Fig. 3. Allele-specific transcriptional activity of ASD noncoding mutations.

Differential expression by proband or sibling alleles in a dual luciferase assay demonstrated that 57 predicted high TRD disease impact mutations fall in active regulatory elements and the mutations confer substantial changes to the regulatory potential of the sequence. Cells were transfected with pGL4.23-based expression plasmid containing 230nt of genomic region as well as a transfection control, and then luminescence was assayed 42h later (Methods). Y-axis shows the magnitude of transcription activation activity normalized to sibling allele. Significance levels were computed based on t-test and Fisher’s combined probability test (two-sided, stars indicate significance level *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0.0001; Methods). Sample sizes for all tests are in Supplementary Table 6. Central values of the box plot represent the median; the box extends from the 25th to the 75th percentile; and whiskers extend to the maximum and minimum values no further than 1.5 * IQR from the hinge (where IQR is the inter-quartile range, or distance between the first and third quartiles).