Genome-wide identification of allele-specific effects on gene expression for single and multiple individuals |
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Authors: | Shaojun Zhang Fang Wang Hongzhi Wang Fan Zhang Bin Xu Xia Li Yadong Wang |
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Affiliation: | 1. School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China;2. Department Of Bioinformatics, Harbin Medical University, Harbin 150086, China |
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Abstract: | The analysis of allele-specific gene expression (ASE) is essential for the mapping of genetic variants that affect gene regulation, and for the identification of alleles that modify disease risk. Although RNA sequencing offers the opportunity to measure expression at allele levels, the availability of powerful statistical methods for mapping ASE in single or multiple individuals is limited. We developed a maximum likelihood model to characterize ASE in the human genome. Approximately 17% of genes displayed an allele-specific effect on gene expression in a single individual. Simulations using our model gave a better performance and improved robustness when compared with the binomial test, with different coverage levels, allelic expression fractions and random noise. In addition, our method can identify ASE in multiple individuals, with enhanced performance. This is helpful in understanding the mechanism of genetic regulation leading to expression changes, alternative splicing variants and even disease susceptibility. |
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Keywords: | ASE, allele-specific gene expression eQTLs, expression quantitative traits loci RT-PCR, real-time polymerase chain reaction CEU, Caucasians of Northern and Western European origin CHB, Chinese individuals from Beijing University JPT, Japanese individuals from Tokyo YRI, Yoruba from Ibadan, Nigeria RNA-seq, high-throughput RNA sequencing SNP, single nucleotide polymorphisms FDR, false discovery rate AUC, the area under the curve HLA-DPA1, major histocompatibility complex, class II, DP alpha 1 MHC, major histocompatibility complex HBV, hepatitis B virus UTR, untranslated region ROC, receiver operating characteristic |
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