CLN1 disease is a rare, neurodegenerative disorder caused by mutations in the PPT1 gene, which encodes a lysosomal enzyme responsible for depalmitoylating proteins. Disease presents at different ages and currently lacks a definitive cure or full molecular understanding. This work adopts a personalised medicine approach to investigate transcript isoform expression in specific CLN1 patients and explores targeted therapeutic strategies. Transcript isoforms are mature mRNA products derived from the same gene through processes such as alternative splicing, making them crucial for gene regulation, protein diversity, and understanding disease mechanisms. iPSCs were generated from skin fibroblasts from a New Zealand juvenile-onset CLN1 patient and their parents. Early-stage validation confirmed expression of key pluripotency markers (OCT4, SOX2, NANOG, and SSEA4), supporting the lines' pluripotency. Western blots of patient-derived cell lysates revealed reduced PPT1 protein levels, with enzyme activity at approximately 4%, supporting a partial loss of function consistent with juvenile onset. RNA-seq differential expression analysis of patient samples from NCBI Geo DataSets utilizing R suggests dysregulation of lysosomal and synaptic pathways. To complement these findings, PPT1 splice isoform usage was assessed using ENCODE long-read RNA-seq data. This revealed 202 valid PPT1 transcript isoforms across normal human tissues, far exceeding the limited three isoforms currently annotated on NCBI. These findings will guide the design of antisense oligonucleotide therapies to modulate harmful or protective transcript isoforms in patient iPSC-derived neurons and astrocytes, currently developing. We aim to unravel the transcript dynamics of CLN1 disease and contribute towards developing precision therapies.