Genomics doc

Tools to analyze SNP data from GWAS (Genome-Wide Association Studies) and TDTs.

Arrays

Babelomics set of tools for Single Nucleotide Polymorphisms (SNP) analysis can be found in the Genomics button of the Tools drop down menu.

This tool allows the study of SNPs applying microarray technology, and through two different analysis: Association Analysis based on SNPs and Genotype Stratification.

Association Analysis

The basic association test is for a disease trait and is based on comparing allele frequencies between cases and controls (empirical p-values are available). Also implemented are the Chi-square case/control association test, Fisher's exact test, Linear, Logistic regression and TDT test (only for family-based analysis). As well some modifications are implemented as the SNP filtering on the basis of minor allele frequency.

In general, the idea of population association studies is to identify patterns of polymorphisms that vary systematically between individuals with different disease states and could therefore represent the effects of risk-enhancing or protective alleles.

The statistical determination of how associated the genotype and phenotype are, it can be analysed with different tests that we propose in this section, where the use of one test or other principally depends on the type of incoming data.

• [More information](Association Analysis doc)

References

Variation

Burden test

• [More information](Burden test)

References