Summary in one sentence:
It is a review generally reviewing the methods for genome-wide allele-specific analysis and the mechanisms causing the allelic biases.

Outlines:
1. eQTL is what researchers are focusing on to find out human genetic variation that affects gene expression. However, direct assessment of cis-regularoty variation requires allele-specific approaches.
2. An example showing why use allele-specific analysis to focus on cis effects in functional assays: transcription is repressed by an incresasing amount of the transcriptional product, therefore the total expression of the transcript varies little across samples with different cis-regulatory genotypes. However, in heterozygotes, allele-specific studies can readily detect differences in expression between the alleles and therefore reveal the effect of cis-regulatory genetic variation.
3. Allele-specific differences among transcripts within an individual can affect up to 30% of loci.
4. To do genome-wide allele-specific analysis, two different types of methods can be used: Polymorphism-directed approaches, Global approaches.
5*. Polymorphism-directed approaches only focus on the specific informative sites, so the information density of genomic data increase (such as the read density become higher than ordinary RNA-Seq data). While using RNA/cDNA data as case sample, the genomic DNA data can be used as control, which can control for the technical biases ingerent in quantitative analysis of allele ratios. These include Genome-wide genotyping arrays, and an alternative approach to assay allelic expression is the use of custom padlock probes to capture known exonic polymorphisms on a large scale, with digital quantification of the alleles in captured sequences from a genomic DNA control and correponding RNA (cDNA) is carried out by NGS.
6*. Global approaches always use NGS of transcriptome (RNA-seq). RNA-seq reads at the polymorphic sites provide digital estimates of allelic abundance, and simple statistical approaches allow the detection of sites that show potentially skewed expression. Chip-seq allows the detection of total binding at specific sequences and also of allele-specific chromatin activity in cases in which heterozygous sites overlap ChIP-seq peaks. Two difficulties are available: 1) all alignment methods for short sequences reads are biased towards the alleles that are represented in the reference genome; 2) the relatively low coverage of polymorphic sites in all global NGS studies to date.
7. With SNP-targeted studies, 20% of sites show 1.5-fold and 30% of measured transcripts show 1.2-fold difference between alleles. With RNA-seq or ChIP-seq data, ranges from 7 to 11% of sites measured (subtle variation may not be detected).
8. In the scale of allelic expression, cell lines from the same individual are more similar than ones from different individuals, which suggests a genetic basis for allelic basis for allelic expression differences. In a previous study, many of the significant differences in allelic expression were observed in genes that were not detected to have eQTLs. It shows that these allelic biases are because of loci variants instead of eQTLs. Allelic biases show more tissue independence, at least half of cis-regulatory SNPs show effects in multiple cell types. The author tends to agree with the view that allelic differences in chromatin would be expected to yield changes in allelic expression statue.

Further reading:
Wiki of "padlock probe": wiki/Molecular_Inversion_Probe#Padlock_Probe
Wiki of "Expression quantitative trait loci": wiki/Expression_quantitative_trait_loci
The two references David gave me for the second time.

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