30Autism is a heterogenous collection of disorders with a complex molecular underpinning. 31Evidence from post mortem studies using adult brains have identified atypical co-expression 32 of genes which may occur during the prenatal period. Recent studies using induced pluripotent 33 stem cells (iPSCs) generated from autistic individuals have suggested that prenatal 34 development is a critical period for the emergence of pathophysiology associated with this 35 condition. However, how early during development these differences emerge and whether such 36 alterations can be seen across the development of multiple brain regions is unclear. In this study 37 we investigated whether early prenatal stages of neurodevelopment differ between iPSCs 38 generated from typically developing and autistic individuals. We specifically selected autistic 39 individuals unrelated to each other with a heterogeneous genetic background and no known 40 comorbidities, to probe for common molecular phenotypes. Differentiation of iPSCs towards a 41 cortical lineage revealed abnormal cell fate acquisition from an early stage of development. 42Interestingly, abnormal differentiation occurred in the absence of alteration in cell proliferation 43 during cortical differentiation, differing from previous studies. Moreover, these effects 44 appeared specific for the acquisition of a cortical fate, as differentiation of iPSCs towards a 45 midbrain lineage was not accompanied by differences in neurogenesis between typically 46 developing and autism iPSC lines. RNA-sequencing on a subset of our cohort further revealed 47 autism-specific signatures during cortical differentiation similar to that observed in post 48 mortem studies, indicating a potential common biological mechanism. Together, these data 49 suggest unique developmental differences associated with autism may establish at an early 50 prenatal stage. 51 52 53 4 54 Recent methodological advances in the field of induced pluripotent stem cell (iPSC) 75technology [15][16][17][18][19][20] has made it possible to study prenatal cellular behaviour in autism in detail, 76 something that was not possible using post mortem brains. IPSCs have similar abilities to 77 5 embryonic stem cells to generate any tissue of the body. These can then be differentiated into 78 neurons of various lineages 15-17, 19, 20 . As the neurons contain the same genetic information as 79 the individual from whom it was derived, typical or autistic, its cellular behaviours is 80 influenced by its genetic background. Using these methods, studies have shown significant 81 anomalies in cellular/molecular behaviour during prenatal-equivalent periods of development 82 in autistic individuals [21][22][23] . One such study generated iPSCs from autistic individuals who were 83 comorbid for macrocephaly, and demonstrated: (1) atypical cortical differentiation and 84 increased cell proliferation of cortical neural precursor cells (NPCs) from iPSCs, and (2) an 85 imbalance in excitatory (glutamate-producing) and inhibitory (GABA-produ...