Bug Hunting with False Negatives Revisited

Safe data abstractions are widely used for verification purposes. Positive verification results can be transferred from the abstract to the concrete system. When a property is violated in the abstract system, one still has to check whether a concrete violation scenario exists. However, even when the violation scenario is not reproducible in the concrete system (a false negative), it may still contain information on possible sources of bugs. Here, we propose a bug hunting framework based on abstract violation scenarios. We first extract a violation pattern from one abstract violation scenario. The violation pattern represents multiple abstract violation scenarios, increasing the chance that a corresponding concrete violation exists. Then, we look for a concrete violation that corresponds to the violation pattern by using constraint solving techniques. Finally, we define the class of counterexamples that we can handle and argue correctness of the proposed framework. Our method combines two formal techniques, model checking and constraint solving. Through an analysis of contracting and precise abstractions, we are able to integrate overapproximation by abstraction with concrete counterexample generation

Bug Hunting with False Negatives Revisited

Safe data abstractions are widely used for verification purposes. Positive verification results can be transferred from the abstract to the concrete system. When a property is violated in the abstract system, one still has to check whether a concrete violation scenario exists. However, even when the violation scenario is not reproducible in the concrete system (a false negative), it may still contain information on possible sources of bugs. Here, we propose a bug hunting framework based on abstract violation scenarios. We first extract a violation pattern from one abstract violation scenario. The violation pattern represents multiple abstract violation scenarios, increasing the chance that a corresponding concrete violation exists. Then, we look for a concrete violation that corresponds to the violation pattern by using constraint solving techniques. Finally, we define the class of counterexamples that we can handle and argue correctness of the proposed framework. Our method combines two formal techniques, model checking and constraint solving. Through an analysis of contracting and precise abstractions, we are able to integrate overapproximation by abstraction with concrete counterexample generation

Broadening the phenotypic and molecular spectrum of FINCA syndrome: Biallelic NHLRC2 variants in 15 novel individuals

FINCA syndrome [MIM: 618278] is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration and cerebral angiomatosis. To date, 13 patients from nine families with biallelic NHLRC2 variants have been published. In all of them, the recurrent missense variant p.(Asp148Tyr) was detected on at least one allele. Common manifestations included lung or muscle fibrosis, respiratory distress, developmental delay, neuromuscular symptoms and seizures often followed by early death due to rapid disease progression.Here, we present 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants identified by exome analysis. All patients described here presented with moderate to severe global developmental delay and variable disease progression. Seizures, truncal hypotonia and movement disorders were frequently observed. Notably, we also present the first eight cases in which the recurrent p.(Asp148Tyr) variant was not detected in either homozygous or compound heterozygous state.We cloned and expressed all novel and most previously published non-truncating variants in HEK293-cells. From the results of these functional studies, we propose a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.Taken together, our findings broaden the known phenotypic and molecular spectrum and emphasize that NHLRC2-related disease should be considered in patients presenting with intellectual disability, movement disorders, neuroregression and epilepsy with or without pulmonary involvement

Biallelic loss-of-function variants in the splicing regulator NSRP1 cause a severe neurodevelopmental disorder with spastic cerebral palsy and epilepsy

Purpose: Alternative splicing plays a critical role in mouse neurodevelopment, regulating neurogenesis, cortical lamination, and synaptogenesis, yet few human neurodevelopmental disorders are known to result from pathogenic variation in splicing regulator genes. Nuclear Speckle Splicing Regulator Protein 1 (NSRP1) is a ubiquitously expressed splicing regulator not known to underlie a Mendelian disorder. Methods: Exome sequencing and rare variant family-based genomics was performed as a part of the Baylor-Hopkins Center for Mendelian Genomics Initiative. Additional families were identified via GeneMatcher. Results: We identified six patients from three unrelated families with homozygous loss-of-function variants in NSRP1. Clinical features include developmental delay, epilepsy, variable microcephaly (Z-scores �0.95 to �5.60), hypotonia, and spastic cerebral palsy. Brain abnormalities included simplified gyral pattern, underopercularization, and/or vermian hypoplasia. Molecular analysis identified three pathogenic NSRP1 predicted loss-of-function variant alleles: c.13591362delAAAG (p.Glu455AlafsTer20), c.1272dupG (p.Lys425GlufsTer5), and c.52C>T (p.Gln18Ter). The two frameshift variants result in a premature termination codon in the last exon, and the mutant transcripts are predicted to escape nonsense mediated decay and cause loss of a C-terminal nuclear localization signal required for NSRP1 function. Conclusion: We establish NSRP1 as a gene for a severe autosomal recessive neurodevelopmental disease trait characterized by developmental delay, epilepsy, microcephaly, and spastic cerebral palsy. © 2021, The Author(s), under exclusive licence to the American College of Medical Genetics and Genomics

A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode.

