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" 'Where is the missing heritability?' is a question asked frequently in genetic research. The difficulty seems to come down to the common disease/common variant hypothesis not holding up." » Read more
Linkage Disequilibrium (LD) and Haplotype Analysis
Multi-marker analyses can increase the power of your findings, but standard programs are limiting from an exploratory perspective, and also make it difficult to work with the increasing size and density of today’s SNP analysis datasets. Powerful new plotting and analytics capabilities in SVS 7 help you perform LD and haplotype analyses with greater ease and depth than ever before.
Learn how to create LD plots, generate haplotype frequency tables, and compare single marker association results with haplotype association results.
Linkage Disequilibrium
Interactively explore LD across the entire genome, at a chromosome level, or around a specific marker or gene of interest. You can add LD plots to other plots (e.g., association results) to assess the correlation structure around significant markers. You can even view multiple LD plots together within the same genome browser to compare LD in your study population to that of a similar population (e.g. HapMap populations). It is also useful for comparing higher and lower density arrays, or comparing haplotype blocks
among two or more populations.
Haplotype Block Analysis
SVS makes it easy to automatically compute haplotype blocks based on correlation between markers and then manually manipulate them within an LD plot using a simple drag-and-drop interface. For any defined block in an LD plot, haplotype frequencies and case/control association results can be computed in real-time. Importantly, all block definitions can be saved and reloaded for subsequent analyses, freeing you to explore various block configurations without losing any work or ever having to start over.
» More about Haplotype Block Detection
Haplotype Frequency Estimation
From a given haplotype block in an LD plot you can generate four separate frequency tables, enabling you to interrogate haplotype and diplotype frequency estimations for individual samples as well as overall haplotype frequency estimations across all samples.
» More about Haplotype Frequency Estimation Methods
Haplotype Association Testing
Though chi-square p-values are generated live within an LD plot, more robust haplotype association methods are available from a spreadsheet for case/control traits. Using pre-defined block definitions or a moving window approach, you can perform haplotype association across your entire dataset employing both per-haplotype (for each haplotype in a block) and per-block tests. Several test statistics and multiple testing corrections are available, ensuring you get the most power out of multi-marker associations.
» More about Haplotype Association Testing
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