Additional file 2 of Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

Additional file 2. Table 1 Numbers of SNPs from each GWAS, and number remaining after QC (retaining SNPs in all of HapMap3 reference, UKB genotyping and AAB genotyping). Table 2 SBayesR parRes output. Table 3 Statistics for tests of comparison of PGS between groups (ASD, SIB, UNR, UKB). Table 4 pTDT analysis results. Table 5 Summary of statistics for PGS correlations. Table 6 Variance explained by the PGS. Table 7a List of ASD/ID-related CNVs aggregated from ClinGen and DECIPHER. b List of ASD/ID/DD-related genes aggregated from Satterstrom et al. (2020) and DDD Study (2017) and overlapping with ENSEMBL hg19 gene set. Note that some genes are repeated as there are multiple transcripts that were considered for overlap. Table 8a: Identified CNVs in the AAB corresponding with CNVs reported by parents in the AAB medical history survey. Please note that this information is limited to that which was reported by parents, and is intended to be used to help assess replication in our pipeline. b Phenotypic correlates of called AAB CNVs overlapping ClinGen and DECIPHER CNVs. clingen_ddd.* provides start, end and widths of reference CNVs; critgene.* provides start and end of critical gene/s within reference CNVs; overlap_pcent refers to the % overlap of the called CNV, as a proportion of the ClinGen and/or DECIPHER-defined CNV. c Large CNVs (>1 Mb) identified within the AAB. d CNVs overlapping ASD/ID/DD-associated genes from Satterstrom et al. (2020) and DDD Study (2017). Table 9 Overlap of Australian Autism Biobank (AAB) phenotypes with the Simons Simplex Collection (SSC) and Simons Foundation Powering Autism Research for Knowledge (SPARK).