In this sense, the vast data generated during the human genome project only provide a minimal help to establish the relationship between sequence variation and susceptibility to disease.
Genevar software was used to determine associations between sequence variation and gene expression (http://www.sanger.ac.uk/resources/software/genevar/) [ 7].
Summary: Genevar (GENe Expression VARiation) is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression.
However an inspection, review and interpretation of the output by an experienced and knowledgeable person is essential to understand the genomic context of these datasets and can be critical to make connections between sequence variation and biological phenomena.
This fact allows in principle to distinguish between sequence variation and bisulfite conversion and therefore to i) avoid wrong inference of the methylation state due to sequence variation and ii) detect sequence variation in the same sample preparation as the methylation levels.
Although we did not find any evidence for association between sequence variation and HTGW in our cohort, we identified three CpG sites whose DNA methylation levels were associated with HTGW, and these associations were largely independent of other metabolic syndrome phenotypes or DNA sequence variation.
Now there are thousands of exome and whole-genome sequences (soon to be tens of thousands, and eventually millions), which have been determined with the aim of identifying disease-causing variants and, more broadly, establishing well-founded correlations between sequence variation and specific phenotypes.
In wild-type, the frequency of crossing over per length of DNA varies as much as ten-fold between the cluster and an arm of chromosome I [ 9], making this species an excellent model for studying the relationship between sequence variation and recombination rate.
Our data on CpCSV appear to be largely in line with the notion of a strict correlation between sequence variation and geographical origin of luteovirus isolates, as recently observed also for Sugarcane yellow leaf virus (ScYLV) [ 22] and Curcurbit aphid-borne yellows virus [ 30].
