisms (SNPs) and examined sample conditions. DMET-Analyzer can genotype function variants in a defined set that comprises genes known to be related to drug absorption, distribution, metabolism and excretion. It returns a list of SNPs candidates and the related p-values whose distribution is different among classes.
An R package for carrying out association analysis of common copy number variants in population-based studies. This package includes functions for testing for association with different classes of response variables (e.g. class status, censored data, counts) under a series of study designs (case-control, cohort, etc) and inheritance models, adjusting for covariates.