Forty non-exclusive patient groups, each group’s patients sharing the same HPO term, amongst whom individual copy number variant candidate genes were each recurrently identified by multiple functional genomics methods and whose recurrently-identified candidate genes demonstrated a significant number of protein-protein interactions.

<p>The dendrogram displays the relationship between categories based upon the number of candidate genes identified by multiple methods that are shared between the phenotype-group patients. Categories are marked if there were significant enrichments using clustering in a gene expression network (Blue), GO (Green) or KEGG (yellow). No phenotype-grouped patients with candidate genes meeting these criteria were identified use mouse KO phenotype (MGI) associations.</p

Clusters of 33 genes whose products have known protein-protein interactions copy changed among 34 (22%) of 154 patients with intellectual disability.

<p>These genes were those identified using two or more methods (from KEGG, GO and Gene Expression clustering) and that were found to contribute to a significant enrichment of interactions identified by the Dapple protein-protein interaction network (<i>p</i> < 1x10^–4).</p

Functional genomics enrichments significantly enriched in genes affected by <i>de novo</i> CNVs in 33 patients presenting with seizures.

<p><b>(A)</b> Significant functional genomics enrichments. Many of these functions have links to seizures or associated phenomena (synaptic deficits, receptor signaling, gustatory aura[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005012#pgen.1005012.ref073" target="_blank">73</a>]) but also to regions prone to copy number variation[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005012#pgen.1005012.ref074" target="_blank">74</a>]. <b>(B)</b> Genes disrupted by short CNVs in patients were also observed to cluster significantly in a brain-specific gene co-expression network. Here we display the strongest clusters (<i>r ></i> 0.92 for all co-expression similarities) of genes from seizure patients from this network. <b>(C)</b> Overall, the functional enrichments identified known (HPO-defined) seizure genes for 11 of the 33 patients, and proposed causal genes for 21 of the remaining 22 patients.</p

Clinical features of Kleefstra syndrome shared by the three affected brothers of family MRQ14.

<p>BMI, body mass index; DD, developmental disability; ID, intellectual disability, VUR, vesico-ureteric reflux</p><p>Clinical features of Kleefstra syndrome shared by the three affected brothers of family MRQ14.</p

Pedigree of families (A) MRQ14, (B) MRQ11 and (C) MRQ15.

<p>The segregation of mutation of <i>KMT2B</i>, <i>ZNF589</i> and <i>HHAT</i> are also in the pedigree. The symbol +/+ represents homozygous ancestral alleles, M/M is for homozygous variant alleles and +/M is for heterozygous carriers. In the panel B, the genotype of the father (III:1) has been deduced.</p

Family MRQ15 homozygous and compound heterozygous variants validation using Sanger sequencing and <i>in silico</i> prediction.

<p>NM, mRNA accession number; PhyloP, Phylogenetic P-values; Polyphen, Polymorphism phenotyping; SIFT, Sorting intolerance from tolerance, Mutation taster (<a href="http://www.mutationtaster.org" target="_blank">http://www.mutationtaster.org</a>).</p><p>Family MRQ15 homozygous and compound heterozygous variants validation using Sanger sequencing and <i>in silico</i> prediction.</p

Family MRQ14 homozygous and compound heterozygous variant validation using Sanger sequencing and <i>in silico</i> pathogenecity predictions.

<p>NM, mRNA accession number; PhyloP, Phylogenetic P-values; Polyphen, Polymorphism phenotyping; SIFT, Sorting intolerance from tolerance, Mutation taster (<a href="http://www.mutationtaster.org" target="_blank">http://www.mutationtaster.org</a>).</p><p>Family MRQ14 homozygous and compound heterozygous variant validation using Sanger sequencing and <i>in silico</i> pathogenecity predictions.</p

The sequencing chromatograms of the families MRQ14, MRQ11 and MRQ15.

<p>(<b>A</b>) Shows the panels containing the region with the identified <i>KMT2B</i> mutation in family MRQ14: ancestral (left panel), heterozygous (middle panel) and variant (right panel) (<b>B</b>) shows the region containing the identified <i>ZNF589</i> mutation in family MRQ11: ancestral (left panel), heterozygous (middle panel) and variant (right panel). (<b>C</b>) shows the <i>de novo</i> variant of <i>HHAT</i> in family MRQ15: ancestral (left panel), heterozygous (right panel).</p

Summary of molecular and clinical features of individuals with <i>KMT2C</i> mutations.

<p>Summary of molecular and clinical features of individuals with <i>KMT2C</i> mutations.</p

Trr is required in the mushroom body for short term memory.

<p>Fluorescent confocal images of control (A-D) and trr knockdown (E-H) adult male brains. UAS-mCD8::GFP calyx (A, E) shows the expression domain of the <i>R14H06-Gal4</i> driver in the mushroom body and is marked by yellow dashed lines and an asterisk. The scale bar represents 10 μm. DAPI (B, F) is shown to identify nuclei and note the low nuclear density in the peduncle, which is indicated with a P. Trr (C, G) is labeled by immunohistochemistry using an anti-trr antibody. The overlay of DAPI and trr signal (D, H) shows a reduction of trr in the target cells (blue and red channels). (I-J) Confocal projections showing the main axonal lobes of the mushroom body that are labeled by <i>UAS-mDC8</i>::<i>GFP</i> through expression with the <i>R14H06-Gal4</i> driver in control flies (I) and trr knockdown flies (J). The scale bar represents 10 μm. (K) Standard boxplots representing the courtship indexes (CIs) resulting from courtship conditioning in control and trr knockdown flies. + indicates the mean. The mean CI for naïve and trained flies was compared using the Mann-Whitney test. (L) Learning Indexes (LI) for controls and trr knockdown flies derived from the CIs. Trr knockdown males have a significantly reduced LI (randomization test, 10,000 bootstrap replicates).</p