Induced pluripotent stem cells (iPSCs) offer powerful platforms for disease modelling, though maintaining genomic stability across varying culture conditions remains challenging. This study aimed to generate and characterize a new human iPSC line from peripheral blood mononuclear cells (PBMCs) of an adenylosuccinate lyase mutation carrier; and to evaluate how different extracellular matrix coatings, Matrigel, Geltrex, and BioLaminin 521, influence the genomic stability of pre-established schizophrenia-derived iPSC lines. PBMCs were reprogrammed using non-integrating Sendai virus vectors, yielding fully characterized, virus-free pluripotent clones with a normal 46, XY karyotype at an average efficiency of 0.126%. In the matrix study, high-resolution quantitative polymerase chain reaction (qPCR)-based genetic screening revealed variations in chromosomal abnormality profiles among different substrates. Across conditions, the most commonly observed recurrent submicroscopic copy number variations involved chromosome 12p (chr12p), chr17q, chr20q, and chrXp. BioLaminin 521 showed the highest overall variability, Matrigel displayed intermediate instability with a chr10p deletion, and Geltrex maintained the greatest genomic stability. However, because these alterations became more pronounced at higher passages, these outcomes are heavily influenced by prolonged passaging alongside potential matrix effects. In conclusion, while a trend suggests that matrix composition influences colony architecture, prolonged culture duration appears to drive selective replication pressures. These preliminary findings highlight the need for further validation and the importance of combining cytogenetics with molecular screening for monitoring genomic integrity.