NCM 2022: Ultra-deep targeted long-read transcriptome sequencing reveals isoform diversity across human neurodevelopment

Alternative splicing dramatically increases transcriptomic and proteomic diversity from the coding genome and is an important mechanism in the control of gene expression in the central nervous system. We used Oxford Nanopore Technologies (ONT) whole-transcriptome sequencing to profile transcript diversity across human brain development. In parallel, we performed ultradeep targeted transcriptome sequencing across a panel of >300 genes associated with schizophrenia, autism, and intellectual disability. ONT-barcoded cDNA was pooled and enriched with a panel of >6000 hybridisation probes before ONT library preparation and sequencing. A bespoke data analysis pipeline was used for isoform visualisation and quantification. We identified widespread transcript diversity in the developing cortex with the detection of novel transcripts not previously described in existing genomic annotations. Our data confirm the importance of alternative splicing in the human cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain.