Human Genetic Variation and Gene Expression

Cross-Species Conservation Indirect Evidence of Regulatory Elements 

An effective and elegantly uncomplicated method for directly assessing allele-specific transcript abundance within a normal chromosomal context has been used by several groups (22,23,25) to examine allele-specific expression in human samples. Cowles et al. (26) have used this method to examine such variation between mouse strains. These groups use SNPs in the transcribed regions of genes as tools to measure allele-specific expression levels of genes 

A group led by Lee and Buetow (28) describes an efficient approach to EAI analysis that uses Affymetrix HuSNP chips to assay for both sample genotype and allele-specific expression level. Of 602 informative (heterozygous) genes expressed in kidney or liver, 54% were found to show EAI in at least one of seven individuals tested. 

The HaploChIP approach does not require the presence of an indicator SNP in a transcribed region SNPs in chromatin outside transcribed 

Neither EAI nor HaploChIP determine which SNP is causing an effect on gene expression additional techniques are required for this. As noted by Hudson (30), such variants may be targets for manipulation of expression levels to restore full gene function. 

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