The leucine-rich glioma-inactivated (LGI) family consists of four highly conserved paralogous genes, LGI1-4, that are highly expressed in mammalian central and/or peripheral nervous systems. LGI1 antibodies are detected in subjects with autoimmune limbic encephalitis and peripheral nerve hyperexcitability syndromes (PNHSs) such as Isaacs and Morvan syndromes. Pathogenic variations of LGI1 and LGI4 are associated with neurological disorders as disease traits including familial temporal lobe epilepsy and neurogenic arthrogryposis multiplex congenita 1 with myelin defects, respectively. No human disease has been reported associated with either LGI2 or LGI3. We implemented exome sequencing and family-based genomics to identify individuals with deleterious variants in LGI3 and utilized GeneMatcher to connect practitioners and researchers worldwide to investigate the clinical and electrophysiological phenotype in affected subjects. We also generated Lgi3-null mice and performed peripheral nerve dissection and immunohistochemistry to examine the juxtaparanode LGI3 microarchitecture. As a result, we identified 16 individuals from eight unrelated families with loss-of-function (LoF) bi-allelic variants in LGI3. Deep phenotypic characterization showed LGI3 LoF causes a potentially clinically recognizable PNHS trait characterized by global developmental delay, intellectual disability, distal deformities with diminished reflexes, visible facial myokymia, and distinctive electromyographic features suggestive of motor nerve instability. Lgi3-null mice showed reduced and mis-localized Kv1 channel complexes in myelinated peripheral axons. Our data demonstrate bi-allelic LoF variants in LGI3 cause a clinically distinguishable disease trait of PNHS, most likely caused by disturbed Kv1 channel distribution in the absence of LGI3

Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia

Objective Human genomics established that pathogenic variation in diverse genes can underlie a single disorder. For example, hereditary spastic paraplegia is associated with >80 genes, with frequently only few affected individuals described for each gene. Herein, we characterize a large cohort of individuals with biallelic variation in ENTPD1, a gene previously linked to spastic paraplegia 64 (Mendelian Inheritance in Man # 615683). Methods Individuals with biallelic ENTPD1 variants were recruited worldwide. Deep phenotyping and molecular characterization were performed. Results A total of 27 individuals from 17 unrelated families were studied; additional phenotypic information was collected from published cases. Twelve novel pathogenic ENTPD1 variants are described (NM 001776.6): c.398_399delinsAA; p.(Gly133Glu), c.540del; p.(Thr181Leufs*18), c.640del; p.(Gly216Glufs*75), c.185 T > G; p.(Leu62*), c.1531 T > C; p.(*511Glnext*100), c.967C > T; p.(Gln323*), c.414-2_414-1del, and c.146 A > G; p.(Tyr49Cys) including 4 recurrent variants c.1109 T > A; p.(Leu370*), c.574-6_574-3del, c.770_771del; p.(Gly257Glufs*18), and c.1041del; p.(Ile348Phefs*19). Shared disease traits include childhood onset, progressive spastic paraplegia, intellectual disability (ID), dysarthria, and white matter abnormalities. In vitro assays demonstrate that ENTPD1 expression and function are impaired and that c.574-6_574-3del causes exon skipping. Global metabolomics demonstrate ENTPD1 deficiency leads to impaired nucleotide, lipid, and energy metabolism. Interpretation The ENTPD1 locus trait consists of childhood disease onset, ID, progressive spastic paraparesis, dysarthria, dysmorphisms, and white matter abnormalities, with some individuals showing neurocognitive regression. Investigation of an allelic series of ENTPD1 (1) expands previously described features of ENTPD1-related neurological disease, (2) highlights the importance of genotype-driven deep phenotyping, (3) documents the need for global collaborative efforts to characterize rare autosomal recessive disease traits, and (4) provides insights into disease trait neurobiology. ANN NEUROL 202

Report from Working Group 2: Higgs Physics at the HL-LHC and HE-LHC

The discovery of the Higgs boson in 2012, by the ATLAS and CMS experiments, was a success achieved with only a percent of the entire dataset foreseen for the LHC. It opened a landscape of possibilities in the study of Higgs boson properties, Electroweak Symmetry breaking and the Standard Model in general, as well as new avenues in probing new physics beyond the Standard Model. Six years after the discovery, with a conspicuously larger dataset collected during LHC Run 2 at a 13 TeV centre-of-mass energy, the theory and experimental particle physics communities have started a meticulous exploration of the potential for precision measurements of its properties. This includes studies of Higgs boson production and decays processes, the search for rare decays and production modes, high energy observables, and searches for an extended electroweak symmetry breaking sector. This report summarises the potential reach and opportunities in Higgs physics during the High Luminosity phase of the LHC, with an expected dataset of pp collisions at 14 TeV, corresponding to an integrated luminosity of 3~ab$^{-1}$. These studies are performed in light of the most recent analyses from LHC collaborations and the latest theoretical developments. The potential of an LHC upgrade, colliding protons at a centre-of-mass energy of 27 TeV and producing a dataset corresponding to an integrated luminosity of 15~ab$^{-1}$, is also discussed

Search for large extra dimensions in dimuon and dielectron events in pp collisions at s=7\sqrt{s} = 7 TeV

Results are presented from a search for large, extra spatial dimensions in events with either two isolated muons or two isolated electrons. The data are from proton-proton interactions at sqrt(s) = 7 TeV collected with the CMS detector at the LHC. The size of the data sample corresponds to an integrated luminosity of approximately 2 inverse femtobarns. The observed dimuon and dielectron mass spectra are found to be consistent with standard-model expectations. Depending on the number of extra dimensions, the 95% confidence level limits from the combined dimuon and dielectron channels range from Ms > 2.4 TeV to Ms > 3.8 TeV, where Ms characterizes the scale for the onset of quantum gravity.Comment: Submitted to Physics Letters