Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis.

Expression quantitative trait loci (eQTL) analyses detect genetic variants (SNPs) associated with RNA expression levels of genes. The conventional eQTL analysis is to perform individual tests for each gene-SNP pair using simple linear regression and to perform the test on each tissue separately ignoring the extensive information known about RNA expression in other tissue(s). Although Bayesian models have been recently developed to improve eQTL prediction on multiple tissues, they are often based on uninformative priors or treat all tissues equally. In this study, we develop a novel tissue augmented Bayesian model for eQTL analysis (TA-eQTL), which takes prior eQTL information from a different tissue into account to better predict eQTL for another tissue. We demonstrate that our modified Bayesian model has comparable performance to several existing methods in terms of sensitivity and specificity using allele-specific expression (ASE) as the gold standard. Furthermore, the tissue augmented Bayesian model improves the power and accuracy for local-eQTL prediction especially when the sample size is small. In summary, TA-eQTL's performance is comparable to existing methods but has additional flexibility to evaluate data from different platforms, can focus prediction on one tissue using only summary statistics from the secondary tissue(s), and provides a closed form solution for estimation.

[Analysis of protein expression feature and construction of procaryotic expression system for human papillomavirus type 16 (HPV-16) E4 gene].

OBJECTIVE: To clone the E4 gene (E4) from human papillomavirus type 16(HPV-16), construct the engineering bacteria of prokaryotic expression, and explore the expression conditions and the characters of expression product. METHODS: The complete E4 gene was cloned by PCR from the sample cell extract of clinical cervical disease that was the positive HPV-16 confirmed by Real-PCR. The E4 DNA fragment was inserted into the pET32a(+) to construct a prokaryotic expression plasmid, called as pET32/E4. Then the expression plasmids were transferred into competent E. coli BL21 (DE3). Recombinant DNA was identified by Bgl II and Hind III digestion, and then sequencing. The recombine bacterium, BL21/E4, was induced with different IPTG concentrations at different temperatures. The expressed proteins were checked and analyzed by SDS-PAGE and Gel-Pro Analyzer 4. His-tag of BL21/E4 expression protein was hybridized to McAb. RESULTS: The E4 gene cloned by PCR was about 342 bp. The blasted result showed that the E4 gene had 99% homology of HVP-16 DNA sequence, the cloned E4 gene expression frame was the same as HVP-16 East Asia strain's. Compared with other HPV-16 strains in GenBank, the homology of E4 gene was above 97%. pET32/E4 could express recombinant E4 (rE4) in BL21. The highest expression, which was 12.2% or 12.8% of total bacterial proteins respectively, was gotten when BL21/E4 was induced by 0.1 mmol/L IPTG at 28 degrees C or 37 degrees C for 18 hours. The results of SDS-PAGE and Western blot showed the rE4 was expressed mainly to form the inclusion body, and to fuse with his-tag (rE4/His), that was soluble and had a molecular weight as about 34 KDa. CONCLUSION: We cloned successfully the E4 gene from HPV-16 and constructed the prokaryotic expression E. coli BL21/E4, which could expression rE4 protein fused with his-tag (rE4/His), effectively. The fused protein could react to McAb recognizing His-tag, which was convenience purified by affinity chromatography. The above research results built a good foundation for preparing the high grade of purity E4 protein and developing the relative study.