webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering

Genotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions. Results webGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups. Availability webGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt.Peer reviewe

In-frame deletion in canine PITRM1 is associated with a severe early-onset epilepsy, mitochondrial dysfunction and neurodegeneration

We investigated the clinical, genetic, and pathological characteristics of a previously unknown severe juvenile brain disorder in several litters of Parson Russel Terriers. The disease started with epileptic seizures at 6–12 weeks of age and progressed rapidly to status epilepticus and death or euthanasia. Histopathological changes at autopsy were restricted to the brain. There was severe acute neuronal degeneration and necrosis diffusely affecting the grey matter throughout the brain with extensive intraneuronal mitochondrial crowding and accumulation of amyloid-β (Aβ). Combined homozygosity mapping and genome sequencing revealed an in-frame 6-bp deletion in the nuclear-encoded pitrilysin metallopeptidase 1 (PITRM1) encoding for a mitochondrial protease involved in mitochondrial targeting sequence processing and degradation. The 6-bp deletion results in the loss of two amino acid residues in the N-terminal part of PITRM1, potentially affecting protein folding and function. Assessment of the mitochondrial function in the affected brain tissue showed a significant deficiency in respiratory chain function. The functional consequences of the mutation were modeled in yeast and showed impaired growth in permissive conditions and an impaired respiration capacity. Loss-of-function variants in human PITRM1 result in a childhood-onset progressive amyloidotic neurological syndrome characterized by spinocerebellar ataxia with behavioral, psychiatric and cognitive abnormalities. Homozygous Pitrm1-knockout mice are embryonic lethal, while heterozygotes show a progressive, neurodegenerative phenotype characterized by impairment in motor coordination and Aβ deposits. Our study describes a novel early-onset PITRM1-related neurodegenerative canine brain disorder with mitochondrial dysfunction, Aβ accumulation, and lethal epilepsy. The findings highlight the essential role of PITRM1 in neuronal survival and strengthen the connection between mitochondrial dysfunction and neurodegeneration

Dominant Distal Myopathy 3 (MPD3) Caused by a Deletion in the HNRNPA1 Gene

Background and Objectives To determine the genetic cause of the disease in the previously reported family with adult-onset autosomal dominant distal myopathy (myopathy, distal, 3; MPD3). Methods Continued clinical evaluation including muscle MRI and muscle pathology. A linkage analysis with single nucleotide polymorphism arrays and genome sequencing were used to identify the genetic defect, which was verified by Sanger sequencing. RNA sequencing was used to investigate the transcriptional effects of the identified genetic defect. Results Small hand muscles (intrinsic, thenar, and hypothenar) were first involved with spread to the lower legs and later proximal muscles. Dystrophic changes with rimmed vacuoles and cytoplasmic inclusions were observed in muscle biopsies at advanced stage. A single nucleotide polymorphism array confirmed the previous microsatellite-based linkage to 8p22-q11 and 12q13-q22. Genome sequencing of three affected family members combined with structural variant calling revealed a small heterozygous deletion of 160 base pairs spanning the second last exon 10 of the heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) gene, which is in the linked region on chromosome 12. Segregation of the mutation with the disease was confirmed by Sanger sequencing. RNA sequencing showed that the mutant allele produces a shorter mutant mRNA transcript compared with the wild-type allele Immunofluorescence studies on muscle biopsies revealed small p62 and larger TDP-43 inclusions. Discussion A small exon 10 deletion in the gene HNRNPA1 was identified as the cause of MPD3 in this family. The new HNRNPA1-related phenotype, upper limb presenting distal myopathy, was thus confirmed, and the family displays the complexities of gene identification.Peer reviewe

Painful swollen leg – think beyond deep vein thrombosis or Baker's cyst

<p>Abstract</p> <p>Background</p> <p>The diagnosis of deep vein thrombosis of leg is very common in clinical practice. Not infrequently a range of pathologies are diagnosed after excluding a thrombosis, often after a period of anticoagulation.</p> <p>Case presentation</p> <p>This is a report of three patients who presented with a painful swollen leg and were initially treated as a deep vein thrombosis or a baker's cyst, but later diagnosed as a pleomorphic sarcoma, a malignant giant cell tumor of the muscle and a myxoid liposarcoma. A brief review of such similar reports and the relevant literature is presented.</p> <p>Conclusion</p> <p>A painful swollen leg is a common clinical scenario and though rare, tumors must be thought of without any delay, in a duplex negative, low risk deep vein thrombosis situation.</p

Identification of a common risk haplotype for canine idiopathic epilepsy in the ADAM23 gene

Background: Idiopathic epilepsy is a common neurological disease in human and domestic dogs but relatively few risk genes have been identified to date. The seizure characteristics, including focal and generalised seizures, are similar between the two species, with gene discovery facilitated by the reduced genetic heterogeneity of purebred dogs. We have recently identified a risk locus for idiopathic epilepsy in the Belgian Shepherd breed on a 4.4 megabase region on CFA37. Results: We have expanded a previous study replicating the association with a combined analysis of 157 cases and 179 controls in three additional breeds: Schipperke, Finnish Spitz and Beagle (p(c) = 2.9e-07, p(GWAS) = 1.74E-02). A targeted resequencing of the 4.4 megabase region in twelve Belgian Shepherd cases and twelve controls with opposite haplotypes identified 37 case-specific variants within the ADAM23 gene. Twenty-seven variants were validated in 285 cases and 355 controls from four breeds, resulting in a strong replication of the ADAM23 locus (p(raw) = 2.76e-15) and the identification of a common 28 kb-risk haplotype in all four breeds. Risk haplotype was present in frequencies of 0.49-0.7 in the breeds, suggesting that ADAM23 is a low penetrance risk gene for canine epilepsy. Conclusions: These results implicate ADAM23 in common canine idiopathic epilepsy, although the causative variant remains yet to be identified. ADAM23 plays a role in synaptic transmission and interacts with known epilepsy genes, LGI1 and LGI2, and should be considered as a candidate gene for human epilepsies.Peer reviewe