Video Poster: Full-length RNA sequencing of Alzheimer brain sample using long reads reveals complex alternative splicing patterns
Long-read mRNA sequencing such as PacBio’s Iso-Seq method offer high-throughput transcriptome profiling that circumvents the transcript assembly problem by sequencing full-length cDNA. The Iso-Seq method has emerged as the most reliable technology for fully characterizing isoforms and, in turn, help shed light on underlying disease mechanisms. Here, we have utilized the Iso-Seq method to sequence an Alzheimer’s disease whole brain?sample. This is a devastating neurodegenerative disease that affects ~44 million people worldwide, making it the most common form of dementia. Studies looking into disease mechanism have shown that changes in gene expression due to alternative splicing likely contribute to the initiation and progression of Alzheimer’s disease. Hence, efforts have been made to better understand the gene expression changes in the Alzheimer brain by sequencing the transcriptome of affected brain regions. In this study, complex alternative splicing patterns emerged, with 162,290?unique transcripts up to 14 kb in?length from 17,670 genes being detected. More than 60% of these transcripts were?novel isoforms, the vast majority of which?have supporting cage peak data and?polyadenylation signals. To further investigate the sample, we also applied the Iso-Seq solution to single cell RNA samples. In this experiment we obtained between 150,000-180,000 unique isoforms from 15,000-17,000 genes. Over 50% of the isoforms categorized as novel isoforms, suggesting a high degree of undiscovered transcripts in the human samples, demonstrating the?utility of long-read RNA sequencing for human?disease research.