The last decade has brought substantial progress in understanding the contributions of human genetic variation to neuropsychiatric conditions including ASD. However, such studies alone do not provide a roadmap for understanding disease mechanisms at the level of the functional genome or neurobiological pathways. The focus of this panel is one of the key missing components in elucidating ASD pathophysiology: an understanding of how molecular alterations play out at the level of brain, and whether molecular alterations converge on specific pathways or cell types. Jonathan Mill will present large scale analysis of methylation patterns in controls throughout development and in ASD brain. Mike Gandal will provide an overview of large-scale transcriptomic studies that define core molecular changes in ASD, and their relationship to other major psychiatric disorders. Dalila Pinto will discuss alterations at the level of lncRNA, which are increasingly recognized as potentially important regulators of gene expression and the implications of these data for future study of ASD. Lastly, Dan Geschwind will summarize work integrating multiple molecular phenotypes using a network fusion framework, as well as emerging single cell sequencing data that we expect will significantly refine our understanding of the cell and circuit level alterations in disease.