Related Experiment Video
Updated: Jan 19, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers
Yanbo Yang1, Qiong Zhang2, Ya-Ru Miao2
1Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China.
Abstract:
Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3' untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3'UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified. By integrating apaQTLs with survival and genome-wide association studies (GWAS) data, we further identified 2154 apaQTLs associated with patient survival time and 151 342 apaQTLs located in GWAS loci. In addition, we designed an online tool to predict the effects of SNPs on PASs by utilizing PAS motif prediction tool. Finally, we developed SNP2APA, a user-friendly and intuitive database (http://gong_lab.hzau.edu.cn/SNP2APA/) for data browsing, searching, and downloading. SNP2APA will significantly improve our understanding of genetic variants and APA in human cancers.
Related Concept Videos
08:35Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
06:41In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
09:19Evaluating the Effectiveness of Cancer Drug Sensitization In Vitro and In Vivo
09:37Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
08:46Genetic Variant Detection in the CALR gene using High Resolution Melting Analysis
07:15Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

