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. 2022 Aug 18;54(9):1305–1319. doi: 10.1038/s41588-022-01148-2

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 2 — Gene sets were defined and grouped by transcriptome proteome, neuronal regulome, ASD gene prediction scores, genetic evidence from neuropsychiatric diseases, and gene level constraint. Analyses were repeated after removing known ASD/NDD genes. Number of genes in each set before and after removing known genes are shown in bracket below gene set. Dots represent fold enrichment of DNVs or odds ratio for over-transmission of LoFs in each set. Horizontal bars indicate 95% confidence interval. For each gene set, also shown are the percentage of excessive DNVs in cases and percentage of over-transmission of rare, inherited LoFs to cases. (A) De novo enrichment analysis was performed by dnEnrich that conditional on the overall increase in burden of de novo damaging variants in cases compared with controls (Methods). P-values were derived from 100,000 random permutations of de novo damaging variants among all 5,754 constrained genes and accounts for the tri-nucleotide sequence context and gene length. (B) Enrichment of rare, inherited LoFs was evaluated by comparing the transmission and non-transmission of ultra-rare LoFs with pExt > =0.1 in the gene set versus those in all other constrained genes using a 2-by-2 table. P-values were given by chi-squared test.