Fig. 1

Detection of transposable element insertions (TEIs) in the SSC cohort. A Pipeline and analysis overview. Quad and trio bam files were analyzed for TEIs using a dockerized version of xTea on the cloud in Amazon Web Services (AWS). Candidate TE insertions were filtered using xTea filters, and filters for regions of the genome with reference and known non-reference TEIs for a high confidence set. A custom pipeline for detection of de novo insertions was used, and candidates were manually inspected on the Integrative Genomics Viewer. Enrichment or depletion of TEIs in ASD genes, high pLI genes, genomic regions, and regulatory regions in fetal brain development was tested by simulation analyses. A subset of candidates was validated by full-length PCR. B Mean number of TEIs detected in the SSC cohort with standard deviation. C Percentage of insertions in the SSC cohort that were not found in previous studies (novel) or overlap with TEIs from previous analyses (known) for all TEIs including those in parents and children (left) and Venn diagram showing overlap with other large cohort studies for TEIs detected in unrelated parental samples in our cohort (right). D Cumulative fraction of TEIs in unrelated parental samples which are found at a certain population allele frequency (PAF) within the SSC cohort. 94% L1, 92% Alu, and 95% SVA insertions show < 1% PAF