Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures.

BACKGROUND: The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. METHODS: Case-control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. RESULTS: Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. CONCLUSIONS: In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. IMPACT: We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis

Solid-Phase C1q/C3d Fixing Readouts Correlate with High Median Fluorescence Intensity (MFI) De Novo Donor-Specific HLA Antibodies and C4d+ Antibody-Mediated Rejection in Kidney Transplant Recipients

BACKGROUND Solid-phase assays to investigate the complement-activating capacity of HLA antibodies have been utilized to optimize organ allocation and improve transplant outcomes. The clinical utility of C1q/C3d-binding characteristics of de novo donor-specific anti-HLA antibodies (dnDSA) associated with C4d-positive antibody-mediated rejection (C4d⁺ AMR) in kidney transplants (KTx) has not been defined. MATERIAL AND METHODS Sera from 120 KTx recipients that had dnDSA concurrent with protocol/cause biopsy (median 3.8 years after transplantation) were screened for C1q and C3d-binding dnDSA. The difference in the incidence of C4d⁺ AMR between recipients with and without C1q/C3d-binding dnDSA was assessed. RESULTS Over 86% of dnDSAs were class II antibodies. The immunodominant dnDSAs characterized by the highest median fluorescence intensity (MFI) in most recipients were HLA-DQ antibodies (67%). Most recipients (62%, n=74) had either C1q⁺ (56%), C3d⁺ (48%), or both C1q⁺C3d⁺ (41.2%) dnDSA, while the remaining 38% were negative for both C1q and C3d. Of those with C1q⁺/C3d⁺ dnDSA, 87% had high-MFI IgG (MFI=14144±5363 and 13932±5278, respectively), while 65% of C1q⁻C3d⁻ dnDSA had low-MFI IgG (MFI=5970±3347). The incidence of C4d+ AMR was significantly higher in recipients with C1q⁺ (66%), C3d+ (74%), and C1q⁺C3d⁺ (72%) dnDSA than in those with C1q⁻C3d⁻ dnDSA (30%) recipients. Recipients with C3d⁺/C1q⁺ dnDSA had higher C4d⁺ scores on biopsy. CONCLUSIONS C1q⁺/C3d⁺ dnDSA were associated with C4d⁺ AMR and high-IgG MFI. Our data call into question the predictive utility of C1q/C3d-binding assays in identifying KTx recipients at risk of allograft failure. In conclusion, IgG MFI is sufficient for clinical management, and the C1q/C3d-assays with added cost do not provide any additional information

Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction

Abstract Background In children with sensory processing dysfunction (SPD), who do not meet criteria for autism spectrum disorder (ASD) or intellectual disability, the contribution of de novo pathogenic mutation in neurodevelopmental genes is unknown and in need of investigation. We hypothesize that children with SPD may have pathogenic variants in genes that have been identified as causing other neurodevelopmental disorders including ASD. This genetic information may provide important insight into the etiology of sensory processing dysfunction and guide clinical evaluation and care. Methods Eleven community-recruited trios (children with isolated SPD and both biological parents) underwent WES to identify candidate de novo variants and inherited rare single nucleotide variants (rSNV) in genes previously associated with ASD. Gene enrichment in these children and their parents for transmitted and non-transmitted mutation burden was calculated. A comparison analysis to assess for enriched rSNV burden was then performed in 2377 children with ASD and their families from the Simons Simplex Collection. Results Of the children with SPD, 2/11 (18%), were identified as having a de novo loss of function or missense mutation in genes previously reported as causative for neurodevelopmental disorders (MBD5 and FMN2). We also found that the parents of children with SPD have significant enrichment of pathogenic rSNV burden in high-risk ASD candidate genes that are inherited by their affected children. Using the same approach, we confirmed enrichment of rSNV burden in a large cohort of children with autism and their parents but not unaffected siblings. Conclusions Our findings suggest that SPD, like autism, has a genetic basis that includes both de novo single gene mutations as well as an accumulated burden of rare inherited variants from their parents

Additional file 1: of Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction

High- Probability Risk ASD Gene Set. Table of seventy-six genes from AutDB determined to be “probably damaging” and included in the high-risk ASD gene set. (XLS 80 kb

Additional file 2: of Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction

Moderate- Probability Risk ASD Gene Set. Table of 292 genes from AutDB categorized as possibly damaging and included as moderate-risk ASD gene set. (XLS 151 kb

Quantitative trait loci for interhemispheric commissure development and social behaviors in the BTBR T⁺ tf/J mouse model of autism.

