Alison Tang: Full-length alternative isoform analysis of RNA (FLAIR) for nanopore reads

Lightning talk: Alison Tang of the University of California, Santa Cruz presented her research on using long nanopore reads to characterise full-length RNA isoforms. Long nanopore reads can span entire RNA molecules thereby facilitating the identification of exon-exon connectivity and allowing discovery and quantification of novel isoforms. Existing short-read RNA analysis tools are ill equipped to work with long nanopore reads. To address this, Alison developed the analysis tool FLAIR (full-length alternative isoform analysis of RNA). FLAIR contains two alignment steps to produce an accurate, nanopore-specific reference. It also incorporates promoter chromatin states to distinguish between 5’ truncations and true transcription start sites. Alison presented data showing how the tool works with both cDNA and native RNA sequencing data, allowing the detection of many novel isoforms (65% using native RNA sequencing of GM12878).

Using FLAIR on cancer samples with splicing factor mutations, the team at UC, Santa Cruz demonstrated that the tool is able to detect subtle splicing aberrations. In closing her presentation, Alison stated that this is ‘one of the many ways in which nanopore sequencing can expand our understanding of the transcriptome’.