Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data

Applications of ENCODE data to Systematic Analyses via Data Integration

Large-scale genomic data have been utilized to generate unprecedented biological findings and new hypotheses. To delineate functional elements in the human genome, the Encyclopedia of DNA Elements (ENCODE) project has generated an enormous amount of genomic data, yielding around 7,000 data profiles in different cell and tissue types. In this article, we reviewed the systematic analyses that have integrated ENCODE data with other data sources to reveal new biological insights, ranging from human genome annotation to the identification of new candidate drugs. These analyses demonstrate the critical impact of ENCODE data on basic biology and translational research.

Genetic variants in lncRNA H19 are associated with the risk of oral squamous cell carcinoma in a Chinese population

To evaluate whether the genetic variants in H19 influence the risk of oral squamous cell carcinoma (OSCC) in a Chinese population, a case-control study was conducted to analyze four functional single nucleotide polymorphisms (SNPs) in H19. The cohort comprised of 444 OSCC cases and 984 healthy controls, and the study further evaluated the biological effect by bioinformatics prediction and functional experiments. Two SNPs, rs217727 and rs2839701, were found to be associated with the risk of OSCC [rs217727: odds ratio (OR) = 1.32, 95% confidence interval (CI) = 1.11-1.58, P = 0.002; rs2839701: OR = 1.23, 95% CI = 1.04-1.46, P = 0.019].Bioinformatics predicted that rs2839701 C>G might alter the secondary structure of H19. In addition, rs2839701 C>G inhibited the transcription activity and was correlated with the decreased expression of downstream gene MRPL23-AS1 that was downregulated in OSCC. The current results suggested that the SNPs in H19 may play a major role in genetic susceptibility to OSCC.