Advances in the identification and analysis of allele-specific expression
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Volume
1
Publisher
Publisher URL
DOI
10.1186/gm56
Journal
GENOME MEDICINE
ISSN
1756-994X
Metadata
Show full item recordAbstract
Allele-specific expression (ASE) is essential for normal development and many cellular processes
but, if impaired, can result in disease. ASE is a feature of organisms with genomes consisting of
more than one set of homologous chromosomes. The higher the number of chromosome sets
(ploidy) per cell, the higher the potential complexity of ASE. Humans, for instance, are diploid
(except germ cells, which are haploid), resulting in multiple possible expression states in time and
space for each set of alleles. ASE is invoked and modulated by both genetic and epigenetic
changes, affecting the underlying DNA sequence or chromatin of each allele, respectively.
Although numerous methods have been developed to assay ASE, they usually require RNA to be
available and are dependent upon genetic polymorphisms (such as single nucleotide polymorphisms (SNPs)) to differentiate between allelic transcripts. The rapid convergence to secondgeneration sequencing as the method of choice to examine genomic, epigenomic and
transcriptomic data enables an integrated and more general approach to define and predict ASE,
independent of SNPs. This ‘Omni-Seq’ approach has the potential to advance our understanding
of the biology and pathophysiology of ASE-mediated processes by elucidating subtle combinatorial effects, leading to the accurate delineation of sub-phenotypes with consequential benefit for
improved insight into disease etiology.