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Main areas: Genomics

fgardos edited this page Dec 30, 2014 · 1 revision

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 purpose of this set of tests is to study association between genetic markers and phenotype or traits.

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.

  • [Detailed information](Association Analysis doc)

Stratification

Another study that one can handle with our tools is a simple but potentially powerful approach to population stratification.

Complete linkage agglomerative clustering is applied, based on pairwise identity-by-state (IBS) distance. In addition, some modifications are taken into account in the clustering process: a significant pairwise population concordance test for whether two individuals belong to the same population (i.e. do not merge clusters that contain significantly different individuals) and also cluster size restrictions (i.e. such that, with a cluster size of 2, for example, the subsequent association test would implicitly match every case with its nearest control, as long as the case and control do not show evidence of belonging to different populations). *

( * taken from PLINK documentation in http://pngu.mgh.harvard.edu/~purcell/plink/ )

  • [Detailed information](SNP stratification doc)

Variation

Burden test

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