Table 1.
Genes with multiple de novo variants.
Fig 1.
Quantile-quantile plot for gene-level association tests interrogating LoF variants.
Black dots represent transformed p values against the expected transformed p values for genes with qualifying LoF variants. The red dot corresponds to the p value associated with SON however all four variants driving this signal were found to be false positives with Sanger sequencing. The red line indicates the expectation under the null model of no effect on risk.
Table 2.
Top associations from the gene-level case-control collapsing analyses.
Fig 2.
Distribution of MAP1B LOF alleles in PVNH cases (red dots), in individuals from ExAC and gnomAD databases (blue dots with number of alleles observed represented by number of dots running vertically at this site), and in the Deciphering Developmental Disorders case (orange dot).
A Sanger confirmed de novo variant is indicated with a white dot in the circle.
Table 3.
MAP1B LoF qualifying variants identified in PVNH patients.
Fig 3.
Brain MRI of subjects pvhnz9000cfc1 (top) and mother (bottom).
Images are coronal T1-weighted (left column) and axial T1-weighted (right column). The images all show bilateral periventricular nodular grey matter heterotopia maximal in the frontal regions (black arrows). The axial images show over-folded cortex in the deep perisylvian/insular region on the right consistent with polymicrogyria (white arrows).
Fig 4.
Ordered correlation matrices for the PVNH query and the fourteen loci significantly co-expressing within this node.
Pairwise Pearson’s correlation represented as a matrix between (a) pairs of the 14 genes within the PVNH gene set (Methods) and (b) the human PVNH query plus the 14 genes whose co-regulatory patterns significantly exceed the eFDR in both the Kang and Miller transcriptomic datasets. Genes are ordered according to hierarchical clustering, with the most positive (+1) and negative (-1) co-regulatory interactions represented as blue and red squares, respectively.