Molecular Characterization of NRXN1 Deletions from 19,263 Clinical Microarray Cases Identifies Exons Important for Neurodevelopmental Disease Expression

PURPOSE: The purpose of the current study was to assess the penetrance of NRXN1 deletions. METHODS: We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant copy-number variations (CNVs) was used as a proxy to estimate the relative penetrance of NRXN1 deletions. RESULTS: We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability that were significantly greater than in controls (odds ratio (OR) = 8.14; 95% confidence interval (CI): 2.91-22.72; P \u3c 0.0001). Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3\u27 end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5\u27 NRXN1 deletion (OR = 7.47; 95% CI: 2.36-23.61; P = 0.0006). The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (P = 0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV at a prevalence twice as high as that for exonic NRXN1 deletion cases (P = 0.0035). CONCLUSIONS: The results support the importance of exons near the 5\u27 end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes.Genet Med 19 1, 53-61

Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disorders

Balanced chromosomal rearrangements (BCRs), including inversions, translocations, and insertions, reorganize large sections of the genome and contribute substantial risk for developmental disorders (DDs). However, the rarity and lack of systematic screening for BCRs in the population has precluded unbiased analyses of the genomic features and mechanisms associated with risk for DDs versus normal developmental outcomes. Here, we sequenced and analyzed 1,420 BCR breakpoints across 710 individuals, including 406 DD cases and the first large-scale collection of 304 control BCR carriers. We found that BCRs were not more likely to disrupt genes in DD cases than controls, but were seven-fold more likely to disrupt genes associated with dominant DDs (21.3% of cases vs. 3.4% of controls; P = 1.60×10$^{−12}$). Moreover, BCRs that did not disrupt a known DD gene were significantly enriched for breakpoints that altered topologically associated domains (TADs) containing dominant DD genes in cases compared to controls (odds ratio [OR] = 1.43, P = 0.036). We discovered six TADs enriched for noncoding BCRs (false discovery rate < 0.1) that contained known DD genes (MEF2C, FOXG1, SOX9, BCL11A, BCL11B, and SATB2) and represent candidate pathogenic long-range positional effect (LRPE) loci. These six TADs were collectively disrupted in 7.4% of the DD cohort. Phased Hi-C analyses of five cases with noncoding BCR breakpoints localized to one of these putative LRPEs, the 5q14.3 TAD encompassing MEF2C, confirmed extensive disruption to local 3D chromatin structures and reduced frequency of contact between the MEF2C promoter and annotated enhancers. We further identified six genomic features enriched in TADs preferentially disrupted by noncoding BCRs in DD cases versus controls and used these features to build a model to predict TADs at risk for LRPEs across the genome. These results emphasize the potential impact of noncoding structural variants to cause LRPEs in unsolved DD cases, as well as the complex interaction of features associated with predicting three-dimensional chromatin structures intolerant to disruption

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10−6). Novel reciprocal case–control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present

Rare copy number variations associated with schizophrenia and intellectual disability

Schizophrenia is a severe psychiatric disorder associated with significant impairments in cognitive functioning. Extensive evidence supports the importance of genetic aetiology, similar to other neurodevelopmental disorders like intellectual disability (ID). Of particular importance are large rare pathogenic copy number variations (CNVs), which have been independently associated with schizophrenia and ID. To date, there have been no studies systematically investigating the genome-wide burden and/or functional impact of rare CNVs on intellect (IQ) in schizophrenia. In this thesis, I used high resolution CNV data from a sample of 546 unrelated subjects of European descent with schizophrenia to investigate multiple IQ groups. The results demonstrated that the yield of pathogenic CNVs increased with decreasing IQ. Notably, the yield of pathogenic CNVs was similar for those with ID and those with a non-verbal learning disability (NVLD). There was a significantly greater burden of rare genic duplications that overlapped genes involved in neurodevelopment in individuals with schizophrenia in the lower IQ group compared to those with higher IQ that persisted after removing all subjects with a pathogenic CNV. I also investigated the variable expression and incomplete penetrance of two rare pathogenic CNVs by compiling every case with a 15q13.3 or a 3q13.31 microdeletion reported in the literature to date. The results of these studies showed ID and schizophrenia to be features of both, with the collective penetrance of 15q13.3 deletions for any neuropsychiatric disorder at over 80.0%. Finally, using two large clinically ascertained cohorts, I demonstrated that the burden of additional rare CNVs located elsewhere in the genome shapes the expression of schizophrenia in 22q11.2 deletion syndrome (22q11.2DS), and, together with the location of the deletion itself, the penetrance of ID in NRXN1 deletions. Collectively, these novel data represent important contributions towards understanding the genetic architecture of schizophrenia and ID.Ph.D

Adult expression of a 3q13.31 microdeletion

Abstract Background The emerging 3q13.31 microdeletion syndrome appears to encompass diverse neurodevelopmental conditions. However, the 3q13.31 deletion is rare and few adult cases have yet been reported. We examined a cohort with schizophrenia (n = 459) and adult control subjects (n = 26,826) using high-resolution microarray technology for deletions and duplications at the 3q13.31 locus. Results We report on the extended adult phenotype associated with a 3q13.31 microdeletion in a 41-year-old male proband with schizophrenia and a nonverbal learning disability. He was noted to have a speech impairment, delayed motor skills, and other features consistent with the 3q13.31 microdeletion syndrome. The 2.06 Mb deletion overlapped two microRNAs and seven RefSeq genes, including GAP43, LSAMP, DRD3, and ZBTB20. No overlapping 3q13.31 deletions or duplications were identified in control subjects. Conclusions Later-onset conditions like schizophrenia are increasingly associated with rare copy number variations and associated genomic disorders like the 3q13.31 microdeletion syndrome. Detailed phenotype information across the lifespan facilitates genotype-phenotype correlations, accurate genetic counselling, and anticipatory care

Mechanistic dissection of chromatin topology disruption in the 5q14.3 MEF2C locus as an indirect driver of neurodevelopmental disorders

Structural variants have the potential to create long-range positional effects, uncouple genes from regulatory elements, and facilitate aberrant 3D chromatin folding. In an independent study, we revealed a significant enrichment of intergenic balanced chromosomal abnormality (BCA) breakpoints from congenital anomaly cases at chromosome 5q14.3. All 11 5q14.3 BCA carriers had breakpoints disrupting the topologically associated domain (TAD) housing MEF2C, a known driver of neurodevelopmental disorders. In a second study, we showed, using 4C-seq, that MEF2C forms proximal and distal interaction loops within this TAD, contacting multiple neuronal enhancers. To understand the functional impact of these BCAs, we performed a mechanistic dissection of the 3D regulatory network at the 5q14.3 locus and its constituent functional elements using Cas9-based genome editing. We generated >200 cell lines, representing deletions of MEF2C alongside five MEF2C TAD boundary and interaction loop targets in iPS-derived neural stem cells (NSCs) and cortical induced neurons (iNs). We profiled changes in expression and 3D chromatin interactions within these models using RNA-seq and 4C-seq. MEF2C was variably differentially expressed upon deletion of proximal and distal MEF2C loop regions, with effects depending on cell type and variant class. Underlying chromatin interaction patterns revealed evidence of loop maintenance in these models, possibly via CTCF buffering, highlighting compensatory mechanisms against 3D chromatin disruption. In contrast, deletion of the proximal TAD boundary facilitated increased contacts with predicted enhancers in the adjacent TAD. Our results suggest novel regulatory mechanisms driving phenotypic outcomes for the 5q14.3 region, with significant implications for interpretation of pathogenic structural variation