By using the unique biological samples of PAE newborns as well as alcohol-exposed both hESCs and differentiated hESCs, our study shows the early effects of alcohol exposure on both embryonic and extraembryonic cells reveal interesting new candidate genes DPPA4, FOXP2, and TACR3 for the effects of PAE as well as brings forth potential biomarkers for PAE or even FASD. Here, FOXP2 is linked to pulmonary artery enlargement.