BackgroundAutism and Agenesis of the Corpus Callosum (AgCC) are interrelated behavioral and anatomic phenotypes whose genetic etiologies are incompletely understood. We used the BTBR T⁺ tf/J (BTBR) strain, exhibiting fully penetrant AgCC, a diminished hippocampal commissure, and abnormal behaviors that may have face validity to autism, to study the genetic basis of these disorders.MethodsWe generated 410 progeny from an F2 intercross between the BTBR and C57BL/6J strains. The progeny were phenotyped for social behaviors (as juveniles and adults) and commisural morphology, and genotyped using 458 markers. Quantitative trait loci (QTL) were identified using genome scans; significant loci were fine-mapped, and the BTBR genome was sequenced and analyzed to identify candidate genes.ResultsSix QTL meeting genome-wide significance for three autism-relevant behaviors in BTBR were identified on chromosomes 1, 3, 9, 10, 12, and X. Four novel QTL for commissural morphology on chromosomes 4, 6, and 12 were also identified. We identified a highly significant QTL (LOD score = 20.2) for callosal morphology on the distal end of chromosome 4.ConclusionsWe identified several QTL and candidate genes for both autism-relevant traits and commissural morphology in the BTBR mouse. Twenty-nine candidate genes were associated with synaptic activity, axon guidance, and neural development. This is consistent with a role for these processes in modulating white matter tract development and aspects of autism-relevant behaviors in the BTBR mouse. Our findings reveal candidate genes in a mouse model that will inform future human and preclinical studies of autism and AgCC

Quantitative Trait Loci for Interhemispheric Commissure Development and Social Behaviors in the BTBR T⁺<i>tf/J</i> Mouse Model of Autism

<div><p>Background</p><p>Autism and Agenesis of the Corpus Callosum (AgCC) are interrelated behavioral and anatomic phenotypes whose genetic etiologies are incompletely understood. We used the BTBR T⁺<i>tf/J</i> (BTBR) strain, exhibiting fully penetrant AgCC, a diminished hippocampal commissure, and abnormal behaviors that may have face validity to autism, to study the genetic basis of these disorders.</p><p>Methods</p><p>We generated 410 progeny from an F2 intercross between the BTBR and C57BL/6J strains. The progeny were phenotyped for social behaviors (as juveniles and adults) and commisural morphology, and genotyped using 458 markers. Quantitative trait loci (QTL) were identified using genome scans; significant loci were fine-mapped, and the BTBR genome was sequenced and analyzed to identify candidate genes.</p><p>Results</p><p>Six QTL meeting genome-wide significance for three autism-relevant behaviors in BTBR were identified on chromosomes 1, 3, 9, 10, 12, and X. Four novel QTL for commissural morphology on chromosomes 4, 6, and 12 were also identified. We identified a highly significant QTL (LOD score = 20.2) for callosal morphology on the distal end of chromosome 4.</p><p>Conclusions</p><p>We identified several QTL and candidate genes for both autism-relevant traits and commissural morphology in the BTBR mouse. Twenty-nine candidate genes were associated with synaptic activity, axon guidance, and neural development. This is consistent with a role for these processes in modulating white matter tract development and aspects of autism-relevant behaviors in the BTBR mouse. Our findings reveal candidate genes in a mouse model that will inform future human and preclinical studies of autism and AgCC.</p></div

Categories of candidate genes for AgCC and autism-relevant phenotypes in the BTBR mouse.

<p>Candidate genes identified in the present study fall into four major protein categories: (1) Developmental proteins, involved in processes of cell cycle regulation, cell adhesion, axon growth, guidance, migration, actin-binding and cytoskeletal organization, (2) Synaptic and receptor proteins, (3) Kinases, and (4) Immune and heat shock proteins. ^*Indicates gene has been previously implicated in ASD (SFARIgene; gene.sfari.org) ^#Indicates gene family member has been previously implicated in ASD (SFARIgene; gene.sfari.org).</p

Gene candidate analysis flowchart.

<p>Following fine mapping, QTL meeting genome-wide significance of 5% were further analyzed to identify a list of gene candidates for future study. Sequencing data from the BTBR T⁺<i>tf/J</i> strain was compared to known SNPs in the C57BL/6J and LP/J strains, and potential pathogenicity of BTBR-specific SNPs were determined (using Polyphen-2). Genes containing potentially pathogenic SNPs were filtered to only those involved in neurological behavior or within the nervous system, and then filtered again to limit genes to only those with cortical expression to develop the final list of gene candidates for AgCC and autism-relevant behaviors in the BTBR T⁺<i>tf/J</i> strain of mouse.</p

QTL for autism-relevant behaviors.

<p>For the related juvenile reciprocal social interaction trait parameters “novel mouse sniff” (the cumulative time spent sniffing the novel mouse) and “diff sniff” (the difference between seconds spent sniffing the novel mouse and seconds spent sniffing the novel object) (A, B), a significant QTL was found on chromosome 3 (LOD = 4.52). (B) An additional QTL was found on the X chromosome (LOD = 4.12) for the “novel mouse sniff” trait, but did not meet genome-wide significance for the trait “diff sniff.” (C) The trait “Juvenile Nose to Nose” displayed a QTL on chromosome 1 (LOD = 4.43) and chromosome 9 (LOD = 3.80). (D) The trait “Juvenile Push Crawl” displayed QTL on chromosome 10 (LOD = 4.77) and chromosome 12 (LOD = 4.09), respectively. Red arrows indicate statistically significant QTL; red hatched arrows indicate transgressive loci.</p